From 99e16d2269fa0416d452a4d774116e82458c1593 Mon Sep 17 00:00:00 2001 From: David Doty Date: Fri, 25 Aug 2023 21:51:30 -0700 Subject: [PATCH 01/25] bumped version --- scadnano/scadnano.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index e6b2bcb..cd3c677 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -53,7 +53,7 @@ # needed to use forward annotations: https://docs.python.org/3/whatsnew/3.7.html#whatsnew37-pep563 from __future__ import annotations -__version__ = "0.18.3" # version line; WARNING: do not remove or change this line or comment +__version__ = "0.18.4" # version line; WARNING: do not remove or change this line or comment import collections import dataclasses From bd12d4dcf1213d77b21728e21f59977a52e1ecea Mon Sep 17 00:00:00 2001 From: David Doty Date: Sat, 26 Aug 2023 14:45:35 -0700 Subject: [PATCH 02/25] Update scadnano.py --- scadnano/scadnano.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index cd3c677..87710d3 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -78,7 +78,7 @@ try: import openpyxl except ImportError as import_error: - raise import_error + pass default_scadnano_file_extension = 'sc' """Default filename extension when writing a scadnano file.""" From dbc105829aa58cf195abdd61390235126dac5d50 Mon Sep 17 00:00:00 2001 From: David Doty Date: Sat, 26 Aug 2023 17:16:55 -0700 Subject: [PATCH 03/25] Update scadnano.py --- scadnano/scadnano.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 87710d3..cc3a50a 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1,7 +1,8 @@ """ The :mod:`scadnano` Python module is a library for describing synthetic DNA nanostructures (e.g., DNA origami). -Installation instructions are at the +To install, type `pip install scadnano` at the command line; +more detailed installation instructions and troubleshooting tips are at the `GitHub repository `_. The scadnano project is developed and maintained by the UC Davis Molecular Computing group. From ddc8eee1d421177bc4bcf0655746a6ae2294b0d9 Mon Sep 17 00:00:00 2001 From: David Doty Date: Sat, 26 Aug 2023 17:18:37 -0700 Subject: [PATCH 04/25] Update README.md --- README.md | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 5c0c63e..9e9df01 100644 --- a/README.md +++ b/README.md @@ -65,7 +65,7 @@ pip install scadnano Read below for troubleshooting suggestions if that didn't work. ### Getting Python -The scadnano Python package requires Python version 3.7 or later (with a workaround available for version 3.6, but not for any lower version). +The scadnano Python package requires Python version 3.7 or later. To check your current version of Python, open a command line and type @@ -79,17 +79,13 @@ If it is version 2.7 or below, type python3 --version ``` -If that fails, or reports Python version 3.5 or below, you will have to install a later version of Python (recommended at least 3.7). Follow [this link](https://www.python.org/downloads/) to install Python. You may also use an alternative Python distribution, such as [Anaconda](https://www.anaconda.com/products/individual#Downloads). - -If you are using Python 3.6 and do not wish to upgrade, you can install a package providing the required features: the [dataclasses backport](https://pypi.org/project/dataclasses/); see `pip` instructions below to see how to install it. -Python 3.7 provides the -[dataclasses module](https://docs.python.org/3/library/dataclasses.html) automatically. +If that fails, or reports Python version 3.6 or below, you will have to install a later version of Python. Follow [this link](https://www.python.org/downloads/) to install Python. You may also use an alternative Python distribution, such as [Anaconda](https://www.anaconda.com/products/individual#Downloads). ### Installing the scadnano Python package -Once Python is installed (and the dataclasses backport if you have Python version 3.6), there are two ways you can install the scadnano Python package: +Once Python is installed, there are two ways you can install the scadnano Python package: 1. pip (recommended) From 34211de71802c8e95db9f1ab7525c17815bf8e59 Mon Sep 17 00:00:00 2001 From: David Doty Date: Sat, 26 Aug 2023 17:25:04 -0700 Subject: [PATCH 05/25] Update scadnano.py --- scadnano/scadnano.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index cc3a50a..5c3d12e 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -173,17 +173,17 @@ class Color(_JSONSerializable): """ Red component: 0-255. - Optional if :py:data:`Color.hex` is given.""" + Optional if :data:`Color.hex_string` is given.""" g: Optional[int] = None """Green component: 0-255. - Optional if :py:data:`Color.hex` is given.""" + Optional if :data:`Color.hex_string` is given.""" b: Optional[int] = None """Blue component: 0-255. - Optional if :py:data:`Color.hex` is given.""" + Optional if :data:`Color.hex_string` is given.""" hex_string: InitVar[str] = None """Hex color preceded by # sign, e.g., "#ff0000" is red. From 3ed8158a018cc88a9e5a6cad5deef538e50f7ce9 Mon Sep 17 00:00:00 2001 From: David Doty Date: Sat, 26 Aug 2023 17:26:37 -0700 Subject: [PATCH 06/25] Update scadnano.py --- scadnano/scadnano.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 5c3d12e..1d4099e 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -362,9 +362,9 @@ class Grid(str, enum.Enum): `v` even and `h` a multiple of 3 or `v` odd and `h` = 1 + a multiple of 3. - However, we use the same convention as cadnano for encoding hex coordinates see `misc/cadnano-format-specs/v2.txt`. + However, we use the same convention as cadnano for encoding honeycomb coordinates; + see `misc/cadnano-format-specs/v2.txt`. That convention is different from simply excluding coordinates from the hex lattice. - """ none = "none" From 0bd7995fc112c0feb4bd264866c561a8ab385ebe Mon Sep 17 00:00:00 2001 From: David Doty Date: Sat, 26 Aug 2023 17:35:29 -0700 Subject: [PATCH 07/25] Update scadnano.py --- scadnano/scadnano.py | 31 +++++++++++++++++++------------ 1 file changed, 19 insertions(+), 12 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 1d4099e..2bb20e0 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -437,7 +437,12 @@ def _rotate_string(string: str, rotation: int) -> str: class M13Variant(enum.Enum): - """Variants of M13mp18 viral genome. "Standard" variant is p7249. Other variants are longer.""" + """ + Variants of M13mp18 viral genome. "Standard" variant is p7249. Other variants are longer. + + To create a string with the DNA sequence of one of these variants, call the function + :func:`m13`. + """ p7249 = "p7249" """"Standard" variant of M13mp18; 7249 bases long, available from, for example @@ -969,17 +974,17 @@ class ModificationType(enum.Enum): @dataclass(frozen=True, eq=True) class Modification(_JSONSerializable, ABC): - """Abstract case class of modifications (to DNA sequences, e.g., biotin or Cy3). + """ + Abstract case class of modifications (to DNA sequences, e.g., biotin or Cy3). Use concrete subclasses :any:`Modification3Prime`, :any:`Modification5Prime`, or :any:`ModificationInternal` to instantiate. If :data:`Modification.id` is not specified, then :data:`Modification.idt_text` is used as - the unique ID. Each :data:`Modification.id` must be unique. For example if you create a 5' "modification" + the unique ID. Each :data:`Modification.id` must be unique. For example if you create a 5' modification to represent 6 T bases: ``t6_5p = Modification5Prime(display_text='6T', idt_text='TTTTTT')`` - (this is a useful hack for putting single-stranded extensions on strands until loopouts on the end - of a strand are supported; - see https://github.com/UC-Davis-molecular-computing/scadnano-python-package/issues/2), + (this was a useful hack for putting single-stranded extensions on strands before the :any:`Extension` + class was created to directly support this idea), then this would clash with a similar 3' modification without specifying unique IDs for them: ``t6_3p = Modification3Prime(display_text='6T', idt_text='TTTTTT') # ERROR``. @@ -2605,7 +2610,7 @@ class Extension(_JSONSerializable): design = sc.Design(helices=[sc.Helix(max_offset=10)]) design.draw_strand(0,0).extension_5p(3).move(10).extension_3p(2) - which makes this strand with an :any:`Extension` on the side of the length-10 :any:`Domain`: + which makes this strand with :any:`Extension`'s on each side of the length-10 :any:`Domain`: .. code-block:: none @@ -2736,7 +2741,13 @@ def _add_key_value_to_json_map_if_not_default( def wc(seq: str) -> str: - """Return reverse Watson-Crick complement of `seq`.""" + """ + Return reverse Watson-Crick complement of `seq`. + For example, ``wc('AACCTG')`` returns ``'CAGGTT'``. + + :param seq: a DNA sequence + :return: reverse Watson-Crick complement of `seq`. + """ return seq.translate(_wctable)[::-1] @@ -2756,8 +2767,6 @@ class IDTFields(_JSONSerializable): Choices supplied by IDT at the time this was written: ``"25nm"``, ``"100nm"``, ``"250nm"``, ``"1um"``, ``"5um"``, ``"10um"``, ``"4nmU"``, ``"20nmU"``, ``"PU"``, ``"25nmS"``. - - Optional field. """ purification: str = default_idt_purification @@ -2765,8 +2774,6 @@ class IDTFields(_JSONSerializable): https://www.idtdna.com/site/order/oligoentry). Choices supplied by IDT at the time this was written: ``"STD"``, ``"PAGE"``, ``"HPLC"``, ``"IEHPLC"``, ``"RNASE"``, ``"DUALHPLC"``, ``"PAGEHPLC"``. - - Optional field. """ plate: Optional[str] = None From d012f170b2a4e6e2dfe4f217029c1c5b9ea05fbd Mon Sep 17 00:00:00 2001 From: David Doty Date: Sat, 26 Aug 2023 17:47:16 -0700 Subject: [PATCH 08/25] Update scadnano.py --- scadnano/scadnano.py | 25 +++++++++++++++++++------ 1 file changed, 19 insertions(+), 6 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 2bb20e0..93531dc 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -2834,10 +2834,13 @@ class StrandBuilder: design.draw_strand(0, 0).to(10).cross(1).to(5).with_modification_5p(mod.biotin_5p).as_scaffold() - :any:`StrandBuilder` should generally not be created directly. + :any:`StrandBuilder` should generally not be created directly by calling its constructor, + but rather by calling the method :meth:`Design.draw_strand`. + Although it is convenient to use chained method calls, it is also sometimes useful to assign the - :any:`StrandBuilder` object into a variable and then call the methods on that variable. For example, - this code is equivalent to the above line: + :any:`StrandBuilder` object into a variable and then call the methods on that variable, particularly + when creating a strand with many domains that are easiest to express in a Python loop (e.g., a long + scaffold strand for a DNA origami). For example, the following code is equivalent to the above line: .. code-block:: Python @@ -3155,7 +3158,6 @@ def with_idt(self, scale: str = default_idt_scale, -> StrandBuilder: """ Gives :any:`IDTFields` value to :any:`Strand` being built. - Only a name is required; other fields are given reasonable default values. :param scale: see :py:data:`IDTFields.scale` @@ -3504,7 +3506,7 @@ class Strand(_JSONSerializable): scaffold_domains = [ ... ] scaffold_strand = sc.Strand(domains=scaffold_domains, is_scaffold=True) - or by calling :py:meth:`Strand.set_scaffold` on the :any:`Strand` object: + or by calling :meth:`Strand.set_scaffold` on the :any:`Strand` object: .. code-block:: Python @@ -3514,7 +3516,18 @@ class Strand(_JSONSerializable): scaffold_strand = sc.Strand(domains=scaffold_domains) scaffold_strand.set_scaffold() - Both will give the strand the same color that + or by calling :meth:`StrandBuilder.as_scaffold` on the :any:`StrandBuilder` object returned by + :meth:`Design.strand`: + + .. code-block:: Python + + import scadnano as sc + + design = sc.Design(helices=[sc.Helix(max_offset=100) for _ in range(2)]) + scaffold_strand = design.strand(0, 0).move(100).cross(1).move(-100).as_scaffold() + + + By default, these will give the strand the same color that `cadnano `_ uses for the scaffold. """ From 1c39fbc024f39016c02fb54259875595972549c0 Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 29 Aug 2023 16:21:58 -0700 Subject: [PATCH 09/25] closes #279: rename IDTFields to VendorFields --- ...helix_origami_barrel_from_algoSST_paper.py | 18 +- ...gami_rectangle_seed_tiles_grow_from_top.py | 12 +- ...ple_1_helix_origami_idt_duplicate_names.py | 12 +- examples/idt-plates-explicit.py | 4 +- scadnano/modifications.py | 32 +- scadnano/scadnano.py | 329 ++++++++++-------- tests/scadnano_tests.py | 123 +++---- tutorial/tutorial.md | 2 +- 8 files changed, 287 insertions(+), 245 deletions(-) diff --git a/examples/16_helix_origami_barrel_from_algoSST_paper.py b/examples/16_helix_origami_barrel_from_algoSST_paper.py index 06b3987..d1bdb73 100644 --- a/examples/16_helix_origami_barrel_from_algoSST_paper.py +++ b/examples/16_helix_origami_barrel_from_algoSST_paper.py @@ -110,8 +110,9 @@ def add_adapters(design: sc.Design) -> None: start=left_outside_seed, end=left_inside_seed) dom_bot = sc.Domain(helix=bot_helix, forward=False, start=left_outside_seed, end=left_inside_seed) - idt = sc.IDTFields(scale='25nm', purification='STD') - adapter = sc.Strand(domains=[dom_bot, dom_top], name=f'adap-left-{top_helix}-{bot_helix}', idt=idt) + idt = sc.VendorFields(scale='25nm', purification='STD') + adapter = sc.Strand(domains=[dom_bot, dom_top], name=f'adap-left-{top_helix}-{bot_helix}', + vendor_fields=idt) design.add_strand(adapter) # right adapters @@ -123,8 +124,9 @@ def add_adapters(design: sc.Design) -> None: start=right_inside_seed, end=right_outside_seed) dom_bot = sc.Domain(helix=bot_helix, forward=False, start=right_inside_seed, end=right_outside_seed) - idt = sc.IDTFields(scale='25nm', purification='STD') - adapter = sc.Strand(domains=[dom_top, dom_bot], name=f'adap-right-{top_helix}-{bot_helix}', idt=idt) + idt = sc.VendorFields(scale='25nm', purification='STD') + adapter = sc.Strand(domains=[dom_top, dom_bot], name=f'adap-right-{top_helix}-{bot_helix}', + vendor_fields=idt) design.add_strand(adapter) @@ -161,9 +163,9 @@ def add_tiles_and_assign_dna(design: sc.Design) -> None: start=left_left, end=left_right) ss_bot = sc.Domain(helix=bot_helix, forward=False, start=left_left, end=left_right) - idt = sc.IDTFields(scale='25nm', purification='STD') + idt = sc.VendorFields(scale='25nm', purification='STD') tile = sc.Strand(domains=[ss_bot, ss_top], name=f'tile-left-{top_helix}-{bot_helix}', - color=sc.Color(0, 0, 0), idt=idt) + color=sc.Color(0, 0, 0), vendor_fields=idt) design.add_strand(tile) design.assign_dna(tile, seq) @@ -176,9 +178,9 @@ def add_tiles_and_assign_dna(design: sc.Design) -> None: start=right_left, end=right_right) ss_bot = sc.Domain(helix=bot_helix, forward=False, start=right_left, end=right_right) - idt = sc.IDTFields(scale='25nm', purification='STD') + idt = sc.VendorFields(scale='25nm', purification='STD') tile = sc.Strand(domains=[ss_bot, ss_top], name=f'tile-right-{top_helix}-{bot_helix}', - color=sc.Color(0, 0, 0), idt=idt) + color=sc.Color(0, 0, 0), vendor_fields=idt) design.add_strand(tile) design.assign_dna(tile, seq) diff --git a/examples/16_helix_origami_rectangle_seed_tiles_grow_from_top.py b/examples/16_helix_origami_rectangle_seed_tiles_grow_from_top.py index 3c133e6..d192839 100644 --- a/examples/16_helix_origami_rectangle_seed_tiles_grow_from_top.py +++ b/examples/16_helix_origami_rectangle_seed_tiles_grow_from_top.py @@ -30,7 +30,7 @@ def set_helix_major_ticks(design: sc.Design) -> None: for helix in design.helices.values(): helix.major_ticks = list(major_ticks) - for _,helix in zip([0,1,2], design.helices.values()): + for _, helix in zip([0, 1, 2], design.helices.values()): ticks = [11, 22, 32, 40, 48] tick = 58 offset = 11 @@ -73,8 +73,9 @@ def add_adapters(design: sc.Design) -> None: start=left_outside_seed, end=left_inside_seed) ss_bot = sc.Domain(helix=bot_helix, forward=False, start=left_outside_seed, end=left_inside_seed) - idt = sc.IDTFields(scale='25nm', purification='STD') - adapter = sc.Strand(domains=[ss_bot, ss_top], name=f'adap-left-{top_helix}-{bot_helix}', idt=idt) + idt = sc.VendorFields(scale='25nm', purification='STD') + adapter = sc.Strand(domains=[ss_bot, ss_top], name=f'adap-left-{top_helix}-{bot_helix}', + vendor_fields=idt) design.add_strand(adapter) # right adapters @@ -86,8 +87,9 @@ def add_adapters(design: sc.Design) -> None: start=right_inside_seed, end=right_outside_seed) ss_bot = sc.Domain(helix=bot_helix, forward=False, start=right_inside_seed, end=right_outside_seed) - idt = sc.IDTFields(scale='25nm', purification='STD') - adapter = sc.Strand(domains=[ss_top, ss_bot], name=f'adap-right-{top_helix}-{bot_helix}', idt=idt) + idt = sc.VendorFields(scale='25nm', purification='STD') + adapter = sc.Strand(domains=[ss_top, ss_bot], name=f'adap-right-{top_helix}-{bot_helix}', + vendor_fields=idt) design.add_strand(adapter) diff --git a/examples/1_staple_1_helix_origami_idt_duplicate_names.py b/examples/1_staple_1_helix_origami_idt_duplicate_names.py index 73238c3..ed7ecac 100644 --- a/examples/1_staple_1_helix_origami_idt_duplicate_names.py +++ b/examples/1_staple_1_helix_origami_idt_duplicate_names.py @@ -1,24 +1,26 @@ import scadnano as sc + def create_design() -> sc.Design: ss1_r = sc.Domain(0, True, 0, 4) ss2_r = sc.Domain(0, True, 4, 8) ss3_r = sc.Domain(0, True, 8, 12) ss_l = sc.Domain(0, False, 0, 12) - s1_r = sc.Strand([ss1_r], idt=sc.IDTFields(), name='s1_r') - s2_r = sc.Strand([ss2_r], idt=sc.IDTFields(), name='s1_r') - s3_r = sc.Strand([ss3_r], idt=sc.IDTFields(), name='s1_r') - s_l = sc.Strand([ss_l], idt=sc.IDTFields(), name='s_l') + s1_r = sc.Strand([ss1_r], vendor_fields=sc.VendorFields(), name='s1_r') + s2_r = sc.Strand([ss2_r], vendor_fields=sc.VendorFields(), name='s1_r') + s3_r = sc.Strand([ss3_r], vendor_fields=sc.VendorFields(), name='s1_r') + s_l = sc.Strand([ss_l], vendor_fields=sc.VendorFields(), name='s_l') strands = [s1_r, s2_r, s3_r, s_l] design = sc.Design(strands=strands, grid=sc.square) - design.assign_dna(s_l, 'AGTT'*3) + design.assign_dna(s_l, 'AGTT' * 3) return design + if __name__ == '__main__': d = create_design() d.write_idt_bulk_input_file(directory='idt') diff --git a/examples/idt-plates-explicit.py b/examples/idt-plates-explicit.py index eb23cae..e4e4a69 100644 --- a/examples/idt-plates-explicit.py +++ b/examples/idt-plates-explicit.py @@ -19,9 +19,9 @@ def create_design() -> sc.Design: row = ROWS[row_idx] col = COLS[col_idx] well = f'{row}{col}' - idt = sc.IDTFields(plate=f'plate{plate}', well=well) + idt = sc.VendorFields(plate=f'plate{plate}', well=well) - strand = sc.Strand(domains=[ss_f, ss_r], idt=idt, name=f'staple{s}') + strand = sc.Strand(domains=[ss_f, ss_r], vendor_fields=idt, name=f'staple{s}') strands.append(strand) row_idx += 1 if row_idx == len(ROWS): diff --git a/scadnano/modifications.py b/scadnano/modifications.py index 02b2854..4ca0dd9 100644 --- a/scadnano/modifications.py +++ b/scadnano/modifications.py @@ -1,23 +1,23 @@ from scadnano import Modification5Prime, Modification3Prime, ModificationInternal -biotin_5p = Modification5Prime(display_text='B', idt_text='/5Biosg/') -biotin_3p = Modification3Prime(display_text='B', idt_text='/3Bio/') -biotin_int = ModificationInternal(display_text='B', idt_text='/iBiodT/', allowed_bases=frozenset('T')) +biotin_5p = Modification5Prime(display_text='B', vendor_code='/5Biosg/') +biotin_3p = Modification3Prime(display_text='B', vendor_code='/3Bio/') +biotin_int = ModificationInternal(display_text='B', vendor_code='/iBiodT/', allowed_bases=frozenset('T')) -cy3_5p = Modification5Prime(display_text='Cy3', idt_text='/5Cy3/') -cy3_3p = Modification3Prime(display_text='Cy3', idt_text='/3Cy3Sp/') -cy3_int = ModificationInternal(display_text='Cy3', idt_text='/iCy3/') +cy3_5p = Modification5Prime(display_text='Cy3', vendor_code='/5Cy3/') +cy3_3p = Modification3Prime(display_text='Cy3', vendor_code='/3Cy3Sp/') +cy3_int = ModificationInternal(display_text='Cy3', vendor_code='/iCy3/') -cy5_5p = Modification5Prime(display_text='Cy5', idt_text='/5Cy5/') -cy5_3p = Modification3Prime(display_text='Cy5', idt_text='/3Cy5Sp/') -cy5_int = ModificationInternal(display_text='Cy5', idt_text='/iCy5/') +cy5_5p = Modification5Prime(display_text='Cy5', vendor_code='/5Cy5/') +cy5_3p = Modification3Prime(display_text='Cy5', vendor_code='/3Cy5Sp/') +cy5_int = ModificationInternal(display_text='Cy5', vendor_code='/iCy5/') -fam_5p = Modification5Prime(display_text='F', idt_text='/56-FAM/') -fam_3p = Modification3Prime(display_text='F', idt_text='/36-FAM/') +fam_5p = Modification5Prime(display_text='F', vendor_code='/56-FAM/') +fam_3p = Modification3Prime(display_text='F', vendor_code='/36-FAM/') -rox_5p = Modification5Prime(display_text='R', idt_text='/56-ROXN/') -rox_3p = Modification3Prime(display_text='R', idt_text='/3Rox_N/') +rox_5p = Modification5Prime(display_text='R', vendor_code='/56-ROXN/') +rox_3p = Modification3Prime(display_text='R', vendor_code='/3Rox_N/') -fluorescein_5p = Modification5Prime(display_text='F', idt_text='/5FluorT/') -fluorescein_3p = Modification3Prime(display_text='F', idt_text='/3FluorT/') -fluorescein_int = ModificationInternal(display_text='F', idt_text='/iFluorT/') \ No newline at end of file +fluorescein_5p = Modification5Prime(display_text='F', vendor_code='/5FluorT/') +fluorescein_3p = Modification3Prime(display_text='F', vendor_code='/3FluorT/') +fluorescein_int = ModificationInternal(display_text='F', vendor_code='/iFluorT/') diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 93531dc..e303bfd 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -54,7 +54,7 @@ # needed to use forward annotations: https://docs.python.org/3/whatsnew/3.7.html#whatsnew37-pep563 from __future__ import annotations -__version__ = "0.18.4" # version line; WARNING: do not remove or change this line or comment +__version__ = "0.19.0" # version line; WARNING: do not remove or change this line or comment import collections import dataclasses @@ -379,8 +379,8 @@ class Grid(str, enum.Enum): ########################################################################## # constants -default_idt_scale = "25nm" -default_idt_purification = "STD" +default_vendor_scale = "25nm" +default_vendor_purification = "STD" def default_major_tick_distance(grid: Grid) -> int: @@ -899,7 +899,8 @@ def m13(rotation: int = 5587, variant: M13Variant = M13Variant.p7249) -> str: legacy_dna_sequence_keys = ['dna_sequence'] # support legacy names for these ideas domains_key = 'domains' legacy_domains_keys = ['substrands'] # support legacy names for these ideas -idt_key = 'idt' +vendor_key = 'vendor' +legacy_vendor_keys = ['idt'] is_scaffold_key = 'is_scaffold' modification_5p_key = '5prime_modification' modification_3p_key = '3prime_modification' @@ -929,20 +930,21 @@ def m13(rotation: int = 5587, variant: M13Variant = M13Variant.p7249) -> str: mod_location_key = 'location' mod_display_text_key = 'display_text' mod_id_key = 'id' -mod_idt_text_key = 'idt_text' +mod_vendor_code_key = 'vendor_code' +legacy_mod_vendor_code_keys = ['idt_text'] mod_font_size_key = 'font_size' mod_display_connector_key = 'display_connector' mod_allowed_bases_key = 'allowed_bases' mod_connector_length_key = 'connector_length' -# IDT keys -idt_scale_key = 'scale' -idt_purification_key = 'purification' -idt_plate_key = 'plate' -idt_well_key = 'well' -# legacy; not written anymore as part of idt, but may be read from older versions of the JSON if -# the Strand has no name but the IDT field does have a name -idt_name_key = 'name' +# vendor keys +vendor_scale_key = 'scale' +vendor_purification_key = 'purification' +vendor_plate_key = 'plate' +vendor_well_key = 'well' +# legacy; not written anymore as part of vendor fields, but may be read from older versions of the JSON if +# the Strand has no name but the VendorField does have a name +vendor_name_key = 'name' # end keys ################## @@ -980,13 +982,13 @@ class Modification(_JSONSerializable, ABC): :any:`Modification3Prime`, :any:`Modification5Prime`, or :any:`ModificationInternal` to instantiate. - If :data:`Modification.id` is not specified, then :data:`Modification.idt_text` is used as + If :data:`Modification.id` is not specified, then :data:`Modification.vendor_code` is used as the unique ID. Each :data:`Modification.id` must be unique. For example if you create a 5' modification - to represent 6 T bases: ``t6_5p = Modification5Prime(display_text='6T', idt_text='TTTTTT')`` + to represent 6 T bases: ``t6_5p = Modification5Prime(display_text='6T', vendor_code='TTTTTT')`` (this was a useful hack for putting single-stranded extensions on strands before the :any:`Extension` class was created to directly support this idea), then this would clash with a similar 3' modification without specifying unique IDs for them: - ``t6_3p = Modification3Prime(display_text='6T', idt_text='TTTTTT') # ERROR``. + ``t6_3p = Modification3Prime(display_text='6T', vendor_code='TTTTTT') # ERROR``. In general it is recommended to create a single :any:`Modification` object for each *type* of modification in the design. For example, if many strands have a 5' biotin, then it is recommended to @@ -994,7 +996,7 @@ class was created to directly support this idea), .. code-block:: python - biotin_5p = Modification5Prime(display_text='B', idt_text='/5Biosg/') + biotin_5p = Modification5Prime(display_text='B', vendor_code='/5Biosg/') design.draw_strand(0, 0).move(8).with_modification_5p(biotin_5p) design.draw_strand(1, 0).move(8).with_modification_5p(biotin_5p) """ @@ -1007,11 +1009,12 @@ class was created to directly support this idea), """ Representation as a string; used to write in :any:`Strand` json representation, while the full description of the modification is written under a global key in the :any:`Design`. - If not specified, but :py:data:`Modification.idt_text` is specified, then it will be set equal to that. + If not specified, but :data:`Modification.vendor_code` is specified, then it will be set equal to that. """ - idt_text: Optional[str] = None - """IDT text string specifying this modification (e.g., '/5Biosg/' for 5' biotin). optional""" + vendor_code: Optional[str] = None + """Text string specifying this modification used by a vendor (a DNA synthesis company such as IDT). + For example, for IDT DNA (https://www.idtdna.com/), use '/5Biosg/' for 5' biotin.""" connector_length: int = default_connector_length """Length of "connector" displayed in web interface. @@ -1021,13 +1024,13 @@ class was created to directly support this idea), text does not overlap.""" def __post_init__(self) -> None: - if self.id == _default_modification_id and self.idt_text is not None: - object.__setattr__(self, 'id', self.idt_text) + if self.id == _default_modification_id and self.vendor_code is not None: + object.__setattr__(self, 'id', self.vendor_code) def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> Dict[str, Any]: ret = {mod_display_text_key: self.display_text} - if self.idt_text is not None: - ret[mod_idt_text_key] = self.idt_text + if self.vendor_code is not None: + ret[mod_vendor_code_key] = self.vendor_code ret[mod_display_connector_key] = False # type: ignore if self.connector_length != default_connector_length: ret[mod_connector_length_key] = self.connector_length @@ -1063,7 +1066,7 @@ class Modification5Prime(Modification): .. code-block:: python - biotin_5p = Modification5Prime(display_text='B', idt_text='/5Biosg/') + biotin_5p = Modification5Prime(display_text='B', vendor_code='/5Biosg/') design.draw_strand(0, 0).move(8).with_modification_5p(biotin_5p) design.draw_strand(1, 0).move(8).with_modification_5p(biotin_5p) """ @@ -1078,9 +1081,10 @@ def from_json(json_map: Dict[str, Any]) -> Modification5Prime: display_text = json_map[mod_display_text_key] location = json_map[mod_location_key] assert location == "5'" - idt_text = json_map.get(mod_idt_text_key) + vendor_code = mandatory_field(Modification5Prime, json_map, mod_vendor_code_key, + legacy_keys=legacy_mod_vendor_code_keys) connector_length = json_map.get(mod_connector_length_key, default_connector_length) - return Modification5Prime(display_text=display_text, idt_text=idt_text, + return Modification5Prime(display_text=display_text, vendor_code=vendor_code, connector_length=connector_length) @staticmethod @@ -1099,7 +1103,7 @@ class Modification3Prime(Modification): .. code-block:: python - biotin_3p = Modification3Prime(display_text='B', idt_text='/3Bio/') + biotin_3p = Modification3Prime(display_text='B', vendor_code='/3Bio/') design.draw_strand(0, 0).move(8).with_modification_3p(biotin_3p) design.draw_strand(1, 0).move(8).with_modification_3p(biotin_3p) """ @@ -1114,9 +1118,10 @@ def from_json(json_map: Dict[str, Any]) -> Modification3Prime: display_text = json_map[mod_display_text_key] location = json_map[mod_location_key] assert location == "3'" - idt_text = json_map.get(mod_idt_text_key) + vendor_code = mandatory_field(Modification3Prime, json_map, mod_vendor_code_key, + legacy_keys=legacy_mod_vendor_code_keys) connector_length = json_map.get(mod_connector_length_key, default_connector_length) - return Modification3Prime(display_text=display_text, idt_text=idt_text, + return Modification3Prime(display_text=display_text, vendor_code=vendor_code, connector_length=connector_length) @staticmethod @@ -1159,11 +1164,13 @@ def from_json(json_map: Dict[str, Any]) -> ModificationInternal: display_text = json_map[mod_display_text_key] location = json_map[mod_location_key] assert location == "internal" - idt_text = json_map.get(mod_idt_text_key) + vendor_code = mandatory_field(Modification5Prime, json_map, mod_vendor_code_key, + legacy_keys=legacy_mod_vendor_code_keys) allowed_bases_list = json_map.get(mod_allowed_bases_key) allowed_bases = frozenset(allowed_bases_list) if allowed_bases_list is not None else None connector_length = json_map.get(mod_connector_length_key, default_connector_length) - return ModificationInternal(display_text=display_text, idt_text=idt_text, allowed_bases=allowed_bases, + return ModificationInternal(display_text=display_text, vendor_code=vendor_code, + allowed_bases=allowed_bases, connector_length=connector_length) @staticmethod @@ -2163,17 +2170,17 @@ def idt_dna_sequence(self) -> Optional[str]: strand_pos = pos + len_dna_prior if strand_pos in strand.modifications_int: # if internal mod attached to base, replace base mod = strand.modifications_int[strand_pos] - if mod.idt_text is not None: - idt_text_with_delim = mod.idt_text + if mod.vendor_code is not None: + vendor_code_with_delim = mod.vendor_code if mod.allowed_bases is not None: if base not in mod.allowed_bases: msg = (f'internal modification {mod} can only replace one of these bases: ' f'{",".join(mod.allowed_bases)}, ' f'but the base at position {strand_pos} is {base}') raise IllegalDesignError(msg) - new_seq_list[-1] = idt_text_with_delim # replace base with modified base + new_seq_list[-1] = vendor_code_with_delim # replace base with modified base else: - new_seq_list.append(idt_text_with_delim) # append modification between two bases + new_seq_list.append(vendor_code_with_delim) # append modification between two bases return ''.join(new_seq_list) @@ -2752,51 +2759,63 @@ def wc(seq: str) -> str: @dataclass -class IDTFields(_JSONSerializable): - """Data required when ordering DNA strands from the synthesis company - `IDT (Integrated DNA Technologies) `_. - This data is used when automatically generating files used to order DNA from IDT. +class VendorFields(_JSONSerializable): + """ + Data required when ordering DNA strands from a synthesis company. + These fields were originally designed for `IDT (Integrated DNA Technologies) `_ + and the default values for :data:`VendorFields.scale` and :data:`VendorFields.purification` reflect that. + However, most vendors have the same concepts of scale, purification, a code to specify the modification + (the field :data:`VendorFields.vendor_code`), + etc., so we use this generic class for any of them. Currently only IDT is supported by methods to + automatically export DNA sequences in the format IDT recognizes, but one should be able to write custom + code to export other formats that reads the fields in this object. When exporting to IDT files via :py:meth:`Design.write_idt_plate_excel_file` - or :py:meth:`Design.write_idt_bulk_input_file`, the field :py:data:`Strand.name` is used for the - name if it exists, otherwise a reasonable default is chosen.""" + or :meth:`Design.write_idt_bulk_input_file`, the field :data:`Strand.name` is used for the + name if it exists, otherwise a reasonable default is chosen. + """ - scale: str = default_idt_scale - """Synthesis scale at which to synthesize the strand (third field in IDT bulk input: + scale: str = default_vendor_scale + """ + Synthesis scale at which to synthesize the strand (third field in IDT bulk input: https://www.idtdna.com/site/order/oligoentry). Choices supplied by IDT at the time this was written: ``"25nm"``, ``"100nm"``, ``"250nm"``, ``"1um"``, ``"5um"``, ``"10um"``, ``"4nmU"``, ``"20nmU"``, ``"PU"``, ``"25nmS"``. """ - purification: str = default_idt_purification - """Purification options (fourth field in IDT bulk input: + purification: str = default_vendor_purification + """ + Purification options (fourth field in IDT bulk input: https://www.idtdna.com/site/order/oligoentry). Choices supplied by IDT at the time this was written: ``"STD"``, ``"PAGE"``, ``"HPLC"``, ``"IEHPLC"``, ``"RNASE"``, ``"DUALHPLC"``, ``"PAGEHPLC"``. """ plate: Optional[str] = None - """Name of plate in case this strand will be ordered on a 96-well or 384-well plate. + """ + Name of plate in case this strand will be ordered on a 96-well or 384-well plate. - Optional field, but non-optional if :py:data:`IDTFields.well` is not ``None``. + Optional field, but non-optional if :data:`VendorFields.well` is not ``None``. """ well: Optional[str] = None - """Well position on plate in case this strand will be ordered on a 96-well or 384-well plate. + """ + Well position on plate in case this strand will be ordered on a 96-well or 384-well plate. + Well position on plate in case this strand will be ordered on a 96-well or 384-well plate. - Optional field, but non-optional if :py:data:`IDTFields.plate` is not ``None``. + Optional field, but non-optional if :data:`VendorFields.plate` is not ``None``. """ def __post_init__(self) -> None: - _check_idt_string_not_none_or_empty(self.scale, 'scale') - _check_idt_string_not_none_or_empty(self.purification, 'purification') + _check_vendor_string_not_none_or_empty(self.scale, 'scale') + _check_vendor_string_not_none_or_empty(self.purification, 'purification') if self.plate is None and self.well is not None: - raise IllegalDesignError(f'IDTFields.plate cannot be None if IDTFields.well is not None\n' - f'IDTFields.well = {self.well}') + raise IllegalDesignError(f'VendorFields.plate cannot be None if VendorFields.well is not None\n' + f'VendorFields.well = {self.well}') if self.plate is not None and self.well is None: - raise IllegalDesignError(f'IDTFields.well cannot be None if IDTFields.plate is not None\n' - f'IDTFields.plate = {self.plate}') + raise IllegalDesignError(f'VendorFields.well cannot be None if VendorFields.plate is not None\n' + f'VendorFields.plate = {self.plate}') def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> Union[NoIndent, Dict[str, Any]]: @@ -2808,19 +2827,19 @@ def to_json_serializable(self, suppress_indent: bool = True, return NoIndent(dct) if suppress_indent else dct @staticmethod - def from_json(json_map: Dict[str, Any]) -> 'IDTFields': - scale = mandatory_field(IDTFields, json_map, idt_scale_key) - purification = mandatory_field(IDTFields, json_map, idt_purification_key) - plate = json_map.get(idt_plate_key) - well = json_map.get(idt_well_key) - return IDTFields(scale=scale, purification=purification, plate=plate, well=well) + def from_json(json_map: Dict[str, Any]) -> VendorFields: + scale = mandatory_field(VendorFields, json_map, vendor_scale_key) + purification = mandatory_field(VendorFields, json_map, vendor_purification_key) + plate = json_map.get(vendor_plate_key) + well = json_map.get(vendor_well_key) + return VendorFields(scale=scale, purification=purification, plate=plate, well=well) -def _check_idt_string_not_none_or_empty(value: str, field_name: str) -> None: +def _check_vendor_string_not_none_or_empty(value: str, field_name: str) -> None: if value is None: - raise IllegalDesignError(f'field {field_name} in IDTFields cannot be None') + raise IllegalDesignError(f'field {field_name} in VendorFields cannot be None') if len(value) == 0: - raise IllegalDesignError(f'field {field_name} in IDTFields cannot be empty') + raise IllegalDesignError(f'field {field_name} in VendorFields cannot be empty') class StrandBuilder: @@ -3152,27 +3171,27 @@ def as_scaffold(self) -> StrandBuilder: self._strand.set_scaffold(True) return self - def with_idt(self, scale: str = default_idt_scale, - purification: str = default_idt_purification, - plate: Optional[str] = None, well: Optional[str] = None) \ + def with_vendor_fields(self, scale: str = default_vendor_scale, + purification: str = default_vendor_purification, + plate: Optional[str] = None, well: Optional[str] = None) \ -> StrandBuilder: """ - Gives :any:`IDTFields` value to :any:`Strand` being built. + Gives :any:`VendorFields` value to :any:`Strand` being built. :param scale: - see :py:data:`IDTFields.scale` + see :py:data:`VendorFields.scale` :param purification: - see :py:data:`IDTFields.purification` + see :py:data:`VendorFields.purification` :param plate: - see :py:data:`IDTFields.plate` + see :py:data:`VendorFields.plate` :param well: - see :py:data:`IDTFields.well` + see :py:data:`VendorFields.well` :return: self """ if self._strand is None: raise ValueError('no Strand created yet; make at least one domain first') - self._strand.idt = IDTFields(scale=scale, purification=purification, - plate=plate, well=well) + self._strand.vendor_fields = VendorFields(scale=scale, purification=purification, + plate=plate, well=well) return self def with_modification_5p(self, mod: Modification5Prime) -> StrandBuilder: @@ -3551,8 +3570,8 @@ def dna_sequence(self) -> Optional[str]: (for complementarity checking) or :any:`Strand.set_dna_sequence` (without complementarity checking, to allow mismatches). - Note that this does not include any IDT codes for :any:`Modification`'s. - To include those call :meth:`Strand.idt_dna_sequence`.""" + Note that this does not include any vendor codes for :any:`Modification`'s. + To include those call :meth:`Strand.vendor_dna_sequence`.""" sequence_list = [] for domain in self.domains: if domain.dna_sequence is None: @@ -3565,16 +3584,23 @@ def dna_sequence(self) -> Optional[str]: a color is assigned by cycling through a list of defaults given by :meth:`ColorCycler.colors`""" - idt: Optional[IDTFields] = None - """Fields used when ordering strands from the synthesis company IDT + vendor_fields: Optional[VendorFields] = None + """ + Fields used when ordering strands from the a DNA synthesis company such as IDT (Integrated DNA Technologies, Coralville, IA). If present (i.e., not equal to :const:`None`) - then the method :py:meth:`Design.write_idt_bulk_input_file` can be called to automatically + then the method :meth:`Design.write_idt_bulk_input_file` can be called to automatically generate an text file for ordering strands in test tubes: https://www.idtdna.com/site/order/oligoentry, as can the method :py:meth:`Design.write_idt_plate_excel_file` for writing a Microsoft Excel file that can be uploaded to IDT's website for describing DNA sequences to be ordered in 96-well or 384-well plates: - https://www.idtdna.com/site/order/plate/index/dna/1800""" + https://www.idtdna.com/site/order/plate/index/dna/1800 + + Currently no other vendors are supported via export methods in the package, + but one could write custom export code based on these fields since most DNA synthesis companies + support the same concepts of scale, purification, and a code for modifications + (such as ``"/5Biosg/"`` for 5' biotin from IDT). + """ is_scaffold: bool = False """Indicates whether this :any:`Strand` is a scaffold for a DNA origami. If any :any:`Strand` in a @@ -3643,7 +3669,7 @@ def dna_sequence(self) -> Optional[str]: def __init__(self, domains: List[Union[Domain, Loopout, Extension]], circular: bool = False, color: Optional[Color] = None, - idt: Optional[IDTFields] = None, + vendor_fields: Optional[VendorFields] = None, is_scaffold: bool = False, modification_5p: Optional[Modification5Prime] = None, modification_3p: Optional[Modification3Prime] = None, modifications_int: Optional[Dict[int, ModificationInternal]] = None, @@ -3654,7 +3680,7 @@ def __init__(self, self.domains = domains self.circular = circular self.color = color - self.idt = idt + self.vendor_fields = vendor_fields self.is_scaffold = is_scaffold self.modification_5p = modification_5p self.modification_3p = modification_3p @@ -3685,8 +3711,8 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D dct[color_key] = self.color.to_json_serializable(suppress_indent) if self.dna_sequence is not None: dct[dna_sequence_key] = self.dna_sequence - if self.idt is not None: - dct[idt_key] = self.idt.to_json_serializable(suppress_indent) + if self.vendor_fields is not None: + dct[vendor_key] = self.vendor_fields.to_json_serializable(suppress_indent) dct[domains_key] = [domain.to_json_serializable(suppress_indent) for domain in self.domains] if hasattr(self, is_scaffold_key) and self.is_scaffold: dct[is_scaffold_key] = self.is_scaffold @@ -3747,19 +3773,21 @@ def from_json(json_map: dict) -> Strand: name = json_map.get(strand_name_key) - idt_dict: Optional[dict] = json_map.get(idt_key) - idt = None if idt_dict is None else IDTFields.from_json(idt_dict) + vendor_dict: Optional[dict] = optional_field(None, json_map, vendor_key, + legacy_keys=legacy_vendor_keys) + vendor_fields = None if vendor_dict is None else VendorFields.from_json(vendor_dict) # legacy: - # if no name is specified, but there's a name field in idt, then use that as the Strand's name - if name is None and idt_dict is not None and idt_name_key in idt_dict: - name = idt_dict[idt_name_key] + # if no name is specified, but there's a name field in vendor fields, + # then use that as the Strand's name + if name is None and vendor_dict is not None and vendor_name_key in vendor_dict: + name = vendor_dict[vendor_name_key] return Strand( domains=substrands, dna_sequence=dna_sequence, circular=circular, color=color, - idt=idt, + vendor_fields=vendor_fields, is_scaffold=is_scaffold, name=name, label=label, @@ -3881,7 +3909,7 @@ def set_domains(self, domains: Iterable[Union[Domain, Loopout]]) -> None: if isinstance(self.domains[-1], Loopout): raise StrandError(self, 'strand cannot end with a loopout') - def idt_export_name(self, unique_names: bool = False) -> str: + def vendor_export_name(self, unique_names: bool = False) -> str: """ :param unique_names: If True and default name is used, @@ -4281,18 +4309,18 @@ def _ensure_domains_nonoverlapping(self) -> None: f'\n{d1}' f'\n{d2}') - def idt_dna_sequence(self, domain_delimiter: str = '') -> str: + def vendor_dna_sequence(self, domain_delimiter: str = '') -> str: """ :param domain_delimiter: string to put in between DNA sequences of each domain, and between 5'/3' modifications and DNA. Note that the delimiter is not put between internal modifications and the next base(s) in the same domain. - :return: DNA sequence as it needs to be typed to order from IDT, with + :return: DNA sequence as it needs to be typed to order from a DNA synthesis vendor, with :py:data:`Modification5Prime`'s, :py:data:`Modification3Prime`'s, and - :py:data:`ModificationInternal`'s represented with text codes, e.g., "/5Biosg/ACGT" for sequence - ACGT with a 5' biotin modification. + :py:data:`ModificationInternal`'s represented with text codes, e.g., for IDT DNA, using + "/5Biosg/ACGT" for sequence ACGT with a 5' biotin modification. """ self._ensure_modifications_legal(check_offsets_legal=True) @@ -4301,14 +4329,14 @@ def idt_dna_sequence(self, domain_delimiter: str = '') -> str: ret_list: List[str] = [] - if self.modification_5p is not None and self.modification_5p.idt_text is not None: - ret_list.append(self.modification_5p.idt_text) + if self.modification_5p is not None and self.modification_5p.vendor_code is not None: + ret_list.append(self.modification_5p.vendor_code) for substrand in self.domains: ret_list.append(substrand.idt_dna_sequence()) - if self.modification_3p is not None and self.modification_3p.idt_text is not None: - ret_list.append(self.modification_3p.idt_text) + if self.modification_3p is not None and self.modification_3p.vendor_code is not None: + ret_list.append(self.modification_3p.vendor_code) return domain_delimiter.join(ret_list) @@ -5010,11 +5038,11 @@ def _plate_map(plate_name: str, strands_in_plate: List[Strand], plate_type: Plat """ well_to_strand = {} for strand in strands_in_plate: - if strand.idt is None: + if strand.vendor_fields is None: raise ValueError(f'strand {strand} has no idt field, so cannot be included in the plate map') - elif strand.idt.well is None: + elif strand.vendor_fields.well is None: raise ValueError(f'strand {strand} has no idt.well field, so cannot be included in the plate map') - well_to_strand[strand.idt.well] = strand + well_to_strand[strand.vendor_fields.well] = strand plate_map = PlateMap( plate_name=plate_name, @@ -6233,24 +6261,25 @@ def plate_maps(self, strand_names_to_plate_and_well = {} plate_names_to_strands = defaultdict(list) for strand in strands: - if strand.idt is not None and strand.idt.plate is not None: - plate_names_to_strands[strand.idt.plate].append(strand) + if strand.vendor_fields is not None and strand.vendor_fields.plate is not None: + plate_names_to_strands[strand.vendor_fields.plate].append(strand) if strand.name is not None and strand.name in strand_names_to_plate_and_well: if warn_duplicate_strand_names: print(f'WARNING: found duplicate instance of strand with name {strand.name}') plate, well = strand_names_to_plate_and_well[strand.name] - if strand.idt.plate != plate: + if strand.vendor_fields.plate != plate: raise ValueError(f'two strands with name {strand.name} exist but have different ' - f'IDT plates "{plate}" and "{strand.idt.plate}"' + f'IDT plates "{plate}" and "{strand.vendor_fields.plate}"' 'duplicate strands with the same name are allowed, ' 'but they must have the same IDT plate and well') - if strand.idt.well != well: + if strand.vendor_fields.well != well: raise ValueError(f'two strands with name {strand.name} exist but have different ' - f'IDT wells "{well}" and "{strand.idt.well}"' + f'IDT wells "{well}" and "{strand.vendor_fields.well}"' 'duplicate strands with the same name are allowed, ' 'but they must have the same IDT plate and well') else: - strand_names_to_plate_and_well[strand.name] = (strand.idt.plate, strand.idt.well) + strand_names_to_plate_and_well[strand.name] = ( + strand.vendor_fields.plate, strand.vendor_fields.well) plate_maps = [_plate_map(name, strands_in_plate, plate_type) for name, strands_in_plate in plate_names_to_strands.items()] @@ -7252,18 +7281,18 @@ def to_idt_bulk_input_format(self, idt_lines: List[str] = [] for strand in strands_to_export: - if strand.idt is None and only_strands_with_idt: + if strand.vendor_fields is None and only_strands_with_idt: raise AssertionError(f'cannot export strand {strand} to IDT because it has no IDT field; ' f'since only_strands_with_idt is True, ' f'this strand should have been filtered out by _idt_strands_to_export') - if strand.idt is not None: - scale = strand.idt.scale - purification = strand.idt.purification + if strand.vendor_fields is not None: + scale = strand.vendor_fields.scale + purification = strand.vendor_fields.purification else: - scale = default_idt_scale - purification = default_idt_purification + scale = default_vendor_scale + purification = default_vendor_purification idt_lines.append(delimiter.join( - [strand.idt_export_name(), strand.idt_dna_sequence(domain_delimiter=domain_delimiter), + [strand.vendor_export_name(), strand.vendor_dna_sequence(domain_delimiter=domain_delimiter), scale, purification] )) @@ -7284,11 +7313,11 @@ def _idt_strands_to_export(self, *, continue # skip strands with no IDT field unless requested to export - if strand.idt is None and only_strands_with_idt: + if strand.vendor_fields is None and only_strands_with_idt: continue # figure out what name to export - name = strand.idt_export_name() + name = strand.vendor_export_name() if name in added_strands: existing_strand = added_strands[name] @@ -7330,24 +7359,24 @@ def _check_strands_with_same_name_agree_on_other_idt_fields(strand: Strand, exis f' strand 2: helix {existing_domain.helix}, 5\' end at offset ' f'{existing_domain.offset_5p()}, ' f'sequence: {existing_strand.dna_sequence}\n') - elif strand.idt is not None \ - and existing_strand.idt is not None: - if strand.idt.scale != existing_strand.idt.scale: + elif strand.vendor_fields is not None \ + and existing_strand.vendor_fields is not None: + if strand.vendor_fields.scale != existing_strand.vendor_fields.scale: raise IllegalDesignError( f'two strands with same name {name} but different IDT scales:\n' f' strand 1: helix {domain.helix}, 5\' end at offset {domain.offset_5p()}, ' - f'scale: {strand.idt.scale}\n' + f'scale: {strand.vendor_fields.scale}\n' f' strand 2: helix {existing_domain.helix}, 5\' end at offset ' f'{existing_domain.offset_5p()}, ' - f'scale: {existing_strand.idt.scale}\n') - elif strand.idt.purification != existing_strand.idt.purification: + f'scale: {existing_strand.vendor_fields.scale}\n') + elif strand.vendor_fields.purification != existing_strand.vendor_fields.purification: raise IllegalDesignError( f'two strands with same name {name} but different purifications:\n' f' strand 1: helix {domain.helix}, 5\' end at offset {domain.offset_5p()}, ' - f'purification: {strand.idt.purification}\n' + f'purification: {strand.vendor_fields.purification}\n' f' strand 2: helix {existing_domain.helix}, 5\' end at offset ' f'{existing_domain.offset_5p()}, ' - f'purification: {existing_strand.idt.purification}\n') + f'purification: {existing_strand.vendor_fields.purification}\n') def write_idt_bulk_input_file(self, *, directory: str = '.', filename: str = None, key: Optional[KeyFunction[Strand]] = None, @@ -7390,7 +7419,7 @@ def write_idt_bulk_input_file(self, *, directory: str = '.', filename: str = Non remaining readable by IDT's website. :param warn_duplicate_name: if ``True`` prints a warning when two different :any:`Strand`'s have the same - :data:`IDTFields.name` and the same :data:`Strand.dna_sequence`. An :any:`IllegalDesignError` is + :data:`VendorFields.name` and the same :data:`Strand.dna_sequence`. An :any:`IllegalDesignError` is raised (regardless of the value of this parameter) if two different :any:`Strand`'s have the same name but different sequences, IDT scales, or IDT purifications. @@ -7455,7 +7484,7 @@ def write_idt_plate_excel_file(self, *, directory: str = '.', filename: Optional :py:meth:`strand_order_key_function` :param warn_duplicate_name: if ``True`` prints a warning when two different :any:`Strand`'s have the same - :py:attr:`IDTFields.name` and the same :any:`Strand.dna_sequence`. An :any:`IllegalDesignError` is + :data:`Strand.name` and the same :any:`Strand.dna_sequence`. An :any:`IllegalDesignError` is raised (regardless of the value of this parameter) if two different :any:`Strand`'s have the same name but different sequences, IDT scales, or IDT purifications. @@ -7476,7 +7505,7 @@ def write_idt_plate_excel_file(self, *, directory: str = '.', filename: Optional the parameter `only_strands_with_idt` must be True. :param warn_using_default_plates: specifies whether, if `use_default_plates` is True, to print a warning for strands whose - :py:data:`Strand.idt` has the fields :py:data:`IDTFields.plate` and :py:data:`IDTFields.well`, + :py:data:`Strand.idt` has the fields :data:`VendorFields.plate` and :data:`VendorFields.well`, since `use_default_plates` directs these fields to be ignored. :param plate_type: a :any:`PlateType` specifying whether to use a 96-well plate or a 384-well plate @@ -7507,8 +7536,9 @@ def write_idt_plate_excel_file(self, *, directory: str = '.', filename: Optional def _write_plates_assuming_explicit_plates_in_each_strand(self, directory: str, filename: Optional[str], strands_to_export: List[Strand]) -> None: - plates = list({strand.idt.plate for strand in strands_to_export if strand.idt is not None if - strand.idt.plate is not None}) + plates = list( + {strand.vendor_fields.plate for strand in strands_to_export if strand.vendor_fields is not None if + strand.vendor_fields.plate is not None}) if len(plates) == 0: raise ValueError('Cannot write a a plate file since no plate data exists in any Strands ' 'in the design.\n' @@ -7521,23 +7551,24 @@ def _write_plates_assuming_explicit_plates_in_each_strand(self, directory: str, worksheet = self._add_new_excel_plate_sheet(plate, workbook) strands_in_plate = [strand for strand in strands_to_export if - strand.idt is not None and strand.idt.plate == plate] + strand.vendor_fields is not None and strand.vendor_fields.plate == plate] - strands_in_plate.sort(key=lambda s: (int(s.idt.well[1:]), s.idt.well[0])) # type: ignore + strands_in_plate.sort( + key=lambda s: (int(s.vendor_fields.well[1:]), s.vendor_fields.well[0])) # type: ignore for row, strand in enumerate(strands_in_plate): - if strand.idt is None: + if strand.vendor_fields is None: raise ValueError(f'cannot export strand {strand} to IDT because it has no idt field') - worksheet.cell(row + 2, 1).value = strand.idt.well - worksheet.cell(row + 2, 2).value = strand.idt_export_name() - worksheet.cell(row + 2, 3).value = strand.idt_dna_sequence() + worksheet.cell(row + 2, 1).value = strand.vendor_fields.well + worksheet.cell(row + 2, 2).value = strand.vendor_export_name() + worksheet.cell(row + 2, 3).value = strand.vendor_dna_sequence() workbook.save(filename_plate) # TODO: fix types when openpyxl supports type hints @staticmethod def _add_new_excel_plate_sheet(plate_name: str, - workbook: 'openpyxl.Workbook') -> 'openpyxl.Worksheet': + workbook: 'openpyxl.Workbook') -> Any: worksheet = workbook.create_sheet(title=plate_name) worksheet.cell(1, 1).value = 'Well Position' worksheet.cell(1, 2).value = 'Name' @@ -7581,20 +7612,20 @@ def _write_plates_default(self, directory: str, filename: Optional[str], strands on_final_plate = num_plates_needed == 1 for strand in strands: - if strand.idt is not None: - if warn_using_default_plates and strand.idt.plate is not None: + if strand.vendor_fields is not None: + if warn_using_default_plates and strand.vendor_fields.plate is not None: print( - f"WARNING: strand {strand} has plate entry {strand.idt.plate}, " + f"WARNING: strand {strand} has plate entry {strand.vendor_fields.plate}, " f"which is being ignored since we are using default plate/well addressing") - if warn_using_default_plates and strand.idt.well is not None: + if warn_using_default_plates and strand.vendor_fields.well is not None: print( - f"WARNING: strand {strand} has well entry {strand.idt.well}, " + f"WARNING: strand {strand} has well entry {strand.vendor_fields.well}, " f"which is being ignored since we are using default plate/well addressing") well = plate_coord.well() worksheet.cell(excel_row + 1, 1).value = well - worksheet.cell(excel_row + 1, 2).value = strand.idt_export_name() - worksheet.cell(excel_row + 1, 3).value = strand.idt_dna_sequence() + worksheet.cell(excel_row + 1, 2).value = strand.vendor_export_name() + worksheet.cell(excel_row + 1, 3).value = strand.vendor_dna_sequence() num_strands_remaining -= 1 # IDT charges extra for a plate with < 24 strands for 96-well plate @@ -7996,12 +8027,12 @@ def add_nick(self, helix: int, offset: int, forward: bool, new_color: bool = Tru # if strand is not circular, we delete it and create two new strands self.strands.remove(strand) - idt_present = strand.idt is not None + idt_present = strand.vendor_fields is not None strand_before: Strand = Strand( domains=domains_before, dna_sequence=seq_before_whole, color=strand.color, - idt=strand.idt if idt_present else None, + vendor_fields=strand.vendor_fields if idt_present else None, ) color_after = next(self.color_cycler) if new_color else strand.color @@ -8252,7 +8283,7 @@ def add_half_crossover(self, helix: int, helix2: int, offset: int, forward: bool 'cannot add crossover between two strands if one has a DNA sequence ' 'and the other does not') new_strand: Strand = Strand(domains=new_domains, color=strand_first.color, - dna_sequence=new_dna, idt=strand_first.idt, + dna_sequence=new_dna, vendor_fields=strand_first.vendor_fields, is_scaffold=strand1.is_scaffold or strand2.is_scaffold) # put new strand in place where strand_first was diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 96aaf0d..b063259 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -692,21 +692,21 @@ def test_mod_illegal_exceptions_raised(self) -> None: def test_Cy3(self) -> None: cy3_5 = mod.cy3_5p - self.assertEqual(r'/5Cy3/', cy3_5.idt_text) + self.assertEqual(r'/5Cy3/', cy3_5.vendor_code) self.assertEqual(r'/5Cy3/', cy3_5.id) self.assertEqual('Cy3', cy3_5.display_text) cy3_3 = mod.cy3_3p - self.assertEqual(r'/3Cy3Sp/', cy3_3.idt_text) + self.assertEqual(r'/3Cy3Sp/', cy3_3.vendor_code) self.assertEqual(r'/3Cy3Sp/', cy3_3.id) self.assertEqual('Cy3', cy3_3.display_text) # cy3_i1 = mod.Cy3(location=sc.ModLocation.internal, offset=1) cy3_i1 = mod.cy3_int - self.assertEqual(r'/iCy3/', cy3_i1.idt_text) + self.assertEqual(r'/iCy3/', cy3_i1.vendor_code) self.assertEqual(r'/iCy3/', cy3_i1.id) self.assertEqual('Cy3', cy3_i1.display_text) # cy3_i2 = mod.Cy3(location=sc.ModLocation.internal, offset=3) cy3_i2 = mod.cy3_int - self.assertEqual(r'/iCy3/', cy3_i2.idt_text) + self.assertEqual(r'/iCy3/', cy3_i2.vendor_code) self.assertEqual(r'/iCy3/', cy3_i2.id) self.assertEqual('Cy3', cy3_i2.display_text) @@ -722,29 +722,29 @@ def test_Cy3(self) -> None: modification_5p=cy3_5, modification_3p=cy3_3, modifications_int={1: cy3_i1, 3: cy3_i2}) - self.assertEqual(r'/5Cy3/ATTGC', strand5.idt_dna_sequence()) - self.assertEqual(r'ATTGC/3Cy3Sp/', strand3.idt_dna_sequence()) - self.assertEqual(r'/5Cy3/ATTGC/3Cy3Sp/', strand53.idt_dna_sequence()) - self.assertEqual(r'AT/iCy3/TG/iCy3/C', strand_i.idt_dna_sequence()) - self.assertEqual(r'/5Cy3/AT/iCy3/TG/iCy3/C/3Cy3Sp/', strand53_i.idt_dna_sequence()) + self.assertEqual(r'/5Cy3/ATTGC', strand5.vendor_dna_sequence()) + self.assertEqual(r'ATTGC/3Cy3Sp/', strand3.vendor_dna_sequence()) + self.assertEqual(r'/5Cy3/ATTGC/3Cy3Sp/', strand53.vendor_dna_sequence()) + self.assertEqual(r'AT/iCy3/TG/iCy3/C', strand_i.vendor_dna_sequence()) + self.assertEqual(r'/5Cy3/AT/iCy3/TG/iCy3/C/3Cy3Sp/', strand53_i.vendor_dna_sequence()) def test_biotin(self) -> None: biotin5 = mod.biotin_5p - self.assertEqual(r'/5Biosg/', biotin5.idt_text) + self.assertEqual(r'/5Biosg/', biotin5.vendor_code) self.assertEqual(r'/5Biosg/', biotin5.id) self.assertEqual('B', biotin5.display_text) biotin3 = mod.biotin_3p - self.assertEqual(r'/3Bio/', biotin3.idt_text) + self.assertEqual(r'/3Bio/', biotin3.vendor_code) self.assertEqual(r'/3Bio/', biotin3.id) self.assertEqual('B', biotin3.display_text) # biotin_i_1 = mod.Biotin(location=sc.ModLocation.internal, offset=1) biotin_i_1 = mod.biotin_int - self.assertEqual(r'/iBiodT/', biotin_i_1.idt_text) + self.assertEqual(r'/iBiodT/', biotin_i_1.vendor_code) self.assertEqual(r'/iBiodT/', biotin_i_1.id) self.assertEqual('B', biotin_i_1.display_text) # biotin_i_2 = mod.Biotin(location=sc.ModLocation.internal, offset=2) biotin_i_2 = mod.biotin_int - self.assertEqual(r'/iBiodT/', biotin_i_2.idt_text) + self.assertEqual(r'/iBiodT/', biotin_i_2.vendor_code) self.assertEqual(r'/iBiodT/', biotin_i_2.id) self.assertEqual('B', biotin_i_2.display_text) @@ -759,31 +759,31 @@ def test_biotin(self) -> None: strand53i = sc.Strand(domains=[sc.Domain(4, True, 0, 5)], dna_sequence='ATTGC', modification_5p=biotin5, modification_3p=biotin3, modifications_int={1: biotin_i_1, 2: biotin_i_2}) - self.assertEqual(r'/5Biosg/ATTGC', strand5.idt_dna_sequence()) - self.assertEqual(r'ATTGC/3Bio/', strand3.idt_dna_sequence()) - self.assertEqual(r'A/iBiodT//iBiodT/GC', strand_i.idt_dna_sequence()) - self.assertEqual(r'/5Biosg/ATTGC/3Bio/', strand53.idt_dna_sequence()) - self.assertEqual(r'/5Biosg/A/iBiodT//iBiodT/GC/3Bio/', strand53i.idt_dna_sequence()) + self.assertEqual(r'/5Biosg/ATTGC', strand5.vendor_dna_sequence()) + self.assertEqual(r'ATTGC/3Bio/', strand3.vendor_dna_sequence()) + self.assertEqual(r'A/iBiodT//iBiodT/GC', strand_i.vendor_dna_sequence()) + self.assertEqual(r'/5Biosg/ATTGC/3Bio/', strand53.vendor_dna_sequence()) + self.assertEqual(r'/5Biosg/A/iBiodT//iBiodT/GC/3Bio/', strand53i.vendor_dna_sequence()) def test_to_json_serializable(self) -> None: biotin5 = mod.biotin_5p biotin5 = dataclasses.replace(biotin5, connector_length=6) - self.assertEqual(r'/5Biosg/', biotin5.idt_text) + self.assertEqual(r'/5Biosg/', biotin5.vendor_code) self.assertEqual(r'/5Biosg/', biotin5.id) self.assertEqual('B', biotin5.display_text) self.assertEqual(6, biotin5.connector_length) biotin3 = mod.biotin_3p - self.assertEqual(r'/3Bio/', biotin3.idt_text) + self.assertEqual(r'/3Bio/', biotin3.vendor_code) self.assertEqual(r'/3Bio/', biotin3.id) self.assertEqual('B', biotin3.display_text) # biotin_i_1 = mod.Biotin(location=sc.ModLocation.internal, offset=1) biotin_i_1 = mod.biotin_int - self.assertEqual(r'/iBiodT/', biotin_i_1.idt_text) + self.assertEqual(r'/iBiodT/', biotin_i_1.vendor_code) self.assertEqual(r'/iBiodT/', biotin_i_1.id) self.assertEqual('B', biotin_i_1.display_text) # biotin_i_2 = mod.Biotin(location=sc.ModLocation.internal, offset=2) biotin_i_2 = mod.biotin_int - self.assertEqual(r'/iBiodT/', biotin_i_2.idt_text) + self.assertEqual(r'/iBiodT/', biotin_i_2.vendor_code) self.assertEqual(r'/iBiodT/', biotin_i_2.id) self.assertEqual('B', biotin_i_2.display_text) @@ -812,12 +812,12 @@ def test_to_json_serializable(self) -> None: self.assertTrue(r'/iBiodT/' in mods_dict) biotin5_json = mods_dict[r'/5Biosg/'] - self.assertEqual('/5Biosg/', biotin5_json[sc.mod_idt_text_key]) + self.assertEqual('/5Biosg/', biotin5_json[sc.mod_vendor_code_key]) self.assertEqual('B', biotin5_json[sc.mod_display_text_key]) self.assertEqual(6, biotin5_json[sc.mod_connector_length_key]) biotin3_json = mods_dict[r'/3Bio/'] - self.assertEqual('/3Bio/', biotin3_json[sc.mod_idt_text_key]) + self.assertEqual('/3Bio/', biotin3_json[sc.mod_vendor_code_key]) self.assertEqual('B', biotin3_json[sc.mod_display_text_key]) self.assertNotIn(sc.mod_connector_length_key, biotin3_json) @@ -1111,9 +1111,9 @@ def test_domain_delimiters(self) -> None: def test_domain_delimiters_modifications(self) -> None: strand_name = 's1' - mod_5 = sc.Modification5Prime(display_text='B', idt_text='/5Biosg/') - mod_3 = sc.Modification3Prime(display_text='Cy3', idt_text='/3Cy3Sp/') - mod_i = sc.ModificationInternal(display_text='B', idt_text='/iBiodT/', allowed_bases={'T'}) + mod_5 = sc.Modification5Prime(display_text='B', vendor_code='/5Biosg/') + mod_3 = sc.Modification3Prime(display_text='Cy3', vendor_code='/3Cy3Sp/') + mod_i = sc.ModificationInternal(display_text='B', vendor_code='/iBiodT/', allowed_bases={'T'}) helices = [sc.Helix(max_offset=100) for _ in range(6)] design = sc.Design(helices=helices, strands=[], grid=sc.square) @@ -1129,7 +1129,7 @@ def test_domain_delimiters_modifications(self) -> None: ) strand = design.strands[0] - strand_idt_dna_sequence = strand.idt_dna_sequence(domain_delimiter=' ') + strand_idt_dna_sequence = strand.vendor_dna_sequence(domain_delimiter=' ') self.assertEqual('/5Biosg/ AAAAA CCCC/iBiodT/ GGGGG /3Cy3Sp/', strand_idt_dna_sequence) idt_content = design.to_idt_bulk_input_format(delimiter=';', domain_delimiter=' ') @@ -1138,7 +1138,7 @@ def test_domain_delimiters_modifications(self) -> None: def test_domain_delimiters_internal_nonbase_modifications(self) -> None: strand_name = 's1' - mod_i = sc.ModificationInternal(display_text='9C', idt_text='/iSp9/') + mod_i = sc.ModificationInternal(display_text='9C', vendor_code='/iSp9/') helices = [sc.Helix(max_offset=100) for _ in range(6)] design = sc.Design(helices=helices, strands=[], grid=sc.square) @@ -1152,7 +1152,7 @@ def test_domain_delimiters_internal_nonbase_modifications(self) -> None: ) strand = design.strands[0] - strand_idt_dna_sequence = strand.idt_dna_sequence(domain_delimiter=' ') + strand_idt_dna_sequence = strand.vendor_dna_sequence(domain_delimiter=' ') self.assertEqual('AAAAA CCCC/iSp9/T GGGGG', strand_idt_dna_sequence) idt_content = design.to_idt_bulk_input_format(delimiter=';', domain_delimiter=' ') @@ -1207,9 +1207,9 @@ def test_to_idt_bulk_input_format__duplicate_names_same_sequence(self) -> None: ss2_r = sc.Domain(0, True, 4, 8) ss_l = sc.Domain(0, False, 0, 4) - s1_r = sc.Strand([ss1_r], idt=sc.IDTFields(), name='s1_r') - s2_r = sc.Strand([ss2_r], idt=sc.IDTFields(), name='s1_r') - s_l = sc.Strand([ss_l], idt=sc.IDTFields(), name='s_l') + s1_r = sc.Strand([ss1_r], vendor_fields=sc.VendorFields(), name='s1_r') + s2_r = sc.Strand([ss2_r], vendor_fields=sc.VendorFields(), name='s1_r') + s_l = sc.Strand([ss_l], vendor_fields=sc.VendorFields(), name='s_l') strands = [s1_r, s2_r, s_l] @@ -1226,9 +1226,9 @@ def test_to_idt_bulk_input_format__duplicate_names_different_sequences(self) -> ss2_r = sc.Domain(0, True, 4, 8) ss_l = sc.Domain(0, False, 0, 4) - s1_r = sc.Strand([ss1_r], idt=sc.IDTFields(), name='s1_r') - s2_r = sc.Strand([ss2_r], idt=sc.IDTFields(), name='s1_r') - s_l = sc.Strand([ss_l], idt=sc.IDTFields(), name='s_l') + s1_r = sc.Strand([ss1_r], vendor_fields=sc.VendorFields(), name='s1_r') + s2_r = sc.Strand([ss2_r], vendor_fields=sc.VendorFields(), name='s1_r') + s_l = sc.Strand([ss_l], vendor_fields=sc.VendorFields(), name='s_l') strands = [s1_r, s2_r, s_l] @@ -1245,9 +1245,9 @@ def test_to_idt_bulk_input_format__duplicate_names_different_scales(self) -> Non ss2_r = sc.Domain(0, True, 4, 8) ss_l = sc.Domain(0, False, 0, 4) - s1_r = sc.Strand([ss1_r], idt=sc.IDTFields(scale='25nm'), name='s1_r') - s2_r = sc.Strand([ss2_r], idt=sc.IDTFields(scale='100nm'), name='s1_r') - s_l = sc.Strand([ss_l], idt=sc.IDTFields(), name='s_l') + s1_r = sc.Strand([ss1_r], vendor_fields=sc.VendorFields(scale='25nm'), name='s1_r') + s2_r = sc.Strand([ss2_r], vendor_fields=sc.VendorFields(scale='100nm'), name='s1_r') + s_l = sc.Strand([ss_l], vendor_fields=sc.VendorFields(), name='s_l') strands = [s1_r, s2_r, s_l] @@ -1266,9 +1266,9 @@ def test_to_idt_bulk_input_format__duplicate_names_different_purifications(self) ss2_r = sc.Domain(0, True, 4, 8) ss_l = sc.Domain(0, False, 0, 4) - s1_r = sc.Strand([ss1_r], idt=sc.IDTFields(purification='STD'), name='s1_r') - s2_r = sc.Strand([ss2_r], idt=sc.IDTFields(purification='HPLC'), name='s1_r') - s_l = sc.Strand([ss_l], idt=sc.IDTFields(), name='s_l') + s1_r = sc.Strand([ss1_r], vendor_fields=sc.VendorFields(purification='STD'), name='s1_r') + s2_r = sc.Strand([ss2_r], vendor_fields=sc.VendorFields(purification='HPLC'), name='s1_r') + s_l = sc.Strand([ss_l], vendor_fields=sc.VendorFields(), name='s_l') strands = [s1_r, s2_r, s_l] @@ -4327,10 +4327,10 @@ def test_legacy_idt_name_import__no_strand_name(self) -> None: self.assertEqual(1, len(design.strands)) strand = design.strands[0] self.assertEqual('staple1', strand.name) - self.assertEqual('100nm', strand.idt.scale) - self.assertEqual('HPLC', strand.idt.purification) - self.assertEqual('plate1', strand.idt.plate) - self.assertEqual('A1', strand.idt.well) + self.assertEqual('100nm', strand.vendor_fields.scale) + self.assertEqual('HPLC', strand.vendor_fields.purification) + self.assertEqual('plate1', strand.vendor_fields.plate) + self.assertEqual('A1', strand.vendor_fields.well) def test_legacy_idt_name_import__strand_name_exists(self) -> None: # tests proper importing of old format when name was a subfield of idt; @@ -4484,19 +4484,19 @@ def test_strand_labels(self) -> None: def test_strand_idt(self) -> None: helices = [sc.Helix(max_offset=100), sc.Helix(max_offset=100)] - idt = sc.IDTFields(scale='25nm', purification='HPLC', plate='plate1', well='A2') - strand0_expected = sc.Strand([sc.Domain(0, True, 0, 10)], name='strand1', idt=idt) + idt = sc.VendorFields(scale='25nm', purification='HPLC', plate='plate1', well='A2') + strand0_expected = sc.Strand([sc.Domain(0, True, 0, 10)], name='strand1', vendor_fields=idt) strands = [strand0_expected] design = sc.Design(helices=helices, strands=strands, grid=sc.square) json_str = design.to_json() design_from_json = sc.Design.from_scadnano_json_str(json_str) strand0 = design_from_json.strands[0] - self.assertEqual(strand0_expected.idt, strand0.idt) - self.assertEqual('strand1', strand0.idt_export_name()) - self.assertEqual('25nm', strand0.idt.scale) - self.assertEqual('HPLC', strand0.idt.purification) - self.assertEqual('plate1', strand0.idt.plate) - self.assertEqual('A2', strand0.idt.well) + self.assertEqual(strand0_expected.vendor_fields, strand0.vendor_fields) + self.assertEqual('strand1', strand0.vendor_export_name()) + self.assertEqual('25nm', strand0.vendor_fields.scale) + self.assertEqual('HPLC', strand0.vendor_fields.purification) + self.assertEqual('plate1', strand0.vendor_fields.plate) + self.assertEqual('A2', strand0.vendor_fields.well) def test_domain_labels(self) -> None: helices = [sc.Helix(max_offset=100), sc.Helix(max_offset=100)] @@ -7795,11 +7795,16 @@ class TestPlateMaps(unittest.TestCase): def setUp(self) -> None: helices = [sc.Helix(max_offset=100)] self.design = sc.Design(helices=helices, strands=[], grid=sc.square) - self.design.draw_strand(0, 0).move(10).with_name('strand 0').with_idt(plate='plate 1', well='A1') - self.design.draw_strand(0, 10).move(10).with_name('strand 1').with_idt(plate='plate 1', well='A2') - self.design.draw_strand(0, 20).move(10).with_name('strand 2').with_idt(plate='plate 1', well='B2') - self.design.draw_strand(0, 30).move(10).with_name('strand 3').with_idt(plate='plate 1', well='B3') - self.design.draw_strand(0, 40).move(10).with_name('strand 4').with_idt(plate='plate 1', well='D7') + self.design.draw_strand(0, 0).move(10).with_name('strand 0').with_vendor_fields(plate='plate 1', + well='A1') + self.design.draw_strand(0, 10).move(10).with_name('strand 1').with_vendor_fields(plate='plate 1', + well='A2') + self.design.draw_strand(0, 20).move(10).with_name('strand 2').with_vendor_fields(plate='plate 1', + well='B2') + self.design.draw_strand(0, 30).move(10).with_name('strand 3').with_vendor_fields(plate='plate 1', + well='B3') + self.design.draw_strand(0, 40).move(10).with_name('strand 4').with_vendor_fields(plate='plate 1', + well='D7') def test_plate_map_markdown(self) -> None: plate_maps = self.design.plate_maps() diff --git a/tutorial/tutorial.md b/tutorial/tutorial.md index a67e4d3..0dae627 100644 --- a/tutorial/tutorial.md +++ b/tutorial/tutorial.md @@ -588,7 +588,7 @@ The Excel file should look similar to this: ![](images/excel_file.png) -To customize further (e.g., purification, synthesis scale), one can write to the field [`Strand.idt`](https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Strand.idt), of type [IDTFields](https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.IDTFields). Strands can also be given custom names through the field [`Strand.name`](https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Strand.name); if the Strand has no name, it is assigned one using the cadnano convention (see Excel screenshot above) based on the helix and offset of the strand's 5' and 3' ends. +To customize further (e.g., purification, synthesis scale), one can write to the field [`Strand.idt`](https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Strand.idt), of type [VendorFields](https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.VendorFields). Strands can also be given custom names through the field [`Strand.name`](https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Strand.name); if the Strand has no name, it is assigned one using the cadnano convention (see Excel screenshot above) based on the helix and offset of the strand's 5' and 3' ends. From 5fefd41798cb038adfb48242bd94258b7c6f8d94 Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 29 Aug 2023 17:31:23 -0700 Subject: [PATCH 10/25] re-ran examples to alter changed name of IDT fields --- examples/consecutive_domains.py | 4 +- ...helix_origami_barrel_from_algoSST_paper.sc | 4694 ++--- .../16_helix_origami_rectangle.sc | 3754 ++-- .../16_helix_origami_rectangle_idt.sc | 3754 ++-- .../16_helix_origami_rectangle_no_seq.sc | 3336 ++-- ...helix_origami_rectangle_no_seq_no_twist.sc | 3336 ++-- .../16_helix_origami_rectangle_no_twist.sc | 3754 ++-- ...gami_rectangle_seed_tiles_grow_from_top.sc | 3950 ++--- ...x_origami_rectangle_shifted_seam_no_seq.sc | 3336 ++-- .../1_staple_1_helix_origami.sc | 50 +- .../1_staple_1_helix_origami_mismatches.sc | 44 +- ...ple_1_helix_origami_position_nondefault.sc | 64 +- .../1_staple_1_helix_origami_roll.sc | 44 +- ...ix_2_strands_multiple_substrands_no_seq.sc | 46 +- .../2_staple_2_helix_modifications.sc | 176 +- .../2_staple_2_helix_origami_6bases_wide.sc | 68 +- .../2_staple_2_helix_origami_deletions.sc | 68 +- ...le_2_helix_origami_deletions_insertions.sc | 72 +- ...lix_origami_deletions_insertions_labels.sc | 78 +- ...helix_origami_deletions_insertions_mods.sc | 90 +- ...letions_insertions_mods_chained_methods.sc | 90 +- ...igami_deletions_insertions_new_geometry.sc | 80 +- ...lix_origami_deletions_insertions_no_seq.sc | 66 +- .../3_helix_deletions_insertions.sc | 178 +- examples/output_designs/4_helix_grid_none.sc | 46 +- ...d_none_min_offset_position_x_nondefault.sc | 70 +- .../4_helix_min_offsets_nonzero.sc | 46 +- .../56_helix_origami_rectangle.sc | 4158 ++--- .../64_helix_origami_rectangle.sc | 3602 ++-- .../6_helix_6_col_origami_rectangle.sc | 354 +- .../6_helix_bundle_honeycomb.sc | 3738 ++-- .../6_helix_origami_rectangle.sc | 562 +- ..._origami_rectangle_helices_out_of_order.sc | 564 +- examples/output_designs/circular.sc | 66 +- .../output_designs/consecutive_domains.sc | 46 +- examples/output_designs/domain_colors.sc | 2 +- .../draw_strand_move_negative.sc | 3 +- examples/output_designs/empty.sc | 10 +- .../extension_and_loopout_oxdna_export.sc | 42 +- examples/output_designs/extensions.sc | 104 +- examples/output_designs/hairpin.sc | 34 +- .../helices_out_of_order_nonconsecutive.sc | 22 +- examples/output_designs/helix_groups.sc | 202 +- examples/output_designs/hex_lattice_10x10.sc | 212 +- .../hex_lattice_10x10_with_negative.sc | 212 +- .../output_designs/honeycomb_lattice_10x10.sc | 212 +- .../honeycomb_lattice_10x10_with_negative.sc | 212 +- .../output_designs/idt-plates-explicit.sc | 418 +- .../output_designs/long_range_crossovers.sc | 382 +- examples/output_designs/loopouts_all_types.sc | 54 +- examples/output_designs/many_big_helices.sc | 72 +- .../many_helices_modifications.sc | 118 +- .../output_designs/names_domains_strands.sc | 142 +- .../output_designs/oxdna_export_with_pitch.sc | 10 +- examples/output_designs/proposal.sc | 3836 ++-- examples/output_designs/relax_helix_rolls.sc | 2 +- examples/output_designs/sst-motif-3_2.sc | 928 +- examples/output_designs/sst-motif-4_1.sc | 928 +- .../output_designs/strand_builder_loop.sc | 154 +- examples/output_designs/very_large_origami.sc | 14430 ++++++++-------- examples/oxdna_export_with_pitch.py | 2 +- 61 files changed, 33561 insertions(+), 33566 deletions(-) diff --git a/examples/consecutive_domains.py b/examples/consecutive_domains.py index 57dc53a..37f9d4e 100644 --- a/examples/consecutive_domains.py +++ b/examples/consecutive_domains.py @@ -1,5 +1,6 @@ import scadnano as sc + def create_design() -> sc.Design: # shows how to make consecutive domains on a helix, separated by a crossover that appears horizontal # this is useful when doing single-stranded tile designs, for instance, or any other design @@ -19,10 +20,11 @@ def create_design() -> sc.Design: # 0 [------------> # # 1 <------------] - design.add_full_crossover(helix=0, helix2=1, offset=8, forward=True) + # design.add_full_crossover(helix=0, helix2=1, offset=8, forward=True) return design + if __name__ == '__main__': d = create_design() d.write_scadnano_file(directory='output_designs') diff --git a/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.sc b/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.sc index 232b8c6..47efa9d 100644 --- a/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.sc +++ b/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.sc @@ -1,2348 +1,2348 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - { - "max_offset": 512, - "grid_position": [0, 0], - "major_ticks": [11, 22, 32, 40, 48, 56, 64, 72, 80, 88, 96, 104, 112, 120, 128, 136, 144, 152, 160, 168, 176, 184, 192, 200, 208, 216, 224, 232, 240, 248, 256, 264, 272, 280, 288, 296, 304, 312, 320, 328, 336, 344, 352, 360, 368, 376, 384, 392, 400, 408, 416, 424, 432, 440, 448, 456, 464, 472, 480, 490, 501] - }, - { - "max_offset": 512, - "grid_position": [0, 1], - "major_ticks": [11, 22, 32, 40, 48, 56, 64, 72, 80, 88, 96, 104, 112, 120, 128, 136, 144, 152, 160, 168, 176, 184, 192, 200, 208, 216, 224, 232, 240, 248, 256, 264, 272, 280, 288, 296, 304, 312, 320, 328, 336, 344, 352, 360, 368, 376, 384, 392, 400, 408, 416, 424, 432, 440, 448, 456, 464, 472, 480, 490, 501] - }, - { - "max_offset": 512, - "grid_position": [0, 2], - "major_ticks": [11, 22, 32, 40, 48, 56, 64, 72, 80, 88, 96, 104, 112, 120, 128, 136, 144, 152, 160, 168, 176, 184, 192, 200, 208, 216, 224, 232, 240, 248, 256, 264, 272, 280, 288, 296, 304, 312, 320, 328, 336, 344, 352, 360, 368, 376, 384, 392, 400, 408, 416, 424, 432, 440, 448, 456, 464, 472, 480, 490, 501] - }, - { - "max_offset": 512, - "grid_position": [0, 3], - "major_ticks": [11, 22, 32, 40, 48, 56, 64, 72, 80, 88, 96, 104, 112, 120, 128, 136, 144, 152, 160, 168, 176, 184, 192, 200, 208, 216, 224, 232, 240, 248, 256, 264, 272, 280, 288, 296, 304, 312, 320, 328, 336, 344, 352, 360, 368, 376, 384, 392, 400, 408, 416, 424, 432, 440, 448, 456, 464, 472, 480, 490, 501] - }, - { - "max_offset": 512, - "grid_position": [0, 4], - "major_ticks": [11, 22, 32, 40, 48, 56, 64, 72, 80, 88, 96, 104, 112, 120, 128, 136, 144, 152, 160, 168, 176, 184, 192, 200, 208, 216, 224, 232, 240, 248, 256, 264, 272, 280, 288, 296, 304, 312, 320, 328, 336, 344, 352, 360, 368, 376, 384, 392, 400, 408, 416, 424, 432, 440, 448, 456, 464, 472, 480, 490, 501] - }, - { - "max_offset": 512, - "grid_position": [0, 5], - "major_ticks": [11, 22, 32, 40, 48, 56, 64, 72, 80, 88, 96, 104, 112, 120, 128, 136, 144, 152, 160, 168, 176, 184, 192, 200, 208, 216, 224, 232, 240, 248, 256, 264, 272, 280, 288, 296, 304, 312, 320, 328, 336, 344, 352, 360, 368, 376, 384, 392, 400, 408, 416, 424, 432, 440, 448, 456, 464, 472, 480, 490, 501] - }, - { - "max_offset": 512, - "grid_position": [0, 6], - "major_ticks": [11, 22, 32, 40, 48, 56, 64, 72, 80, 88, 96, 104, 112, 120, 128, 136, 144, 152, 160, 168, 176, 184, 192, 200, 208, 216, 224, 232, 240, 248, 256, 264, 272, 280, 288, 296, 304, 312, 320, 328, 336, 344, 352, 360, 368, 376, 384, 392, 400, 408, 416, 424, 432, 440, 448, 456, 464, 472, 480, 490, 501] - }, - { - "max_offset": 512, - "grid_position": [0, 7], - "major_ticks": [11, 22, 32, 40, 48, 56, 64, 72, 80, 88, 96, 104, 112, 120, 128, 136, 144, 152, 160, 168, 176, 184, 192, 200, 208, 216, 224, 232, 240, 248, 256, 264, 272, 280, 288, 296, 304, 312, 320, 328, 336, 344, 352, 360, 368, 376, 384, 392, 400, 408, 416, 424, 432, 440, 448, 456, 464, 472, 480, 490, 501] - }, - { - "max_offset": 512, - "grid_position": [0, 8], - "major_ticks": [11, 22, 32, 40, 48, 56, 64, 72, 80, 88, 96, 104, 112, 120, 128, 136, 144, 152, 160, 168, 176, 184, 192, 200, 208, 216, 224, 232, 240, 248, 256, 264, 272, 280, 288, 296, 304, 312, 320, 328, 336, 344, 352, 360, 368, 376, 384, 392, 400, 408, 416, 424, 432, 440, 448, 456, 464, 472, 480, 490, 501] - }, - { - "max_offset": 512, - "grid_position": [0, 9], - "major_ticks": 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], - "strands": [ - { - "color": "#0066cc", - "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGTCGTGTGACTGGTGAATCTGCCAATGTAAATAATCCATTTCAGACGATTGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCGGTAATATTGTTCTGGATATTACCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTGCTACAACGGTTAATTTGCGTGATGGACAGACTCTTTTACTCGGTGGCCTCACTGATTATAAAA", 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{"helix": 14, "forward": true, "start": 11, "end": 32} - ] - }, - { - "name": "tile-left-16-17", - "color": "#000000", - "sequence": "TGGATTTGTTTACGGAAAGATAAGCATGGTAAAATTGGTCAA", - "idt": {"scale": "25nm", "purification": "STD"}, - "domains": [ - {"helix": 17, "forward": false, "start": 11, "end": 32}, - {"helix": 16, "forward": true, "start": 11, "end": 32} - ] - }, - { - "name": "tile-right-2-3", - "color": "#000000", - "sequence": "TTGTCTAGAGTTTGGGATGTTAGTTCTTGGTATTGTTGACAA", - "idt": {"scale": "25nm", "purification": "STD"}, - "domains": [ - {"helix": 3, "forward": false, "start": 480, "end": 501}, - {"helix": 2, "forward": true, "start": 480, "end": 501} - ] - }, - { - "name": "tile-right-4-5", - "color": "#000000", - "sequence": "AAGGAAGTAGATTCGAAAGGTACGTGGATAAAATAGGAGGAA", - "idt": {"scale": "25nm", "purification": "STD"}, - "domains": [ - {"helix": 5, "forward": false, "start": 480, "end": 501}, - {"helix": 4, "forward": true, "start": 480, "end": 501} - ] - }, - { - "name": 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"TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGTCGTGTGACTGGTGAATCTGCCAATGTAAATAATCCATTTCAGACGATTGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCGGTAATATTGTTCTGGATATTACCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTGCTACAACGGTTAATTTGCGTGATGGACAGACTCTTTTACTCGGTGGCCTCACTGATTATAAAA", + "domains": [ + {"helix": 17, "forward": false, "start": 32, "end": 102, "deletions": [68]}, + {"helix": 16, "forward": true, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 59, 91, 123, 155, 187, 219], "insertions": [[75, 1], [107, 1], [139, 1], [171, 1], [203, 1], [235, 1]]}, + {"helix": 15, "forward": false, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 75, 107, 139, 171, 203, 235], "insertions": [[59, 1], [91, 1], [123, 1], [155, 1], [187, 1], [219, 1]]}, + {"helix": 14, "forward": true, "start": 32, "end": 240, "deletions": [68, 115, 163, 212]}, + {"helix": 13, "forward": false, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 75, 107, 139, 171, 203, 235], "insertions": [[59, 1], [91, 1], [123, 1], [155, 1], [187, 1], [219, 1]]}, + {"helix": 12, "forward": true, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 59, 91, 123, 155, 187, 219], "insertions": [[75, 1], [107, 1], [139, 1], [171, 1], [203, 1], [235, 1]]}, + {"helix": 11, "forward": false, "start": 32, "end": 240, "deletions": [68, 115, 163, 212]}, + {"helix": 10, "forward": true, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 59, 91, 123, 155, 187, 219], "insertions": [[75, 1], [107, 1], [139, 1], [171, 1], [203, 1], [235, 1]]}, + {"helix": 9, "forward": false, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 75, 107, 139, 171, 203, 235], "insertions": [[59, 1], [91, 1], [123, 1], [155, 1], [187, 1], [219, 1]]}, + {"helix": 8, "forward": true, "start": 32, "end": 240, "deletions": [68, 115, 163, 212]}, + {"helix": 7, "forward": false, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 75, 107, 139, 171, 203, 235], "insertions": [[59, 1], [91, 1], [123, 1], [155, 1], [187, 1], [219, 1]]}, + {"helix": 6, "forward": true, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 59, 91, 123, 155, 187, 219], "insertions": [[75, 1], [107, 1], [139, 1], [171, 1], [203, 1], [235, 1]]}, + {"helix": 5, "forward": false, "start": 32, "end": 240, "deletions": [68, 115, 163, 212]}, + {"helix": 4, "forward": true, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 59, 91, 123, 155, 187, 219], "insertions": [[75, 1], [107, 1], [139, 1], [171, 1], [203, 1], [235, 1]]}, + {"helix": 3, "forward": false, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 75, 107, 139, 171, 203, 235], "insertions": [[59, 1], [91, 1], [123, 1], [155, 1], [187, 1], [219, 1]]}, + {"helix": 2, "forward": true, "start": 32, "end": 480, "deletions": [68, 115, 163, 212, 259, 307, 355, 403, 451]}, + {"helix": 3, "forward": false, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451, 267, 299, 331, 363, 395, 427], "insertions": [[251, 1], [283, 1], [315, 1], [347, 1], [379, 1], [411, 1]]}, + {"helix": 4, "forward": true, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451, 251, 283, 315, 347, 379, 411], "insertions": [[267, 1], [299, 1], [331, 1], [363, 1], [395, 1], [427, 1]]}, + {"helix": 5, "forward": false, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451]}, + {"helix": 6, "forward": true, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451, 251, 283, 315, 347, 379, 411], "insertions": [[267, 1], [299, 1], [331, 1], [363, 1], [395, 1], [427, 1]]}, + {"helix": 7, "forward": false, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451, 267, 299, 331, 363, 395, 427], "insertions": [[251, 1], [283, 1], [315, 1], [347, 1], [379, 1], [411, 1]]}, + {"helix": 8, "forward": true, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451]}, + {"helix": 9, "forward": false, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451, 267, 299, 331, 363, 395, 427], "insertions": [[251, 1], [283, 1], [315, 1], [347, 1], [379, 1], [411, 1]]}, + {"helix": 10, "forward": true, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451, 251, 283, 315, 347, 379, 411], "insertions": [[267, 1], [299, 1], [331, 1], [363, 1], [395, 1], [427, 1]]}, + {"helix": 11, "forward": false, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451]}, + {"helix": 12, "forward": true, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451, 251, 283, 315, 347, 379, 411], "insertions": [[267, 1], [299, 1], [331, 1], [363, 1], [395, 1], [427, 1]]}, + {"helix": 13, "forward": false, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451, 267, 299, 331, 363, 395, 427], "insertions": [[251, 1], [283, 1], [315, 1], [347, 1], [379, 1], [411, 1]]}, + {"helix": 14, "forward": true, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451]}, + {"helix": 15, "forward": false, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451, 267, 299, 331, 363, 395, 427], "insertions": [[251, 1], [283, 1], [315, 1], [347, 1], [379, 1], [411, 1]]}, + {"helix": 16, "forward": true, "start": 240, "end": 480, "deletions": [259, 307, 355, 403, 451, 251, 283, 315, 347, 379, 411], "insertions": [[267, 1], [299, 1], [331, 1], [363, 1], [395, 1], [427, 1]]}, + {"helix": 17, "forward": false, "start": 102, "end": 480, "deletions": [115, 163, 212, 259, 307, 355, 403, 451]} + ], + "is_scaffold": true + }, + { + "color": "#f74308", + "sequence": "TGTTAGTGACAATATTACCGATAGTTGCGCCGACAATGAC", + "domains": [ + {"helix": 18, "forward": false, "start": 248, "end": 256}, + {"helix": 17, "forward": true, "start": 248, "end": 256}, + {"helix": 2, "forward": false, "start": 232, "end": 256} + ] + }, + { + "color": "#57bb00", + "sequence": "CTTTGAAATCATAAGGGAACCGAATAAGTAT", + "domains": [ + {"helix": 4, "forward": false, "start": 224, "end": 232}, + {"helix": 3, "forward": true, "start": 224, "end": 248, "deletions": [235]} + ] + }, + { + "color": "#888888", + "sequence": "AGCCCGGAAGTCGAGAGGGTTGATACTGACCAA", + "domains": [ + {"helix": 3, "forward": true, "start": 248, "end": 256, "insertions": [[251, 1]]}, + {"helix": 4, "forward": false, "start": 232, "end": 256, "deletions": [251], "insertions": [[235, 1]]} + ] + }, + { + "color": "#32b86c", + "sequence": "AACACTATAGGAATTACGAGGCATTCAAAATC", + "domains": [ + {"helix": 6, "forward": false, "start": 224, "end": 232}, + {"helix": 5, "forward": true, "start": 224, "end": 248} + ] + }, + { + "color": "#333333", + "sequence": "ACCGGAACGCCATCTTTTCATAAAGTAAGAGC", + "domains": [ + {"helix": 5, "forward": true, "start": 248, "end": 256}, + {"helix": 6, "forward": false, "start": 232, "end": 256, "deletions": [251], "insertions": [[235, 1]]} + ] + }, + { + "color": "#320096", + "sequence": "TAGAGCTTAGAGGTCATTTTTGCGGAATACC", + "domains": [ + {"helix": 8, "forward": false, "start": 224, "end": 232}, + {"helix": 7, "forward": true, "start": 224, "end": 248, "deletions": [235]} + ] + }, + { + "color": "#03b6a2", + "sequence": "CAAAAGAACGAAACGCAATAATAACGGATGGCT", + "domains": [ + {"helix": 7, "forward": true, "start": 248, "end": 256, "insertions": [[251, 1]]}, + {"helix": 8, "forward": false, "start": 232, "end": 256} + ] + }, + { + "color": "#7300de", + "sequence": "AAATGCAAATTTTTAGAACCCTCTTTAGCGA", + "domains": [ + {"helix": 10, "forward": false, "start": 224, "end": 232}, + {"helix": 9, "forward": true, "start": 224, "end": 248, "deletions": [235]} + ] + }, + { + "color": "#aaaa00", + "sequence": "ACCTCCCGAAAGAACGCGAGGCGTATATATTTT", + "domains": [ + {"helix": 9, "forward": true, "start": 248, "end": 256, "insertions": [[251, 1]]}, + {"helix": 10, "forward": false, "start": 232, "end": 256, "deletions": [251], "insertions": [[235, 1]]} + ] + }, + { + "color": "#b8056c", + "sequence": "CTTTCATCTCGCGTCTGGCCTTCCTGTTTAGT", + "domains": [ + {"helix": 12, "forward": false, "start": 224, "end": 232}, + {"helix": 11, "forward": true, "start": 224, "end": 248} + ] + }, + { + "color": "#007200", + "sequence": "ATCATATGTTACTAGAAAAAGCCTGTAGCCAG", + "domains": [ + {"helix": 11, "forward": true, "start": 248, "end": 256}, + {"helix": 12, "forward": false, "start": 232, "end": 256, "deletions": [251], "insertions": [[235, 1]]} + ] + }, + { + "color": "#cc0000", + "sequence": "TAGAGGATCTTGCATGCCTGCAGTACCTGAG", + "domains": [ + {"helix": 14, "forward": false, "start": 224, "end": 232}, + {"helix": 13, "forward": true, "start": 224, "end": 248, "deletions": [235]} + ] + }, + { + "color": "#f7931e", + "sequence": "CAAAAGAAGAATTATTCATTTCAATGTCGACTC", + "domains": [ + {"helix": 13, "forward": true, "start": 248, "end": 256, "insertions": [[251, 1]]}, + {"helix": 14, "forward": false, "start": 232, "end": 256} + ] + }, + { + "color": "#f74308", + "sequence": "CCCTTATATGGTGGTTCCGAAATATATCTTT", + "domains": [ + {"helix": 16, "forward": false, "start": 224, "end": 232}, + {"helix": 15, "forward": true, "start": 224, "end": 248, "deletions": [235]} + ] + }, + { + "color": "#57bb00", + "sequence": "AGGAGCACTGGAAGGTTATCTAAACGGCAAAAT", + "domains": [ + {"helix": 15, "forward": true, "start": 248, "end": 256, "insertions": [[251, 1]]}, + {"helix": 16, "forward": false, "start": 232, "end": 256, "deletions": [251], "insertions": [[235, 1]]} + ] + }, + { + "color": "#888888", + "sequence": "GGTGAGTTAACAACCATCGGCCTTGCTGGTAATATCCAGA", + "domains": [ + {"helix": 1, "forward": true, "start": 224, "end": 232}, + {"helix": 2, "forward": false, "start": 224, "end": 232}, + {"helix": 17, "forward": true, "start": 224, "end": 248} + ] + }, + { + "color": "#32b86c", + "sequence": "ATGAATAAAGCTTGACAGTTTCCATTAAACGGACCTAAAA", + "domains": [ + {"helix": 18, "forward": false, "start": 56, "end": 64}, + {"helix": 17, "forward": true, "start": 56, "end": 64}, + {"helix": 2, "forward": false, "start": 48, "end": 64}, + {"helix": 3, "forward": true, "start": 48, "end": 56} + ] + }, + { + "color": "#333333", + "sequence": "CGAAAGAGGGTAGTAAATTGGGCTGAATTACC", + "domains": [ + {"helix": 3, "forward": true, "start": 56, "end": 64, "insertions": [[59, 1]]}, + {"helix": 4, "forward": false, "start": 48, "end": 64, "deletions": [59]}, + {"helix": 5, "forward": true, "start": 48, "end": 56} + ] + }, + { + "color": "#320096", + "sequence": 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"end": 456, "deletions": [451]}, + {"helix": 11, "forward": true, "start": 448, "end": 464, "deletions": [451]}, + {"helix": 10, "forward": false, "start": 456, "end": 464} + ] + }, + { + "color": "#cc0000", + "sequence": "ACTTCTGGCTGAGAAGAGTCAAACTACCTT", + "domains": [ + {"helix": 14, "forward": false, "start": 448, "end": 456, "deletions": [451]}, + {"helix": 13, "forward": true, "start": 448, "end": 464, "deletions": [451]}, + {"helix": 12, "forward": false, "start": 456, "end": 464} + ] + }, + { + "color": "#f7931e", + "sequence": "ATTAAAATCCTGATTATCAGATTGGATTAT", + "domains": [ + {"helix": 16, "forward": false, "start": 448, "end": 456, "deletions": [451]}, + {"helix": 15, "forward": true, "start": 448, "end": 464, "deletions": [451]}, + {"helix": 14, "forward": false, "start": 456, "end": 464} + ] + }, + { + "name": "adap-left-17-2", + "color": "#f74308", + "sequence": "GTAAAATACGTAATGCTTGTCAACAAAACAAATCCACCCTAAAGGGAGCCCC", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 2, "forward": false, "start": 22, "end": 48}, + {"helix": 17, "forward": true, "start": 22, "end": 48} + ] + }, + { + "name": "adap-left-3-4", + "color": "#57bb00", + "sequence": "TGAGATGGTTTAATTTTTCCTCCTATCTCTAGACAACACTACGAAGGCACCA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 4, "forward": false, "start": 22, "end": 48}, + {"helix": 3, "forward": true, "start": 22, "end": 48} + ] + }, + { + "name": "adap-left-5-6", + "color": "#888888", + "sequence": "AAAACGAGAATGACCATACCAGATTCCTACTTCCTTCAACTTTAATCATTGT", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 6, "forward": false, "start": 22, "end": 48}, + {"helix": 5, "forward": true, "start": 22, "end": 48} + ] + }, + { + "name": "adap-left-7-8", + "color": "#32b86c", + "sequence": "CATTTGGGGCGCGAGCTCTGATCTCTCGACTATTCTTAAATCAAAAATCAGG", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 8, "forward": false, "start": 22, "end": 48}, + {"helix": 7, "forward": true, "start": 22, "end": 48} + ] + }, + { + "name": "adap-left-9-10", + "color": "#333333", + "sequence": "AAACAAGAGAATCGATTATCCTTAGCCCTATCCATTTGAAAAGGTGGCATCA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 10, "forward": false, "start": 22, "end": 48}, + {"helix": 9, "forward": true, "start": 22, "end": 48} + ] + }, + { + "name": "adap-left-11-12", + "color": "#320096", + "sequence": "GCTTTCCGGCACCGCTTTCCTGATACGATCATCACTGAACGGTAATCGTAAA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 12, "forward": false, "start": 22, "end": 48}, + {"helix": 11, "forward": true, "start": 22, "end": 48} + ] + }, + { + "name": "adap-left-13-14", + "color": "#03b6a2", + "sequence": "TCCAGTCGGGAAACCTATCGTCTCATTTTTAACGCATCTGGTGCCGGAAACC", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 14, "forward": false, "start": 22, "end": 48}, + {"helix": 13, "forward": true, "start": 22, "end": 48} + ] + }, + { + "name": "adap-left-15-16", + "color": "#7300de", + "sequence": "AAGCACTAAATCGGAATTGACCAATTCTCTCTGAATGTCGTGCCAGCTGCAT", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 16, "forward": false, "start": 22, "end": 48}, + {"helix": 15, "forward": true, "start": 22, "end": 48} + ] + }, + { + "name": "adap-right-17-2", + "color": "#aaaa00", + "sequence": "TAGTCTTTAATGCGCGATCTTTCCGTACCAAGAACTTCGTCTTTCCAGACGT", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 17, "forward": true, "start": 464, "end": 490}, + {"helix": 2, "forward": false, "start": 464, "end": 490} + ] + }, + { + "name": "adap-right-3-4", + "color": "#b8056c", + "sequence": "ACGATCTAAAGTTTTGAACATCCCAATTATCCACGTAGTAAGCGTCATACAT", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 3, "forward": true, "start": 464, "end": 490}, + {"helix": 4, "forward": false, "start": 464, "end": 490} + ] + }, + { + "name": "adap-right-5-6", + "color": "#007200", + "sequence": "CTGAATTTACCGTTCCACCTTTCGAAAACCTCGAATTAAAGGTGAATTATCA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 5, "forward": true, "start": 464, "end": 490}, + {"helix": 6, "forward": false, "start": 464, "end": 490} + ] + }, + { + "name": "adap-right-7-8", + "color": "#cc0000", + "sequence": "GACGGAAATTATTCATACACTGACAAATCTGCTCATATAAAAACAGGGAAGC", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 7, "forward": true, "start": 464, "end": 490}, + {"helix": 8, "forward": false, "start": 464, "end": 490} + ] + }, + { + "name": "adap-right-9-10", + "color": "#f7931e", + "sequence": "TTACAGAGAGAATAACAAAGACACCTTCAAGTTCCATAGATAAGTCCTGAAC", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 9, "forward": true, "start": 464, "end": 490}, + {"helix": 10, "forward": false, "start": 464, "end": 490} + ] + }, + { + "name": "adap-right-11-12", + "color": "#f74308", + "sequence": "GCCTGTTTATCAACAAACAGCCTAAAACCCATTCATATCATAGGTCTGAGAG", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 11, "forward": true, "start": 464, "end": 490}, + {"helix": 12, "forward": false, "start": 464, "end": 490} + ] + }, + { + "name": "adap-right-13-14", + "color": "#57bb00", + "sequence": "TAGTGAATTTATCAAAATACGCATCTAACCTTCACATATAATCCTGATTGTT", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 13, "forward": true, "start": 464, "end": 490}, + {"helix": 14, "forward": false, "start": 464, "end": 490} + ] + }, + { + "name": "adap-right-15-16", + "color": "#888888", + "sequence": "GATGGCAATTCATCAATATCATGCCATACCATGCTTAACTGATAGCCCTAAA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 15, "forward": true, "start": 464, "end": 490}, + {"helix": 16, "forward": false, "start": 464, "end": 490} + ] + }, + { + "name": "tile-left-2-3", + "color": "#000000", + "sequence": "TTGTCTAGAGTTTGGGATGTTAGTTCTTGGTATTGTTGACAA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 3, "forward": false, "start": 11, "end": 32}, + {"helix": 2, "forward": true, "start": 11, "end": 32} + ] + }, + { + "name": "tile-left-4-5", + "color": "#000000", + "sequence": "AAGGAAGTAGATTCGAAAGGTACGTGGATAAAATAGGAGGAA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 5, "forward": false, "start": 11, "end": 32}, + {"helix": 4, "forward": true, "start": 11, "end": 32} + ] + }, + { + "name": "tile-left-6-7", + "color": "#000000", + "sequence": "AGAATAGTCGTTTGTCAGTGTATTCGAGGTTAGAATCTGGTA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 7, "forward": false, "start": 11, "end": 32}, + {"helix": 6, "forward": true, "start": 11, "end": 32} + ] + }, + { + "name": "tile-left-8-9", + "color": "#000000", + "sequence": "AATGGATAGGTAGGTGTCTTTATGAGCAGATAAGAGATCAGA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 9, "forward": false, "start": 11, "end": 32}, + {"helix": 8, "forward": true, "start": 11, "end": 32} + ] + }, + { + "name": "tile-left-10-11", + "color": "#000000", + "sequence": "AGTGATGATCTTTTAGGCTGTTGGAACTTGATGCTAAGGATA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 11, "forward": false, "start": 11, "end": 32}, + {"helix": 10, "forward": true, "start": 11, "end": 32} + ] + }, + { + "name": "tile-left-12-13", + "color": "#000000", + "sequence": "TGCGTTAAAATAGATGCGTATATGAATGGGTAGTATCAGGAA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 13, "forward": false, "start": 11, "end": 32}, + {"helix": 12, "forward": true, "start": 11, "end": 32} + ] + }, + { + "name": "tile-left-14-15", + "color": "#000000", + "sequence": "ATTCAGAGAGTTGGCATGATATGTGAAGGTTTATGAGACGAT", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 15, "forward": false, "start": 11, "end": 32}, + {"helix": 14, "forward": true, "start": 11, "end": 32} + ] + }, + { + "name": "tile-left-16-17", + "color": "#000000", + "sequence": "TGGATTTGTTTACGGAAAGATAAGCATGGTAAAATTGGTCAA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 17, "forward": false, "start": 11, "end": 32}, + {"helix": 16, "forward": true, "start": 11, "end": 32} + ] + }, + { + "name": "tile-right-2-3", + "color": "#000000", + "sequence": "TTGTCTAGAGTTTGGGATGTTAGTTCTTGGTATTGTTGACAA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 3, "forward": false, "start": 480, "end": 501}, + {"helix": 2, "forward": true, "start": 480, "end": 501} + ] + }, + { + "name": "tile-right-4-5", + "color": "#000000", + "sequence": "AAGGAAGTAGATTCGAAAGGTACGTGGATAAAATAGGAGGAA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 5, "forward": false, "start": 480, "end": 501}, + {"helix": 4, "forward": true, "start": 480, "end": 501} + ] + }, + { + "name": "tile-right-6-7", + "color": "#000000", + "sequence": "AGAATAGTCGTTTGTCAGTGTATTCGAGGTTAGAATCTGGTA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 7, "forward": false, "start": 480, "end": 501}, + {"helix": 6, "forward": true, "start": 480, "end": 501} + ] + }, + { + "name": "tile-right-8-9", + "color": "#000000", + "sequence": "AATGGATAGGTAGGTGTCTTTATGAGCAGATAAGAGATCAGA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 9, "forward": false, "start": 480, "end": 501}, + {"helix": 8, "forward": true, "start": 480, "end": 501} + ] + }, + { + "name": "tile-right-10-11", + "color": "#000000", + "sequence": "AGTGATGATCTTTTAGGCTGTTGGAACTTGATGCTAAGGATA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 11, "forward": false, "start": 480, "end": 501}, + {"helix": 10, "forward": true, "start": 480, "end": 501} + ] + }, + { + "name": "tile-right-12-13", + "color": "#000000", + "sequence": "TGCGTTAAAATAGATGCGTATATGAATGGGTAGTATCAGGAA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 13, "forward": false, "start": 480, "end": 501}, + {"helix": 12, "forward": true, "start": 480, "end": 501} + ] + }, + { + "name": "tile-right-14-15", + "color": "#000000", + "sequence": "ATTCAGAGAGTTGGCATGATATGTGAAGGTTTATGAGACGAT", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 15, "forward": false, "start": 480, "end": 501}, + {"helix": 14, "forward": true, "start": 480, "end": 501} + ] + }, + { + "name": "tile-right-16-17", + "color": "#000000", + "sequence": "TGGATTTGTTTACGGAAAGATAAGCATGGTAAAATTGGTCAA", + "vendor": {"scale": "25nm", "purification": "STD"}, + "domains": [ + {"helix": 17, "forward": false, "start": 480, "end": 501}, + {"helix": 16, "forward": true, "start": 480, "end": 501} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/16_helix_origami_rectangle.sc b/examples/output_designs/16_helix_origami_rectangle.sc index f9dcf06..f629261 100644 --- a/examples/output_designs/16_helix_origami_rectangle.sc +++ b/examples/output_designs/16_helix_origami_rectangle.sc @@ -1,1878 +1,1878 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 448, "grid_position": [0, 0]}, - {"max_offset": 448, "grid_position": [0, 1]}, - {"max_offset": 448, "grid_position": [0, 2]}, - {"max_offset": 448, "grid_position": [0, 3]}, - {"max_offset": 448, "grid_position": [0, 4]}, - {"max_offset": 448, "grid_position": [0, 5]}, - {"max_offset": 448, "grid_position": [0, 6]}, - {"max_offset": 448, "grid_position": [0, 7]}, - {"max_offset": 448, "grid_position": [0, 8]}, - {"max_offset": 448, "grid_position": [0, 9]}, - {"max_offset": 448, "grid_position": [0, 10]}, - {"max_offset": 448, "grid_position": [0, 11]}, - {"max_offset": 448, "grid_position": [0, 12]}, - {"max_offset": 448, "grid_position": [0, 13]}, - {"max_offset": 448, "grid_position": [0, 14]}, - {"max_offset": 448, "grid_position": [0, 15]} - ], - "strands": [ - { - "color": "#0066cc", - "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCG", - "domains": [ - {"helix": 15, "forward": false, "start": 16, "end": 224}, - {"helix": 14, "forward": true, "start": 16, "end": 224}, - {"helix": 13, "forward": false, "start": 16, "end": 224}, - {"helix": 12, "forward": true, "start": 16, "end": 224}, - {"helix": 11, "forward": false, "start": 16, "end": 224}, - {"helix": 10, "forward": true, "start": 16, "end": 224}, - {"helix": 9, "forward": false, "start": 16, "end": 224}, - {"helix": 8, "forward": true, "start": 16, "end": 224}, - {"helix": 7, "forward": false, "start": 16, "end": 224}, - {"helix": 6, "forward": true, "start": 16, "end": 224}, - {"helix": 5, "forward": false, "start": 16, "end": 224}, - {"helix": 4, "forward": true, "start": 16, "end": 224}, - {"helix": 3, "forward": false, "start": 16, "end": 224}, - {"helix": 2, "forward": true, "start": 16, "end": 224}, - {"helix": 1, "forward": false, "start": 16, "end": 224}, - {"helix": 0, "forward": true, "start": 16, "end": 432}, - {"helix": 1, "forward": false, "start": 224, "end": 432}, - {"helix": 2, "forward": true, "start": 224, "end": 432}, - {"helix": 3, "forward": false, "start": 224, "end": 432}, - {"helix": 4, "forward": true, "start": 224, "end": 432}, - {"helix": 5, "forward": false, "start": 224, "end": 432}, - {"helix": 6, "forward": true, "start": 224, "end": 432}, - {"helix": 7, "forward": false, "start": 224, "end": 432}, - {"helix": 8, "forward": true, "start": 224, "end": 432}, - {"helix": 9, "forward": false, "start": 224, "end": 432}, - {"helix": 10, "forward": true, "start": 224, "end": 432}, - {"helix": 11, "forward": false, "start": 224, "end": 432}, - {"helix": 12, "forward": true, "start": 224, "end": 432}, - {"helix": 13, "forward": false, "start": 224, "end": 432}, - {"helix": 14, "forward": true, "start": 224, "end": 432}, - {"helix": 15, "forward": false, "start": 224, "end": 432} - ], - "is_scaffold": true - }, - { - "color": "#f74308", - "sequence": "ACAACCATCGCCCACGTGCGCCGACAATGACA", - "domains": [ - {"helix": 1, "forward": true, "start": 16, "end": 32}, - {"helix": 0, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#57bb00", - "sequence": "GAGGACAGATGAACGGCTGACCAACTTTGAAA", - "domains": [ - {"helix": 3, "forward": true, "start": 16, "end": 32}, - {"helix": 2, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#888888", - "sequence": "TCGTTTACCAGACGACAACACTATCATAACCC", - "domains": [ - {"helix": 5, "forward": true, "start": 16, "end": 32}, - {"helix": 4, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#32b86c", - "sequence": "CTGTAGCTCAACATGTATTGCTGAATATAATG", - "domains": [ - {"helix": 7, "forward": true, "start": 16, "end": 32}, - {"helix": 6, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#333333", - "sequence": "ATTCAAAAGGGTGAGATAATGTGTAGGTAAAG", - "domains": [ - {"helix": 9, "forward": true, "start": 16, "end": 32}, - {"helix": 8, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#320096", - "sequence": "GATTCTCCGTGGGAACGAGTAACAACCCGTCG", - "domains": [ - {"helix": 11, "forward": true, "start": 16, "end": 32}, - {"helix": 10, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#03b6a2", - "sequence": "GTTTCCTGTGTGAAATAATCATGGTCATAGCT", - "domains": [ - {"helix": 13, "forward": true, "start": 16, "end": 32}, - {"helix": 12, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#7300de", - "sequence": "ACAAGAGTCCACTATTGTTGTTCCAGTTTGGA", - "domains": [ - {"helix": 15, "forward": true, "start": 16, "end": 32}, - {"helix": 14, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#aaaa00", - "sequence": "ACCGCCACCCTCAGAATACCGCCACCCTCAGA", - "domains": [ - {"helix": 0, "forward": false, "start": 416, "end": 432}, - {"helix": 1, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#b8056c", - "sequence": "CCGCCGCCAGCATTGAAGAACCACCACCAGAG", - "domains": [ - {"helix": 2, "forward": false, "start": 416, "end": 432}, - {"helix": 3, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#007200", - "sequence": "AGACAAAAGGGCGACAGGTTTACCAGCGCCAA", - "domains": [ - {"helix": 4, "forward": false, "start": 416, "end": 432}, - {"helix": 5, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#cc0000", - "sequence": "AGAGAATAACATAAAAATAGCAGCCTTTACAG", - "domains": [ - {"helix": 6, "forward": false, "start": 416, "end": 432}, - {"helix": 7, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#f7931e", - "sequence": "CGAGCATGTAGAAACCATCCCATCCTAATTTA", - "domains": [ - {"helix": 8, "forward": false, "start": 416, "end": 432}, - {"helix": 9, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#f74308", - "sequence": "CGCGAGAAAACTTTTTATCGCAAGACAAAGAA", - "domains": [ - {"helix": 10, "forward": false, "start": 416, "end": 432}, - {"helix": 11, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#57bb00", - "sequence": "TCGGGAGAAACAATAAAACAGTACCTTTTACA", - "domains": [ - {"helix": 12, "forward": false, "start": 416, "end": 432}, - {"helix": 13, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#888888", - "sequence": "TTGAAAGGAATTGAGGGTTGGCAAATCAACAG", - "domains": [ - {"helix": 14, "forward": false, "start": 416, "end": 432}, - {"helix": 15, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#32b86c", - "sequence": "ACGTTAGTAAATGAATTTTCTGTATGGGATTT", - "domains": [ - {"helix": 0, "forward": false, "start": 216, "end": 248} - ] - }, - { - "color": "#333333", - "sequence": "AAACGAAATGCCACTACGAAGGCAAAACAGTT", - "domains": [ - {"helix": 2, "forward": false, "start": 208, "end": 216}, - {"helix": 1, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#320096", - "sequence": "AATGCCCCGTAACAGTGCCCGTATCCAACCTA", - "domains": [ - {"helix": 1, "forward": true, "start": 232, "end": 240}, - {"helix": 2, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#03b6a2", - "sequence": "CGATTTTATTAATCATTGTGAATTATCAAGTT", - "domains": [ - {"helix": 4, "forward": false, "start": 208, "end": 216}, - {"helix": 3, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#7300de", - "sequence": "TGCCTTTAAATCAGTAGCGACAGAACCTTATG", - "domains": [ - {"helix": 3, "forward": true, "start": 232, "end": 240}, - {"helix": 4, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#aaaa00", - "sequence": "TCAGAAGCAGGTCTTTACCCTGACAGTTACCA", - "domains": [ - {"helix": 6, "forward": false, "start": 208, "end": 216}, - {"helix": 5, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#b8056c", - "sequence": "GAAGGAAAGCAGATAGCCGAACAATATTATAG", - "domains": [ - {"helix": 5, "forward": true, "start": 232, "end": 240}, - {"helix": 6, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#007200", - "sequence": "CAATAAATACTAATAGTAGTAGCACTTGCGGG", - "domains": [ - {"helix": 8, "forward": false, "start": 208, "end": 216}, - {"helix": 7, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#cc0000", - "sequence": "AGGTTTTGTTAGCGAACCTCCCGATTAACATC", - "domains": [ - {"helix": 7, "forward": true, "start": 232, "end": 240}, - {"helix": 8, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#f7931e", - "sequence": "AGAAAAGCTCATATGTACCCCGGTAGAATCGC", - "domains": [ - {"helix": 10, "forward": false, "start": 208, "end": 216}, - {"helix": 9, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#f74308", - "sequence": "CATATTTACAGTAGGGCTTAATTGTGATAATC", - "domains": [ - {"helix": 9, "forward": true, "start": 232, "end": 240}, - {"helix": 10, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#57bb00", - "sequence": "GGCGATCGTCAGGCTGCGCAACTGCCTTGCTT", - "domains": [ - {"helix": 12, "forward": false, "start": 208, "end": 216}, - {"helix": 11, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#888888", - "sequence": "CTGTAAATATATGTGAGTGAATAATTGGGAAG", - "domains": [ - {"helix": 11, "forward": true, "start": 232, "end": 240}, - {"helix": 12, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#32b86c", - "sequence": "TGGTTTTTCGGTTTGCGTATTGGGAGAAGGAG", - "domains": [ - {"helix": 14, "forward": false, "start": 208, "end": 216}, - {"helix": 13, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#333333", - "sequence": "CGGAATTAGAACAAAGAAACCACCCGCCAGGG", - "domains": [ - {"helix": 13, "forward": true, "start": 232, "end": 240}, - {"helix": 14, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#320096", - "sequence": "GAACGTGGCGAGAAAGGAAGGGAACGAACTGA", - "domains": [ - {"helix": 15, "forward": true, "start": 200, "end": 232} - ] - }, - { - "color": "#03b6a2", - "sequence": "CTTAAACAGCTTGATACCGATAGTCATAACCG", - "domains": [ - {"helix": 0, "forward": false, "start": 32, "end": 56}, - {"helix": 1, "forward": true, "start": 32, "end": 40} - ] - }, - { - "color": "#7300de", - "sequence": "ATATATTCTCATAAGGGAACCGAATGTACAGA", - "domains": [ - {"helix": 1, "forward": true, "start": 40, "end": 48}, - {"helix": 2, "forward": false, "start": 32, "end": 48}, - {"helix": 3, "forward": true, "start": 32, "end": 40} - ] - }, - { - "color": "#aaaa00", - "sequence": "CCAGGCGCGAGGCATAGTAAGAGCGATAAAAA", - "domains": [ - {"helix": 3, "forward": true, "start": 40, "end": 48}, - {"helix": 4, "forward": false, "start": 32, "end": 48}, - {"helix": 5, "forward": true, "start": 32, "end": 40} - ] - }, - { - "color": "#b8056c", - "sequence": "CCAAAATAGATGGCTTAGAGCTTATTTAAATA", - "domains": [ - {"helix": 5, "forward": true, "start": 40, "end": 48}, - {"helix": 6, "forward": false, "start": 32, "end": 48}, - {"helix": 7, "forward": true, "start": 32, "end": 40} - ] - }, - { - "color": "#007200", - "sequence": "TGCAACTAAAATGCAATGCCTGAGAAGGCCGG", - "domains": [ - {"helix": 7, "forward": true, "start": 40, "end": 48}, - {"helix": 8, "forward": false, "start": 32, 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"TCACAATCGACGGGAGAATTAACTAAACGATT", - "domains": [ - {"helix": 5, "forward": true, "start": 392, "end": 400}, - {"helix": 6, "forward": false, "start": 384, "end": 400}, - {"helix": 7, "forward": true, "start": 384, "end": 392} - ] - }, - { - "color": "#57bb00", - "sequence": "TTTTGTTTTCTTTCCTTATCATTCACAATAGA", - "domains": [ - {"helix": 7, "forward": true, "start": 392, "end": 400}, - {"helix": 8, "forward": false, "start": 384, "end": 400}, - {"helix": 9, "forward": true, "start": 384, "end": 392} - ] - }, - { - "color": "#888888", - "sequence": "TAAGTCCTAATTTCATCTTCTGACTATAACTA", - "domains": [ - {"helix": 9, "forward": true, "start": 392, "end": 400}, - {"helix": 10, "forward": false, "start": 384, "end": 400}, - {"helix": 11, "forward": true, "start": 384, "end": 392} - ] - }, - { - "color": "#32b86c", - "sequence": "TATGTAAACTTTGAATACCAAGTTTTTTCAGG", - "domains": [ - {"helix": 11, "forward": true, "start": 392, "end": 400}, - {"helix": 12, "forward": false, "start": 384, "end": 400}, - {"helix": 13, "forward": true, "start": 384, "end": 392} - ] - }, - { - "color": "#333333", - "sequence": "TTTAACGTTCTTTAGGAGCACTAACAAATATC", - "domains": [ - {"helix": 13, "forward": true, "start": 392, "end": 400}, - {"helix": 14, "forward": false, "start": 384, "end": 400}, - {"helix": 15, "forward": true, "start": 384, "end": 392} - ] - }, - { - "color": "#320096", - "sequence": "AAACCCTCAATCAATATCTGGTCAAAGGTTAT", - "domains": [ - {"helix": 15, "forward": true, "start": 392, "end": 416}, - {"helix": 14, "forward": false, "start": 408, "end": 416} - ] - }, - { - "color": "#03b6a2", - "sequence": "TGAGGCAGTACTCAGGAGGTTTAGCCGCCACC", - "domains": [ - {"helix": 2, "forward": false, "start": 400, "end": 408}, - {"helix": 1, "forward": true, "start": 400, "end": 416}, - {"helix": 0, "forward": false, "start": 408, "end": 416} - ] - }, - { - "color": "#7300de", - "sequence": "ATTGAGGGCCTCAGAGCCGCCACCCAGGAGGT", - "domains": [ - {"helix": 4, "forward": false, "start": 400, "end": 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"TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCG", 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"sequence": "CCTGATTGTGCTGATGCAAATCCACAAATATA", + "domains": [ + {"helix": 12, "forward": false, "start": 400, "end": 408}, + {"helix": 11, "forward": true, "start": 400, "end": 416}, + {"helix": 10, "forward": false, "start": 408, "end": 416} + ] + }, + { + "color": "#f7931e", + "sequence": "CTAAAATACAGATGAATATACAGTCGGATTCG", + "domains": [ + {"helix": 14, "forward": false, "start": 400, "end": 408}, + {"helix": 13, "forward": true, "start": 400, "end": 416}, + {"helix": 12, "forward": false, "start": 408, "end": 416} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/16_helix_origami_rectangle_idt.sc b/examples/output_designs/16_helix_origami_rectangle_idt.sc index f9dcf06..f629261 100644 --- a/examples/output_designs/16_helix_origami_rectangle_idt.sc +++ b/examples/output_designs/16_helix_origami_rectangle_idt.sc @@ -1,1878 +1,1878 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 448, "grid_position": [0, 0]}, - {"max_offset": 448, "grid_position": [0, 1]}, - {"max_offset": 448, "grid_position": [0, 2]}, - {"max_offset": 448, "grid_position": [0, 3]}, - {"max_offset": 448, "grid_position": [0, 4]}, - {"max_offset": 448, "grid_position": [0, 5]}, - {"max_offset": 448, "grid_position": [0, 6]}, - {"max_offset": 448, "grid_position": [0, 7]}, - {"max_offset": 448, "grid_position": [0, 8]}, - {"max_offset": 448, "grid_position": [0, 9]}, - {"max_offset": 448, "grid_position": [0, 10]}, - {"max_offset": 448, "grid_position": [0, 11]}, - {"max_offset": 448, "grid_position": [0, 12]}, - {"max_offset": 448, "grid_position": [0, 13]}, - {"max_offset": 448, "grid_position": [0, 14]}, - {"max_offset": 448, "grid_position": [0, 15]} - ], - "strands": [ - { - "color": "#0066cc", - "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCG", - "domains": [ - {"helix": 15, "forward": false, "start": 16, "end": 224}, - {"helix": 14, "forward": true, "start": 16, "end": 224}, - {"helix": 13, "forward": false, "start": 16, "end": 224}, - {"helix": 12, "forward": true, "start": 16, "end": 224}, - {"helix": 11, "forward": false, "start": 16, "end": 224}, - {"helix": 10, "forward": true, "start": 16, "end": 224}, - {"helix": 9, "forward": false, "start": 16, "end": 224}, - {"helix": 8, "forward": true, "start": 16, "end": 224}, - {"helix": 7, "forward": false, "start": 16, "end": 224}, - {"helix": 6, "forward": true, "start": 16, "end": 224}, - {"helix": 5, "forward": false, "start": 16, "end": 224}, - {"helix": 4, "forward": true, "start": 16, "end": 224}, - {"helix": 3, "forward": false, "start": 16, "end": 224}, - {"helix": 2, "forward": true, "start": 16, "end": 224}, - {"helix": 1, "forward": false, "start": 16, "end": 224}, - {"helix": 0, "forward": true, "start": 16, "end": 432}, - {"helix": 1, "forward": false, "start": 224, "end": 432}, - {"helix": 2, "forward": true, "start": 224, "end": 432}, - {"helix": 3, "forward": false, "start": 224, "end": 432}, - {"helix": 4, "forward": true, "start": 224, "end": 432}, - {"helix": 5, "forward": false, "start": 224, "end": 432}, - {"helix": 6, "forward": true, "start": 224, "end": 432}, - {"helix": 7, "forward": false, "start": 224, "end": 432}, - {"helix": 8, "forward": true, "start": 224, "end": 432}, - {"helix": 9, "forward": false, "start": 224, "end": 432}, - {"helix": 10, "forward": true, "start": 224, "end": 432}, - {"helix": 11, "forward": false, "start": 224, "end": 432}, - {"helix": 12, "forward": true, "start": 224, "end": 432}, - {"helix": 13, "forward": false, "start": 224, "end": 432}, - {"helix": 14, "forward": true, "start": 224, "end": 432}, - {"helix": 15, "forward": false, "start": 224, "end": 432} - ], - "is_scaffold": true - }, - { - "color": "#f74308", - "sequence": "ACAACCATCGCCCACGTGCGCCGACAATGACA", - "domains": [ - {"helix": 1, "forward": true, "start": 16, "end": 32}, - {"helix": 0, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#57bb00", - "sequence": "GAGGACAGATGAACGGCTGACCAACTTTGAAA", - "domains": [ - {"helix": 3, "forward": true, "start": 16, "end": 32}, - {"helix": 2, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#888888", - "sequence": "TCGTTTACCAGACGACAACACTATCATAACCC", - "domains": [ - {"helix": 5, "forward": true, "start": 16, "end": 32}, - {"helix": 4, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#32b86c", - "sequence": "CTGTAGCTCAACATGTATTGCTGAATATAATG", - "domains": [ - {"helix": 7, "forward": true, "start": 16, "end": 32}, - {"helix": 6, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#333333", - "sequence": "ATTCAAAAGGGTGAGATAATGTGTAGGTAAAG", - "domains": [ - {"helix": 9, "forward": true, "start": 16, "end": 32}, - {"helix": 8, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#320096", - "sequence": "GATTCTCCGTGGGAACGAGTAACAACCCGTCG", - "domains": [ - {"helix": 11, "forward": true, "start": 16, "end": 32}, - {"helix": 10, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#03b6a2", - "sequence": "GTTTCCTGTGTGAAATAATCATGGTCATAGCT", - "domains": [ - {"helix": 13, "forward": true, "start": 16, "end": 32}, - {"helix": 12, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#7300de", - "sequence": "ACAAGAGTCCACTATTGTTGTTCCAGTTTGGA", - "domains": [ - {"helix": 15, "forward": true, "start": 16, "end": 32}, - {"helix": 14, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#aaaa00", - "sequence": "ACCGCCACCCTCAGAATACCGCCACCCTCAGA", - "domains": [ - {"helix": 0, "forward": false, "start": 416, "end": 432}, - {"helix": 1, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#b8056c", - "sequence": "CCGCCGCCAGCATTGAAGAACCACCACCAGAG", - "domains": [ - {"helix": 2, "forward": false, "start": 416, "end": 432}, - {"helix": 3, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#007200", - "sequence": "AGACAAAAGGGCGACAGGTTTACCAGCGCCAA", - "domains": [ - {"helix": 4, "forward": false, "start": 416, "end": 432}, - {"helix": 5, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#cc0000", - "sequence": "AGAGAATAACATAAAAATAGCAGCCTTTACAG", - "domains": [ - {"helix": 6, "forward": false, "start": 416, "end": 432}, - {"helix": 7, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#f7931e", - "sequence": "CGAGCATGTAGAAACCATCCCATCCTAATTTA", - "domains": [ - {"helix": 8, "forward": false, "start": 416, "end": 432}, - {"helix": 9, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#f74308", - "sequence": "CGCGAGAAAACTTTTTATCGCAAGACAAAGAA", - "domains": [ - {"helix": 10, "forward": false, "start": 416, "end": 432}, - {"helix": 11, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#57bb00", - "sequence": "TCGGGAGAAACAATAAAACAGTACCTTTTACA", - "domains": [ - {"helix": 12, "forward": false, "start": 416, "end": 432}, - {"helix": 13, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#888888", - "sequence": "TTGAAAGGAATTGAGGGTTGGCAAATCAACAG", - "domains": [ - {"helix": 14, "forward": false, "start": 416, "end": 432}, - {"helix": 15, "forward": true, "start": 416, "end": 432} - ] - }, - { - "color": "#32b86c", - "sequence": "ACGTTAGTAAATGAATTTTCTGTATGGGATTT", - "domains": [ - {"helix": 0, "forward": false, "start": 216, "end": 248} - ] - }, - { - "color": "#333333", - "sequence": "AAACGAAATGCCACTACGAAGGCAAAACAGTT", - "domains": [ - {"helix": 2, "forward": false, "start": 208, "end": 216}, - {"helix": 1, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#320096", - "sequence": "AATGCCCCGTAACAGTGCCCGTATCCAACCTA", - "domains": [ - {"helix": 1, "forward": true, "start": 232, "end": 240}, - {"helix": 2, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#03b6a2", - "sequence": "CGATTTTATTAATCATTGTGAATTATCAAGTT", - "domains": [ - {"helix": 4, "forward": false, "start": 208, "end": 216}, - {"helix": 3, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#7300de", - "sequence": "TGCCTTTAAATCAGTAGCGACAGAACCTTATG", - "domains": [ - {"helix": 3, "forward": true, "start": 232, "end": 240}, - {"helix": 4, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#aaaa00", - "sequence": "TCAGAAGCAGGTCTTTACCCTGACAGTTACCA", - "domains": [ - {"helix": 6, "forward": false, "start": 208, "end": 216}, - {"helix": 5, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#b8056c", - "sequence": "GAAGGAAAGCAGATAGCCGAACAATATTATAG", - "domains": [ - {"helix": 5, "forward": true, "start": 232, "end": 240}, - {"helix": 6, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#007200", - "sequence": "CAATAAATACTAATAGTAGTAGCACTTGCGGG", - "domains": [ - {"helix": 8, "forward": false, "start": 208, "end": 216}, - {"helix": 7, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#cc0000", - "sequence": "AGGTTTTGTTAGCGAACCTCCCGATTAACATC", - "domains": [ - {"helix": 7, "forward": true, "start": 232, "end": 240}, - {"helix": 8, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#f7931e", - "sequence": "AGAAAAGCTCATATGTACCCCGGTAGAATCGC", - "domains": [ - {"helix": 10, "forward": false, "start": 208, "end": 216}, - {"helix": 9, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#f74308", - "sequence": "CATATTTACAGTAGGGCTTAATTGTGATAATC", - "domains": [ - {"helix": 9, "forward": true, "start": 232, "end": 240}, - {"helix": 10, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#57bb00", - "sequence": "GGCGATCGTCAGGCTGCGCAACTGCCTTGCTT", - "domains": [ - {"helix": 12, "forward": false, "start": 208, "end": 216}, - {"helix": 11, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#888888", - "sequence": "CTGTAAATATATGTGAGTGAATAATTGGGAAG", - "domains": [ - {"helix": 11, "forward": true, "start": 232, "end": 240}, - {"helix": 12, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#32b86c", - "sequence": "TGGTTTTTCGGTTTGCGTATTGGGAGAAGGAG", - "domains": [ - {"helix": 14, "forward": false, "start": 208, "end": 216}, - {"helix": 13, "forward": true, "start": 208, "end": 232} - ] - }, - { - "color": "#333333", - "sequence": "CGGAATTAGAACAAAGAAACCACCCGCCAGGG", - "domains": [ - {"helix": 13, "forward": true, "start": 232, "end": 240}, - {"helix": 14, "forward": false, "start": 216, "end": 240} - ] - }, - { - "color": "#320096", - "sequence": "GAACGTGGCGAGAAAGGAAGGGAACGAACTGA", - "domains": [ - {"helix": 15, "forward": true, "start": 200, "end": 232} - ] - }, - { - "color": "#03b6a2", - "sequence": "CTTAAACAGCTTGATACCGATAGTCATAACCG", - "domains": [ - {"helix": 0, "forward": false, "start": 32, "end": 56}, - {"helix": 1, "forward": true, "start": 32, "end": 40} - ] - }, - { - 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"#888888", - "sequence": "CTAAAGCATCACCTTGCTGAACCTCAACTAAT", - "domains": [ - {"helix": 15, "forward": true, "start": 360, "end": 384}, - {"helix": 14, "forward": false, "start": 376, "end": 384} - ] - }, - { - "color": "#32b86c", - "sequence": "ACAAACAATATAAGTATAGCCCGGAGGGATAG", - "domains": [ - {"helix": 2, "forward": false, "start": 368, "end": 376}, - {"helix": 1, "forward": true, "start": 368, "end": 384}, - {"helix": 0, "forward": false, "start": 376, "end": 384} - ] - }, - { - "color": "#333333", - "sequence": "TTATTCATACCCTCAGAACCGCCATGATATTC", - "domains": [ - {"helix": 4, "forward": false, "start": 368, "end": 376}, - {"helix": 3, "forward": true, "start": 368, "end": 384}, - {"helix": 2, "forward": false, "start": 376, "end": 384} - ] - }, - { - "color": "#320096", - "sequence": "TGAACAAAACACCACGGAATAAGTGACGGAAA", - "domains": [ - {"helix": 6, "forward": false, "start": 368, "end": 376}, - {"helix": 5, "forward": true, "start": 368, "end": 384}, - {"helix": 4, "forward": false, "start": 376, "end": 384} - ] - }, - { - "color": "#03b6a2", - "sequence": "GGTATTAATCCCAATCCAAATAAGGAACACCC", - "domains": [ - {"helix": 8, "forward": false, "start": 368, "end": 376}, - {"helix": 7, "forward": true, "start": 368, "end": 384}, - {"helix": 6, "forward": false, "start": 376, "end": 384} - ] - }, - { - "color": "#7300de", - "sequence": "AATGGTTTACGCGCCTGTTTATCACAAGAACG", - "domains": [ - {"helix": 10, "forward": false, "start": 368, "end": 376}, - {"helix": 9, "forward": true, "start": 368, "end": 384}, - {"helix": 8, "forward": false, "start": 376, "end": 384} - ] - }, - { - "color": "#aaaa00", - "sequence": "GCGCAGAGGGCTTAGGTTGGGTTACTAAATTT", - "domains": [ - {"helix": 12, "forward": false, "start": 368, "end": 376}, - {"helix": 11, "forward": true, "start": 368, "end": 384}, - {"helix": 10, "forward": false, "start": 376, "end": 384} - ] - }, - { - "color": "#b8056c", - "sequence": "AGATTAGAAAAGAAATTGCGTAGAACAAAATC", - "domains": [ - {"helix": 14, "forward": 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"TCACAATCGACGGGAGAATTAACTAAACGATT", - "domains": [ - {"helix": 5, "forward": true, "start": 392, "end": 400}, - {"helix": 6, "forward": false, "start": 384, "end": 400}, - {"helix": 7, "forward": true, "start": 384, "end": 392} - ] - }, - { - "color": "#57bb00", - "sequence": "TTTTGTTTTCTTTCCTTATCATTCACAATAGA", - "domains": [ - {"helix": 7, "forward": true, "start": 392, "end": 400}, - {"helix": 8, "forward": false, "start": 384, "end": 400}, - {"helix": 9, "forward": true, "start": 384, "end": 392} - ] - }, - { - "color": "#888888", - "sequence": "TAAGTCCTAATTTCATCTTCTGACTATAACTA", - "domains": [ - {"helix": 9, "forward": true, "start": 392, "end": 400}, - {"helix": 10, "forward": false, "start": 384, "end": 400}, - {"helix": 11, "forward": true, "start": 384, "end": 392} - ] - }, - { - "color": "#32b86c", - "sequence": "TATGTAAACTTTGAATACCAAGTTTTTTCAGG", - "domains": [ - {"helix": 11, "forward": true, "start": 392, "end": 400}, - {"helix": 12, "forward": false, "start": 384, "end": 400}, - {"helix": 13, "forward": true, "start": 384, "end": 392} - ] - }, - { - "color": "#333333", - "sequence": "TTTAACGTTCTTTAGGAGCACTAACAAATATC", - "domains": [ - {"helix": 13, "forward": true, "start": 392, "end": 400}, - {"helix": 14, "forward": false, "start": 384, "end": 400}, - {"helix": 15, "forward": true, "start": 384, "end": 392} - ] - }, - { - "color": "#320096", - "sequence": "AAACCCTCAATCAATATCTGGTCAAAGGTTAT", - "domains": [ - {"helix": 15, "forward": true, "start": 392, "end": 416}, - {"helix": 14, "forward": false, "start": 408, "end": 416} - ] - }, - { - "color": "#03b6a2", - "sequence": "TGAGGCAGTACTCAGGAGGTTTAGCCGCCACC", - "domains": [ - {"helix": 2, "forward": false, "start": 400, "end": 408}, - {"helix": 1, "forward": true, "start": 400, "end": 416}, - {"helix": 0, "forward": false, "start": 408, "end": 416} - ] - }, - { - "color": "#7300de", - "sequence": "ATTGAGGGCCTCAGAGCCGCCACCCAGGAGGT", - "domains": [ - {"helix": 4, "forward": false, "start": 400, "end": 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"sequence": "CCTGATTGTGCTGATGCAAATCCACAAATATA", - "domains": [ - {"helix": 12, "forward": false, "start": 400, "end": 408}, - {"helix": 11, "forward": true, "start": 400, "end": 416}, - {"helix": 10, "forward": false, "start": 408, "end": 416} - ] - }, - { - "color": "#f7931e", - "sequence": "CTAAAATACAGATGAATATACAGTCGGATTCG", - "domains": [ - {"helix": 14, "forward": false, "start": 400, "end": 408}, - {"helix": 13, "forward": true, "start": 400, "end": 416}, - {"helix": 12, "forward": false, "start": 408, "end": 416} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"max_offset": 448, "grid_position": [0, 0]}, + {"max_offset": 448, "grid_position": [0, 1]}, + {"max_offset": 448, "grid_position": [0, 2]}, + {"max_offset": 448, "grid_position": [0, 3]}, + {"max_offset": 448, "grid_position": [0, 4]}, + {"max_offset": 448, "grid_position": [0, 5]}, + {"max_offset": 448, "grid_position": [0, 6]}, + {"max_offset": 448, "grid_position": [0, 7]}, + {"max_offset": 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"TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCG", 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b/examples/output_designs/16_helix_origami_rectangle_no_twist.sc index 7ab8cc6..3d2537b 100644 --- a/examples/output_designs/16_helix_origami_rectangle_no_twist.sc +++ b/examples/output_designs/16_helix_origami_rectangle_no_twist.sc @@ -1,1878 +1,1878 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 448, "grid_position": [0, 0]}, - {"max_offset": 448, "grid_position": [0, 1]}, - {"max_offset": 448, "grid_position": [0, 2]}, - {"max_offset": 448, "grid_position": [0, 3]}, - {"max_offset": 448, "grid_position": [0, 4]}, - {"max_offset": 448, "grid_position": [0, 5]}, - {"max_offset": 448, "grid_position": [0, 6]}, - {"max_offset": 448, "grid_position": [0, 7]}, - {"max_offset": 448, "grid_position": [0, 8]}, - {"max_offset": 448, "grid_position": [0, 9]}, - {"max_offset": 448, "grid_position": [0, 10]}, - {"max_offset": 448, "grid_position": [0, 11]}, - {"max_offset": 448, "grid_position": [0, 12]}, - {"max_offset": 448, "grid_position": [0, 13]}, - {"max_offset": 448, "grid_position": [0, 14]}, - {"max_offset": 448, "grid_position": [0, 15]} - ], - "strands": [ - { - "color": "#0066cc", - "sequence": 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GTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGA", 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"TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGA", + "domains": [ + {"helix": 15, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 14, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 13, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 12, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 11, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 10, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 9, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 8, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 7, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 6, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 5, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 4, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 3, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 2, "forward": true, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 1, "forward": false, "start": 16, "end": 224, "deletions": [33, 81, 129, 177]}, + {"helix": 0, "forward": true, "start": 16, "end": 432, "deletions": [33, 81, 129, 177, 225, 273, 321, 369, 417]}, + {"helix": 1, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 2, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 3, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 4, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 5, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 6, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 7, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 8, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 9, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 10, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 11, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 12, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 13, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 14, "forward": true, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]}, + {"helix": 15, "forward": false, "start": 224, "end": 432, "deletions": [225, 273, 321, 369, 417]} + ], + "is_scaffold": true + }, + { + "color": "#f74308", + "sequence": "GCCGCTTTTGCGGGATTTGCAGGGAGTTAAAG", + "domains": [ + {"helix": 1, "forward": true, "start": 16, "end": 32}, + {"helix": 0, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#57bb00", + "sequence": "CAAGAGTAATCTTGACGCTGGCTGACCTTCAT", + "domains": [ + {"helix": 3, "forward": true, "start": 16, "end": 32}, + {"helix": 2, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#888888", + "sequence": "TGCAAAAGAAGTTTTGAATAGCGAGAGGCTTT", + "domains": [ + {"helix": 5, "forward": true, "start": 16, "end": 32}, + {"helix": 4, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#32b86c", + "sequence": "ACGGTGTCTGGAAGTTAATATGCAACTAAAGT", + "domains": [ + {"helix": 7, "forward": true, "start": 16, "end": 32}, + {"helix": 6, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#333333", + "sequence": "AGTCAAATCACCATCAGAGAAAGGCCGGAGAC", + "domains": [ + {"helix": 9, "forward": true, "start": 16, "end": 32}, + {"helix": 8, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#320096", + "sequence": "GGCGGATTGACCGTAACTCCGTGGGAACAAAC", + "domains": [ + {"helix": 11, "forward": true, "start": 16, "end": 32}, + {"helix": 10, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#03b6a2", + "sequence": "AAATTGTTATCCGCTCAGCTGTTTCCTGTGTG", + "domains": [ + {"helix": 13, "forward": true, "start": 16, "end": 32}, + {"helix": 12, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#7300de", + "sequence": "GAGTCCACTATTAAAGTTCCAGTTTGGAACAA", + "domains": [ + {"helix": 15, "forward": true, "start": 16, "end": 32}, + {"helix": 14, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#aaaa00", + "sequence": "AACCCATGTACCGTAAGCAAGCCCAATAGG", + "domains": [ + {"helix": 0, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 1, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#b8056c", + "sequence": "AGCCAGAATGGAAAGATAAATCCTCATTAA", + "domains": [ + {"helix": 2, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 3, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#007200", + "sequence": "ACTTGAGCCATTTGGTTATCACCGTCACCG", + "domains": [ + {"helix": 4, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 5, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#cc0000", + "sequence": "AACCCACAAGAATTGTAATATCAGAGAGAT", + "domains": [ + {"helix": 6, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 7, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#f7931e", + "sequence": "CATCGTAGGAATCATAGCCGTTTTTATTTT", + "domains": [ + {"helix": 8, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 9, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#f74308", + "sequence": "TAATTACTAGAAAAATAAACACCGGAATCA", + "domains": [ + {"helix": 10, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 11, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#57bb00", + "sequence": "TTAATTACATTTAACATCAAGAAAACAAAA", + "domains": [ + {"helix": 12, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 13, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#888888", + "sequence": "CTTTGCCCGAACGTTAACTCGTATTAAATC", + "domains": [ + {"helix": 14, "forward": false, "start": 416, "end": 432, "deletions": [417]}, + {"helix": 15, "forward": true, "start": 416, "end": 432, "deletions": [417]} + ] + }, + { + "color": "#32b86c", + "sequence": "AGAATAGAAAGGAACAACTAAAGGAATTGCG", + "domains": [ + {"helix": 0, "forward": false, "start": 216, "end": 248, "deletions": [225]} + ] + }, + { + "color": "#333333", + "sequence": "TACCAAGCCTCATCTTTGACCCCCTCAAGAG", + "domains": [ + {"helix": 2, "forward": false, "start": 208, "end": 216}, + {"helix": 1, "forward": true, "start": 208, "end": 232, "deletions": [225]} + ] + }, + { + "color": "#320096", + "sequence": "AAGGATTAAGAGGCTGAGACTCCAGCGATTA", + "domains": [ + {"helix": 1, "forward": true, "start": 232, "end": 240}, + {"helix": 2, "forward": false, "start": 216, "end": 240, "deletions": [225]} + ] + }, + { + "color": "#03b6a2", + "sequence": "AATCTACGACCAGTCAGGACGTTGTTCATAA", + "domains": [ + {"helix": 4, "forward": false, "start": 208, "end": 216}, + {"helix": 3, "forward": true, "start": 208, "end": 232, "deletions": [225]} + ] + }, + { + "color": "#7300de", + "sequence": "TCAAAATCAGCGTTTGCCATCTTGGAAGAAA", + "domains": [ + {"helix": 3, "forward": true, "start": 232, "end": 240}, + {"helix": 4, "forward": false, "start": 216, "end": 240, "deletions": [225]} + ] + }, + { + "color": "#aaaa00", + "sequence": "GCCCGAAATTGCATCAAAAAGATTACGTAGA", + "domains": [ + {"helix": 6, "forward": false, "start": 208, "end": 216}, + {"helix": 5, "forward": true, "start": 208, "end": 232, "deletions": [225]} + ] + }, + { + "color": "#b8056c", + "sequence": "AAATACATGCAGTATGTTAGCAAAAGAGGAA", + "domains": [ + {"helix": 5, "forward": true, "start": 232, "end": 240}, + {"helix": 6, "forward": false, "start": 216, "end": 240, "deletions": [225]} + ] + }, + { + "color": "#007200", + "sequence": "CAAAATTACATACAGGCAAGGCAACCTAATT", + "domains": [ + {"helix": 8, "forward": false, "start": 208, "end": 216}, + {"helix": 7, "forward": true, "start": 208, "end": 232, "deletions": [225]} + ] + }, + { + "color": "#cc0000", + "sequence": "TGCCAGTTAGCGTCTTTCCAGAGAGAATTAG", + "domains": [ + {"helix": 7, "forward": true, "start": 232, "end": 240}, + {"helix": 8, "forward": false, "start": 216, "end": 240, "deletions": [225]} + ] + }, + { + "color": "#f7931e", + "sequence": "TTGTATAAAGAAAAGCCCCAAAAAACAATAA", + "domains": [ + 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408, "end": 416} + ] + }, + { + "color": "#f7931e", + "sequence": "TAAAAGTTAGATGATGAAACAAACAATTTCAT", + "domains": [ + {"helix": 14, "forward": false, "start": 400, "end": 408}, + {"helix": 13, "forward": true, "start": 400, "end": 416}, + {"helix": 12, "forward": false, "start": 408, "end": 416} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.sc b/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.sc index 7332ea2..fa644bd 100644 --- a/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.sc +++ b/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.sc @@ -1,1976 +1,1976 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - { - "max_offset": 512, - "grid_position": [0, 0], - "major_ticks": [11, 22, 32, 40, 48, 58, 69, 79, 90, 100, 111, 121, 132, 142, 153, 163, 174, 184, 195, 205, 216, 226, 237, 247, 258, 268, 279, 289, 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GTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGTCGTGTGACTGGTGAATCTGCCAATGTAAATAATCCATTTCAGACGATTGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCGGTAATATTGTTCTGGATATTACCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTGCTACAACGGTTAATTTGCGTGATGGACAGACTCTTTTACTCGGTGGCCTCACTGATTATAAAAACACTTCTCAGGATTCTGGCGTACCGTTCCTGTCTAAAATCCCTTTAATCGGCCTCCTGTTTAGCTCCCGCTCTGATTCTAACGAGGAAAGCACGTTATACGTGCTCGTCAAAGCAACCATAGTACGCGCCCTGTAGCGGCGCA", 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"TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGTCGTGTGACTGGTGAATCTGCCAATGTAAATAATCCATTTCAGACGATTGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCGGTAATATTGTTCTGGATATTACCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTGCTACAACGGTTAATTTGCGTGATGGACAGACTCTTTTACTCGGTGGCCTCACTGATTATAAAAACACTTCTCAGGATTCTGGCGTACCGTTCCTGTCTAAAATCCCTTTAATCGGCCTCCTGTTTAGCTCCCGCTCTGATTCTAACGAGGAAAGCACGTTATACGTGCTCGTCAAAGCAACCATAGTACGCGCCCTGTAGCGGCGCA", 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"forward": false, "start": 232, "end": 264} + ] + }, + { + "color": "#57bb00", + "sequence": "ACTTAGCCGAAATCCGCGACCTGCTCAAGAGA", + "domains": [ + {"helix": 4, "forward": false, "start": 224, "end": 232}, + {"helix": 3, "forward": true, "start": 224, "end": 248} + ] + }, + { + "color": "#888888", + "sequence": "AGGATTAGAAGAGGCTGAGACTCCTCCATGTT", + "domains": [ + {"helix": 3, "forward": true, "start": 248, "end": 256}, + {"helix": 4, "forward": false, "start": 232, "end": 256} + ] + }, + { + "color": "#32b86c", + "sequence": "ATGCAGATATTTAGGAATACCACACCTTTAGC", + "domains": [ + {"helix": 6, "forward": false, "start": 224, "end": 232}, + {"helix": 5, "forward": true, "start": 224, "end": 248} + ] + }, + { + "color": "#333333", + "sequence": "GTCAGACTGACAGAATCAAGTTTGTTCAACTA", + "domains": [ + {"helix": 5, "forward": true, "start": 248, "end": 256}, + {"helix": 6, "forward": false, "start": 232, "end": 256} + ] + }, + { + "color": "#320096", + "sequence": "TGCTCCTTTCAGGATTAGAGAGTAAATAGCTA", 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"end": 248} + ] + }, + { + "color": "#007200", + "sequence": "TTTCATCTCTTTTTCAAATATATTATAATTCG", + "domains": [ + {"helix": 11, "forward": true, "start": 248, "end": 256}, + {"helix": 12, "forward": false, "start": 232, "end": 256} + ] + }, + { + "color": "#cc0000", + "sequence": "TGCAGGTCCGGCCAGTGCCAAGCTTAACGTCA", + "domains": [ + {"helix": 14, "forward": false, "start": 224, "end": 232}, + {"helix": 13, "forward": true, "start": 224, "end": 248} + ] + }, + { + "color": "#f7931e", + "sequence": "GATGAATACGTAGATTTTCAGGTTTGCATGCC", + "domains": [ + {"helix": 13, "forward": true, "start": 248, "end": 256}, + {"helix": 14, "forward": false, "start": 232, "end": 256} + ] + }, + { + "color": "#f74308", + "sequence": "CAAAATCCGTTTGATGGTGGTTCCCACGCTGA", + "domains": [ + {"helix": 16, "forward": false, "start": 224, "end": 232}, + {"helix": 15, "forward": true, "start": 224, "end": 248} + ] + }, + { + "color": "#57bb00", + "sequence": "GAGCCAGCCCGCCTGCAACAGTGCGAAATCGG", + "domains": [ + {"helix": 15, "forward": true, "start": 248, "end": 256}, + {"helix": 16, "forward": false, "start": 232, "end": 256} + ] + }, + { + "color": "#888888", + "sequence": "GGAACGGTACGCCAGAATCCTGAGAAGTGTTT", + "domains": [ + {"helix": 17, "forward": true, "start": 216, "end": 248} + ] + }, + { + "color": "#32b86c", + "sequence": "CAGCATCGGAACGAGGGTAGCAACTCATGAGG", + "domains": [ + {"helix": 2, "forward": false, "start": 48, "end": 72}, + {"helix": 3, "forward": true, "start": 48, "end": 56} + ] + }, + { + "color": "#333333", + "sequence": "AAGTTTCCGCTGCTCATTCAGTGAGAGTAGTA", + "domains": [ + {"helix": 3, "forward": true, "start": 56, "end": 64}, + {"helix": 4, "forward": false, "start": 48, "end": 64}, + {"helix": 5, "forward": true, "start": 48, "end": 56} + ] + }, + { + "color": "#320096", + "sequence": "AATTGGGCCTGCGGAATCGTCATAACAGTTCA", + "domains": [ + {"helix": 5, "forward": true, "start": 56, "end": 64}, + {"helix": 6, "forward": false, "start": 48, "end": 64}, + {"helix": 7, "forward": true, "start": 48, "end": 56} + ] + }, + { + "color": "#03b6a2", + "sequence": "GAAAACGACCATTAGATACATTTCTCATTTGG", + "domains": [ + {"helix": 7, "forward": true, "start": 56, "end": 64}, + {"helix": 8, "forward": false, "start": 48, "end": 64}, + {"helix": 9, "forward": true, "start": 48, "end": 56} + ] + }, + { + "color": "#7300de", + "sequence": "GGCGCGAGATCTACAAAGGCTATCAGAATCGA", + "domains": [ + {"helix": 9, "forward": true, "start": 56, "end": 64}, + {"helix": 10, "forward": false, "start": 48, "end": 64}, + {"helix": 11, "forward": true, "start": 48, "end": 56} + ] + }, + { + "color": "#aaaa00", + "sequence": "TGAACGGTAGTATCGGCCTCAGGATTCTGGTG", + "domains": [ + {"helix": 11, "forward": true, "start": 56, "end": 64}, + {"helix": 12, "forward": false, "start": 48, "end": 64}, + {"helix": 13, "forward": true, "start": 48, "end": 56} + ] + }, + { + "color": "#b8056c", + "sequence": "CCGGAAACATTGCGTTGCGCTCACCAGCTGCA", + "domains": [ + {"helix": 13, "forward": true, "start": 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a/examples/output_designs/1_staple_1_helix_origami_mismatches.sc +++ b/examples/output_designs/1_staple_1_helix_origami_mismatches.sc @@ -1,23 +1,23 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"grid_position": [0, 0]} - ], - "strands": [ - { - "color": "#f74308", - "sequence": "ATTCTCTTGCTTTTTTCA", - "domains": [ - {"helix": 0, "forward": true, "start": 0, "end": 10, "insertions": [[2, 4], [8, 4]]} - ] - }, - { - "color": "#0066cc", - "sequence": "AGAAAAAAAAAAAAAAAA", - "domains": [ - {"helix": 0, "forward": false, "start": 0, "end": 10, "insertions": [[2, 4], [8, 4]]} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]} + ], + "strands": [ + { + "color": "#f74308", + "sequence": "ATTCTCTTGCTTTTTTCA", + "domains": [ + {"helix": 0, "forward": true, "start": 0, "end": 10, "insertions": [[2, 4], [8, 4]]} + ] + }, + { + "color": "#0066cc", + "sequence": "AGAAAAAAAAAAAAAAAA", + "domains": [ + {"helix": 0, "forward": false, "start": 0, "end": 10, "insertions": [[2, 4], [8, 4]]} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/1_staple_1_helix_origami_position_nondefault.sc b/examples/output_designs/1_staple_1_helix_origami_position_nondefault.sc index bddd964..33dadf6 100644 --- a/examples/output_designs/1_staple_1_helix_origami_position_nondefault.sc +++ b/examples/output_designs/1_staple_1_helix_origami_position_nondefault.sc @@ -1,33 +1,33 @@ -{ - "version": "0.16.0", - "groups": { - "pitch90": { - "position": {"x": 0, "y": 0, "z": 0}, - "pitch": 90, - "grid": "none" - } - }, - "helices": [ - { - "group": "pitch90", - "position": {"x": 1, "y": 2, "z": 3}, - "major_ticks": [2, 5] - } - ], - "strands": [ - { - "color": "#f74308", - "sequence": "?AGTTAGTT", - "domains": [ - {"helix": 0, "forward": true, "start": 0, "end": 9} - ] - }, - { - "color": "#0066cc", - "sequence": "AACTAACT?", - "domains": [ - {"helix": 0, "forward": false, "start": 0, "end": 9} - ] - } - ] +{ + "version": "0.19.0", + "groups": { + "pitch90": { + "position": {"x": 0, "y": 0, "z": 0}, + "pitch": 90, + "grid": "none" + } + }, + "helices": [ + { + "group": "pitch90", + "position": {"x": 1, "y": 2, "z": 3}, + "major_ticks": [2, 5] + } + ], + "strands": [ + { + "color": "#f74308", + "sequence": "?AGTTAGTT", + "domains": [ + {"helix": 0, "forward": true, "start": 0, "end": 9} + ] + }, + { + "color": "#0066cc", + "sequence": "AACTAACT?", + "domains": [ + {"helix": 0, "forward": false, "start": 0, "end": 9} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/1_staple_1_helix_origami_roll.sc b/examples/output_designs/1_staple_1_helix_origami_roll.sc index 29cacbb..b88403f 100644 --- a/examples/output_designs/1_staple_1_helix_origami_roll.sc +++ b/examples/output_designs/1_staple_1_helix_origami_roll.sc @@ -1,23 +1,23 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"grid_position": [0, 0], "roll": 90} - ], - "strands": [ - { - "color": 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8} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/2_staple_2_helix_modifications.sc b/examples/output_designs/2_staple_2_helix_modifications.sc index 9225c95..fc18166 100644 --- a/examples/output_designs/2_staple_2_helix_modifications.sc +++ b/examples/output_designs/2_staple_2_helix_modifications.sc @@ -1,89 +1,89 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"grid_position": [0, 0]}, - {"grid_position": [0, 1]} - ], - "modifications_in_design": { - "/iCy3/": { - "display_text": "Cy3", - "idt_text": "/iCy3/", - "display_connector": false, - "location": "internal" - }, - "/iBiodT/": { - "display_text": "B", - "idt_text": "/iBiodT/", - "display_connector": false, - "location": "internal", - "allowed_bases": ["T"] - }, - "/iCy5/": { - "display_text": "Cy5", - "idt_text": "/iCy5/", - "display_connector": false, - "location": "internal" - }, - "/3Bio/": { - "display_text": "B", - "idt_text": "/3Bio/", - "display_connector": false, - 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+ "display_text": "B", + "vendor_code": "/5Biosg/", + "display_connector": false, + "location": "5'" + }, + "/3Bio/": { + "display_text": "B", + "vendor_code": "/3Bio/", + "display_connector": false, + "location": "3'" + }, + "/iBiodT/": { + "display_text": "B", + "vendor_code": "/iBiodT/", + "display_connector": false, + "location": "internal", + "allowed_bases": ["T"] + }, + "/iCy3/": { + "display_text": "Cy3", + "vendor_code": "/iCy3/", + "display_connector": false, + "location": "internal" + }, + "/iCy5/": { + "display_text": "Cy5", + "vendor_code": "/iCy5/", + "display_connector": false, + "location": "internal" + }, + "/3Cy3Sp/": { + "display_text": "Cy3", + "vendor_code": "/3Cy3Sp/", + "display_connector": false, + "location": "3'" + }, + "/5Cy5/": { + "display_text": "Cy5", + "vendor_code": "/5Cy5/", + "display_connector": false, + "location": "5'" + } + }, + "strands": [ + { + "color": "#0066cc", + "sequence": "AACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTA", + "domains": [ + {"helix": 1, "forward": false, "start": 0, "end": 16, "deletions": [12], "insertions": [[2, 1]]}, + {"helix": 0, "forward": true, "start": 0, "end": 32, "deletions": [11, 12, 24], "insertions": [[29, 1]]}, + {"helix": 1, "forward": false, "start": 16, "end": 32, "deletions": [24]} + ], + "5prime_modification": "/5Biosg/", + "3prime_modification": "/3Cy3Sp/", + "internal_modifications": {"5": "/iCy5/", "32": "/iCy3/"} + }, + { + "color": "#f74308", + "sequence": "AGTTAGTTAGTTAGTTTTAGTTAGTTAGTT", + "domains": [ + {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[2, 1]]}, + {"helix": 0, "forward": false, "start": 0, "end": 16, "deletions": [11, 12]} + ], + "5prime_modification": "/5Biosg/", + "3prime_modification": "/3Cy3Sp/", + "internal_modifications": {"9": "/iCy3/", "10": "/iBiodT/", "11": "/iCy3/", "12": "/iCy5/", "4": "/iCy3/", "26": "/iCy5/"} + }, + { + "color": "#57bb00", + "sequence": "TTAGTTAGTTAGTTAGTAGTTAGTTAGTTAG", + "domains": [ + {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[29, 1]]}, + {"helix": 1, "forward": true, "start": 16, "end": 32, "deletions": [24]} + ], + "5prime_modification": "/5Cy5/", + "3prime_modification": "/3Bio/", + "internal_modifications": {"5": "/iCy3/"} + } + ] } \ No newline at end of file diff --git a/examples/output_designs/2_staple_2_helix_origami_6bases_wide.sc b/examples/output_designs/2_staple_2_helix_origami_6bases_wide.sc index 27496e4..36d40fc 100644 --- a/examples/output_designs/2_staple_2_helix_origami_6bases_wide.sc +++ b/examples/output_designs/2_staple_2_helix_origami_6bases_wide.sc @@ -1,35 +1,35 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"grid_position": [0, 0]}, - {"grid_position": [0, 1]} - ], - "strands": [ - { - "color": "#f74308", - "sequence": "TTTG", - "domains": [ - {"helix": 1, "forward": true, "start": 0, "end": 3, "deletions": [1]}, - {"helix": 0, "forward": false, "start": 0, "end": 3, "deletions": [1]} - ] - }, - { - "color": "#57bb00", - "sequence": "GAAC", - "domains": [ - {"helix": 0, "forward": false, "start": 3, "end": 6, "deletions": [4]}, - {"helix": 1, "forward": true, "start": 3, "end": 6, "deletions": [4]} - ] - }, - { - "color": "#0066cc", - "sequence": "AACATCGT", - "domains": [ - {"helix": 1, "forward": false, "start": 0, "end": 3, "deletions": [1]}, - {"helix": 0, "forward": true, "start": 0, "end": 6, "deletions": [1, 4]}, - {"helix": 1, "forward": false, "start": 3, "end": 6, "deletions": [4]} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]} + ], + "strands": [ + { + "color": "#f74308", + "sequence": "TTTG", + "domains": [ + {"helix": 1, "forward": true, "start": 0, "end": 3, "deletions": [1]}, + {"helix": 0, "forward": false, "start": 0, "end": 3, "deletions": [1]} + ] + }, + { + "color": "#57bb00", + "sequence": "GAAC", + "domains": [ + {"helix": 0, "forward": false, "start": 3, "end": 6, "deletions": [4]}, + {"helix": 1, "forward": true, "start": 3, "end": 6, "deletions": [4]} + ] + }, + { + "color": "#0066cc", + "sequence": "AACATCGT", + "domains": [ + {"helix": 1, "forward": false, "start": 0, "end": 3, "deletions": [1]}, + {"helix": 0, "forward": true, "start": 0, "end": 6, "deletions": [1, 4]}, + {"helix": 1, "forward": false, "start": 3, "end": 6, "deletions": [4]} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions.sc b/examples/output_designs/2_staple_2_helix_origami_deletions.sc index 358dff3..8b6339c 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions.sc +++ b/examples/output_designs/2_staple_2_helix_origami_deletions.sc @@ -1,35 +1,35 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"grid_position": [0, 0]}, - {"grid_position": [0, 1]} - ], - "strands": [ - { - "color": "#f74308", - "sequence": "GTTAGTTAGTTAGTTTAGTTAGTTAGTTA", - "domains": [ - {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12]}, - {"helix": 0, "forward": false, "start": 0, "end": 16, "deletions": [11, 12]} - ] - }, - { - "color": "#57bb00", - "sequence": "AGTTAGTTAGTTAGTGTTAGTTAGTTAGTT", - "domains": [ - {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24]}, - {"helix": 1, "forward": true, "start": 16, "end": 32, "deletions": [24]} - ] - }, - { - "color": "#0066cc", - "sequence": "AACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAAC", - "domains": [ - {"helix": 1, "forward": false, "start": 0, "end": 16, "deletions": [12]}, - {"helix": 0, "forward": true, "start": 0, "end": 32, "deletions": [11, 12, 24]}, - {"helix": 1, "forward": false, "start": 16, "end": 32, "deletions": [24]} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]} + ], + "strands": [ + { + "color": "#f74308", + "sequence": "GTTAGTTAGTTAGTTTAGTTAGTTAGTTA", + "domains": [ + {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12]}, + {"helix": 0, "forward": false, "start": 0, "end": 16, "deletions": [11, 12]} + ] + }, + { + "color": "#57bb00", + "sequence": "AGTTAGTTAGTTAGTGTTAGTTAGTTAGTT", + "domains": [ + {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24]}, + {"helix": 1, "forward": true, "start": 16, "end": 32, "deletions": [24]} + ] + }, + { + "color": "#0066cc", + "sequence": "AACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAAC", + "domains": [ + {"helix": 1, "forward": false, "start": 0, "end": 16, "deletions": [12]}, + {"helix": 0, "forward": true, "start": 0, "end": 32, "deletions": [11, 12, 24]}, + {"helix": 1, "forward": false, "start": 16, "end": 32, "deletions": [24]} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.sc b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.sc index b2d6ed7..be823f7 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.sc +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.sc @@ -1,37 +1,37 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 48, "grid_position": [0, 0]}, - {"max_offset": 48, "grid_position": [0, 1]} - ], - "strands": [ - { - "color": "#0066cc", - "sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG", - "domains": [ - {"helix": 1, "forward": false, "start": 8, "end": 24, "deletions": [20]}, - {"helix": 0, "forward": true, "start": 8, "end": 40, "insertions": [[14, 1], [26, 2]]}, - {"loopout": 3}, - {"helix": 1, "forward": false, "start": 24, "end": 40} - ], - "is_scaffold": true - }, - { - "color": "#f74308", - "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", - "domains": [ - {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, - {"helix": 0, "forward": false, "start": 8, "end": 24, "insertions": [[14, 1]]} - ] - }, - { - "color": "#57bb00", - "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", - "domains": [ - {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, - {"helix": 1, "forward": true, "start": 24, "end": 40} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"max_offset": 48, "grid_position": [0, 0]}, + {"max_offset": 48, "grid_position": [0, 1]} + ], + "strands": [ + { + "color": "#0066cc", + "sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG", + "domains": [ + {"helix": 1, "forward": false, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": true, "start": 8, "end": 40, "insertions": [[14, 1], [26, 2]]}, + {"loopout": 3}, + {"helix": 1, "forward": false, "start": 24, "end": 40} + ], + "is_scaffold": true + }, + { + "color": "#f74308", + "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", + "domains": [ + {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": false, "start": 8, "end": 24, "insertions": [[14, 1]]} + ] + }, + { + "color": "#57bb00", + "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", + "domains": [ + {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, + {"helix": 1, "forward": true, "start": 24, "end": 40} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.sc b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.sc index 9af6a19..2bcd854 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.sc +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.sc @@ -1,40 +1,40 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 48, "grid_position": [0, 0]}, - {"max_offset": 48, "grid_position": [0, 1]} - ], - "strands": [ - { - "color": "#0066cc", - "sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG", - "domains": [ - {"helix": 1, "forward": false, "start": 8, "end": 24, "deletions": [20]}, - {"helix": 0, "forward": true, "start": 8, "end": 40, "insertions": [[14, 1], [26, 2]]}, - {"loopout": 3}, - {"helix": 1, "forward": false, "start": 24, "end": 40} - ], - "is_scaffold": true, - "label": "scaffold label" - }, - { - "color": "#f74308", - "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", - "domains": [ - {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, - {"helix": 0, "forward": false, "start": 8, "end": 24, "insertions": [[14, 1]]} - ], - "label": "left staple" - }, - { - "color": "#57bb00", - "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", - "domains": [ - {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, - {"helix": 1, "forward": true, "start": 24, "end": 40} - ], - "label": "right staple" - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"max_offset": 48, "grid_position": [0, 0]}, + {"max_offset": 48, "grid_position": [0, 1]} + ], + "strands": [ + { + "color": "#0066cc", + "sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG", + "domains": [ + {"helix": 1, "forward": false, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": true, "start": 8, "end": 40, "insertions": [[14, 1], [26, 2]]}, + {"loopout": 3}, + {"helix": 1, "forward": false, "start": 24, "end": 40} + ], + "is_scaffold": true, + "label": "scaffold label" + }, + { + "color": "#f74308", + "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", + "domains": [ + {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": false, "start": 8, "end": 24, "insertions": [[14, 1]]} + ], + "label": "left staple" + }, + { + "color": "#57bb00", + "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", + "domains": [ + {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, + {"helix": 1, "forward": true, "start": 24, "end": 40} + ], + "label": "right staple" + } + ] } \ No newline at end of file diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.sc b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.sc index 2930c9c..3de2c40 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.sc +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.sc @@ -1,46 +1,46 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 48, "grid_position": [0, 0]}, - {"max_offset": 48, "grid_position": [0, 1]} - ], - "modifications_in_design": { - "/5Biosg/": { - "display_text": "B", - "idt_text": "/5Biosg/", - "display_connector": false, - "location": "5'" - } - }, - "strands": [ - { - "color": "#0066cc", - "sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG", - "domains": [ - {"helix": 1, "forward": false, "start": 8, "end": 24, "deletions": [20]}, - {"helix": 0, "forward": true, "start": 8, "end": 40, "insertions": [[14, 1], [26, 2]]}, - {"loopout": 3}, - {"helix": 1, "forward": false, "start": 24, "end": 40} - ], - "is_scaffold": true - }, - { - "color": "#f74308", - "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", - "domains": [ - {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, - {"helix": 0, "forward": false, "start": 8, "end": 24, "insertions": [[14, 1]]} - ] - }, - { - "color": "#57bb00", - "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", - "domains": [ - {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, - {"helix": 1, "forward": true, "start": 24, "end": 40} - ], - "5prime_modification": "/5Biosg/" - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"max_offset": 48, "grid_position": [0, 0]}, + {"max_offset": 48, "grid_position": [0, 1]} + ], + "modifications_in_design": { + "/5Biosg/": { + "display_text": "B", + "vendor_code": "/5Biosg/", + "display_connector": false, + "location": "5'" + } + }, + "strands": [ + { + "color": "#0066cc", + "sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG", + "domains": [ + {"helix": 1, "forward": false, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": true, "start": 8, "end": 40, "insertions": [[14, 1], [26, 2]]}, + {"loopout": 3}, + {"helix": 1, "forward": false, "start": 24, "end": 40} + ], + "is_scaffold": true + }, + { + "color": "#f74308", + "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", + "domains": [ + {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": false, "start": 8, "end": 24, "insertions": [[14, 1]]} + ] + }, + { + "color": "#57bb00", + "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", + "domains": [ + {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, + {"helix": 1, "forward": true, "start": 24, "end": 40} + ], + "5prime_modification": "/5Biosg/" + } + ] } \ No newline at end of file diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.sc b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.sc index 970f10c..d3a1a4c 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.sc +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.sc @@ -1,46 +1,46 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 48, "grid_position": [0, 0]}, - {"max_offset": 48, "grid_position": [0, 1]} - ], - "modifications_in_design": { - "/5Biosg/": { - "display_text": "B", - "idt_text": "/5Biosg/", - "display_connector": false, - "location": "5'" - } - }, - "strands": [ - { - "color": "#f74308", - "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", - "domains": [ - {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, - {"helix": 0, "forward": false, "start": 8, "end": 24, "insertions": [[14, 1]]} - ] - }, - { - "color": "#57bb00", - "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", - "domains": [ - {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, - {"helix": 1, "forward": true, "start": 24, "end": 40} - ], - "5prime_modification": "/5Biosg/" - }, - { - "color": "#0066cc", - "sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG", - "domains": [ - {"helix": 1, "forward": false, "start": 8, "end": 24, "deletions": [20]}, - {"helix": 0, "forward": true, "start": 8, "end": 40, "insertions": [[14, 1], [26, 2]]}, - {"loopout": 3}, - {"helix": 1, "forward": false, "start": 24, "end": 40} - ], - "is_scaffold": true - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"max_offset": 48, "grid_position": [0, 0]}, + {"max_offset": 48, "grid_position": [0, 1]} + ], + "modifications_in_design": { + "/5Biosg/": { + "display_text": "B", + "vendor_code": "/5Biosg/", + "display_connector": false, + "location": "5'" + } + }, + "strands": [ + { + "color": "#f74308", + "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", + "domains": [ + {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": false, "start": 8, "end": 24, "insertions": [[14, 1]]} + ] + }, + { + "color": "#57bb00", + "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", + "domains": [ + {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, + {"helix": 1, "forward": true, "start": 24, "end": 40} + ], + "5prime_modification": "/5Biosg/" + }, + { + "color": "#0066cc", + "sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG", + "domains": [ + {"helix": 1, "forward": false, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": true, "start": 8, "end": 40, "insertions": [[14, 1], [26, 2]]}, + {"loopout": 3}, + {"helix": 1, "forward": false, "start": 24, "end": 40} + ], + "is_scaffold": true + } + ] } \ No newline at end of file diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.sc b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.sc index a1b970b..5c003b1 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.sc +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.sc @@ -1,41 +1,41 @@ -{ - "version": "0.15.0", - "grid": "square", - "geometry": { - "rise_per_base_pair": 0.2, - "helix_radius": 1.2 - }, - "helices": [ - {"max_offset": 48, "grid_position": [0, 0]}, - {"max_offset": 48, "grid_position": [0, 1]} - ], - "strands": [ - { - "color": "#0066cc", - "sequence": 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{"max_offset": 48, "grid_position": [0, 0]}, + {"max_offset": 48, "grid_position": [0, 1]} + ], + "strands": [ + { + "color": "#0066cc", + "sequence": "AACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACGTAACG", + "domains": [ + {"helix": 1, "forward": false, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": true, "start": 8, "end": 40, "insertions": [[14, 1], [26, 2]]}, + {"loopout": 3}, + {"helix": 1, "forward": false, "start": 24, "end": 40} + ], + "is_scaffold": true + }, + { + "color": "#f74308", + "sequence": "ACGTTACGTTACGTTTTACGTTACGTTACGTT", + "domains": [ + {"helix": 1, "forward": true, "start": 8, "end": 24, "deletions": [20]}, + {"helix": 0, "forward": false, "start": 8, "end": 24, "insertions": [[14, 1]]} + ] + }, + { + "color": "#57bb00", + "sequence": "ACGTTACGTTACGTTACGCGTTACGTTACGTTAC", + "domains": [ + {"helix": 0, "forward": false, "start": 24, "end": 40, "insertions": [[26, 2]]}, + {"helix": 1, "forward": true, "start": 24, "end": 40} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.sc b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.sc index 38af353..d8986f0 100644 --- a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.sc +++ b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.sc @@ -1,34 +1,34 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"grid_position": [0, 0]}, - {"grid_position": [0, 1]} - ], - "strands": [ - { - "color": "#0066cc", - "domains": [ - {"helix": 1, "forward": false, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, - {"helix": 0, "forward": true, "start": 0, "end": 32, "deletions": [11, 12, 24], "insertions": [[6, 1], [18, 2]]}, - {"loopout": 3}, - {"helix": 1, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 4]]} - ], - "is_scaffold": true - }, - { - "color": "#f74308", - "domains": [ - {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, - {"helix": 0, "forward": false, "start": 0, "end": 16, "deletions": [11, 12], "insertions": [[6, 1]]} - ] - }, - { - "color": "#57bb00", - "domains": [ - {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, - {"helix": 1, "forward": true, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 4]]} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]} + ], + "strands": [ + { + "color": "#0066cc", + "domains": [ + {"helix": 1, "forward": false, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, + {"helix": 0, "forward": true, "start": 0, "end": 32, "deletions": [11, 12, 24], "insertions": [[6, 1], [18, 2]]}, + {"loopout": 3}, + {"helix": 1, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 4]]} + ], + "is_scaffold": true + }, + { + "color": "#f74308", + "domains": [ + {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, + {"helix": 0, "forward": false, "start": 0, "end": 16, "deletions": [11, 12], "insertions": [[6, 1]]} + ] + }, + { + "color": "#57bb00", + "domains": [ + {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, + {"helix": 1, "forward": true, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 4]]} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/3_helix_deletions_insertions.sc b/examples/output_designs/3_helix_deletions_insertions.sc index 94069ff..589eb46 100644 --- a/examples/output_designs/3_helix_deletions_insertions.sc +++ b/examples/output_designs/3_helix_deletions_insertions.sc @@ -1,90 +1,90 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"grid_position": [0, 0]}, - {"grid_position": [0, 1]}, - {"grid_position": [0, 2]} - ], - "strands": [ - { - "color": "#0066cc", - "sequence": "AACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACT", - "domains": [ - {"helix": 1, "forward": false, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, - {"helix": 0, "forward": true, "start": 0, "end": 32, "deletions": [11, 12, 24], "insertions": [[6, 1], [18, 2]]}, - {"loopout": 3}, - {"helix": 1, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 4]]} - ], - "is_scaffold": true - }, - { - "color": "#f74308", - "sequence": "TTAGTTAGTTAGTTAGTTTAGTTAGTTAGTTAG", - "domains": [ - {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, - {"helix": 0, "forward": false, "start": 0, "end": 16, "deletions": [11, 12], "insertions": [[6, 1]]} - ] - }, - { - "color": "#57bb00", - "sequence": "TTAGTTAGTTAGTTAGTAGTTAGTTAGTTAGTTAGT", - "domains": [ - {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, - {"helix": 1, "forward": true, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 4]]} - ] - }, - { - "color": "#888888", - "sequence": "AACTAACTAACTAACT", - "domains": [ - {"helix": 1, "forward": true, "start": 32, "end": 48} - ] - }, - { - "color": "#32b86c", - "sequence": "GGTAGGTAGGTAGGTA", - "domains": [ - {"helix": 1, "forward": true, "start": 48, "end": 64} - ] - }, - { - "color": "#333333", - "domains": [ - {"helix": 2, "forward": false, "start": 32, "end": 48} - ] - }, - { - "color": "#320096", - "domains": [ - {"helix": 2, "forward": true, "start": 16, "end": 32} - ] - }, - { - "color": "#03b6a2", - "sequence": "AGTTAGTTAGTTAGTT", - "domains": [ - {"helix": 1, "forward": false, "start": 32, "end": 48} - ] - }, - { - "color": "#7300de", - "sequence": "TACCTACCTACCTACC", - "domains": [ - {"helix": 1, "forward": false, "start": 48, "end": 64} - ] - }, - { - "color": "#aaaa00", - "domains": [ - {"helix": 2, "forward": true, "start": 32, "end": 48} - ] - }, - { - "color": "#b8056c", - "domains": [ - {"helix": 2, "forward": true, "start": 0, "end": 16} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]}, + {"grid_position": [0, 2]} + ], + "strands": [ + { + "color": "#0066cc", + "sequence": "AACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACTAACT", + "domains": [ + {"helix": 1, "forward": false, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, + {"helix": 0, "forward": true, "start": 0, "end": 32, "deletions": [11, 12, 24], "insertions": [[6, 1], [18, 2]]}, + {"loopout": 3}, + {"helix": 1, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 4]]} + ], + "is_scaffold": true + }, + { + "color": "#f74308", + "sequence": "TTAGTTAGTTAGTTAGTTTAGTTAGTTAGTTAG", + "domains": [ + {"helix": 1, "forward": true, "start": 0, "end": 16, "deletions": [12], "insertions": [[6, 3]]}, + {"helix": 0, "forward": false, "start": 0, "end": 16, "deletions": [11, 12], "insertions": [[6, 1]]} + ] + }, + { + "color": "#57bb00", + "sequence": "TTAGTTAGTTAGTTAGTAGTTAGTTAGTTAGTTAGT", + "domains": [ + {"helix": 0, "forward": false, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 2]]}, + {"helix": 1, "forward": true, "start": 16, "end": 32, "deletions": [24], "insertions": [[18, 4]]} + ] + }, + { + "color": "#888888", + "sequence": "AACTAACTAACTAACT", + "domains": [ + {"helix": 1, "forward": true, "start": 32, "end": 48} + ] + }, + { + "color": "#32b86c", + "sequence": "GGTAGGTAGGTAGGTA", + "domains": [ + {"helix": 1, "forward": true, "start": 48, "end": 64} + ] + }, + { + "color": "#333333", + "domains": [ + {"helix": 2, "forward": false, "start": 32, "end": 48} + ] + }, + { + "color": "#320096", + "domains": [ + {"helix": 2, "forward": true, "start": 16, "end": 32} + ] + }, + { + "color": "#03b6a2", + "sequence": "AGTTAGTTAGTTAGTT", + "domains": [ + {"helix": 1, "forward": false, "start": 32, "end": 48} + ] + }, + { + "color": "#7300de", + "sequence": "TACCTACCTACCTACC", + "domains": [ + {"helix": 1, "forward": false, "start": 48, "end": 64} + ] + }, + { + "color": "#aaaa00", + "domains": [ + {"helix": 2, "forward": true, "start": 32, "end": 48} + ] + }, + { + "color": "#b8056c", + "domains": [ + {"helix": 2, "forward": true, "start": 0, "end": 16} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/4_helix_grid_none.sc b/examples/output_designs/4_helix_grid_none.sc index fd83e5d..d738929 100644 --- a/examples/output_designs/4_helix_grid_none.sc +++ b/examples/output_designs/4_helix_grid_none.sc @@ -1,24 +1,24 @@ -{ - "version": "0.15.0", - "grid": "none", - "helices": [ - {"position": {"x": 0, "y": 0, "z": 2.5}}, - {"position": {"x": 3, "y": 3, "z": 0}}, - {"position": {"x": 8, "y": -3, "z": 0}}, - {"position": {"x": 11, "y": 1, "z": 0}} - ], - "strands": [ - { - "color": "#f74308", - "domains": [ - {"helix": 0, "forward": true, "start": 0, "end": 10} - ] - }, - { - "color": "#0066cc", - "domains": [ - {"helix": 0, "forward": false, "start": 0, "end": 10} - ] - } - ] +{ + "version": "0.19.0", + "grid": "none", + "helices": [ + {"position": {"x": 0, "y": 0, "z": 2.5}}, + {"position": {"x": 3, "y": 3, "z": 0}}, + {"position": {"x": 8, "y": -3, "z": 0}}, + {"position": {"x": 11, "y": 1, "z": 0}} + ], + "strands": [ + { + "color": "#f74308", + "domains": [ + {"helix": 0, "forward": true, "start": 0, "end": 10} + ] + }, + { + "color": "#0066cc", + "domains": [ + {"helix": 0, "forward": false, "start": 0, "end": 10} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.sc b/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.sc index 087feda..4953025 100644 --- a/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.sc +++ b/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.sc @@ -1,36 +1,36 @@ -{ - "version": "0.15.0", - "grid": "none", - "helices": [ - {"position": {"x": 0, "y": 0, "z": 0}, "major_tick_distance": 4}, - {"min_offset": 8, "position": {"x": 3, "y": 3, "z": 0}, "major_tick_distance": 4}, - {"position": {"x": 8, "y": -3, "z": 2.5}, "major_tick_distance": 4}, - {"min_offset": 8, "position": {"x": 11, "y": 1, "z": 2.5}, "major_tick_distance": 4} - ], - "strands": [ - { - "color": "#f74308", - "domains": [ - {"helix": 0, "forward": true, "start": 0, "end": 16} - ] - }, - { - "color": "#57bb00", - "domains": [ - {"helix": 1, "forward": true, "start": 8, "end": 16} - ] - }, - { - "color": "#888888", - "domains": [ - {"helix": 2, "forward": true, "start": 0, "end": 16} - ] - }, - { - "color": "#32b86c", - "domains": [ - {"helix": 3, "forward": true, "start": 8, "end": 16} - ] - } - ] +{ + "version": "0.19.0", + "grid": "none", + "helices": [ + {"position": {"x": 0, "y": 0, "z": 0}, "major_tick_distance": 4}, + {"min_offset": 8, "position": {"x": 3, "y": 3, "z": 0}, "major_tick_distance": 4}, + {"position": {"x": 8, "y": -3, "z": 2.5}, "major_tick_distance": 4}, + {"min_offset": 8, "position": {"x": 11, "y": 1, "z": 2.5}, "major_tick_distance": 4} + ], + "strands": [ + { + "color": "#f74308", + "domains": [ + {"helix": 0, "forward": true, "start": 0, "end": 16} + ] + }, + { + "color": "#57bb00", + "domains": [ + {"helix": 1, "forward": true, "start": 8, "end": 16} + ] + }, + { + "color": "#888888", + "domains": [ + {"helix": 2, "forward": true, "start": 0, "end": 16} + ] + }, + { + "color": "#32b86c", + "domains": [ + {"helix": 3, "forward": true, "start": 8, "end": 16} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/4_helix_min_offsets_nonzero.sc b/examples/output_designs/4_helix_min_offsets_nonzero.sc index a03fa76..f823000 100644 --- a/examples/output_designs/4_helix_min_offsets_nonzero.sc +++ b/examples/output_designs/4_helix_min_offsets_nonzero.sc @@ -1,24 +1,24 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 30, "grid_position": [0, 0]}, - {"min_offset": 1, "max_offset": 30, "grid_position": [0, 1]}, - {"min_offset": 2, "max_offset": 30, "grid_position": [0, 2]}, - {"min_offset": 3, "max_offset": 30, "grid_position": [0, 3]} - ], - "strands": [ - { - "color": "#f74308", - "domains": [ - {"helix": 0, "forward": true, "start": 0, "end": 29} - ] - }, - { - "color": "#0066cc", - "domains": [ - {"helix": 0, "forward": false, "start": 0, "end": 29} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"max_offset": 30, "grid_position": [0, 0]}, + {"min_offset": 1, "max_offset": 30, "grid_position": [0, 1]}, + {"min_offset": 2, "max_offset": 30, "grid_position": [0, 2]}, + {"min_offset": 3, "max_offset": 30, "grid_position": [0, 3]} + ], + "strands": [ + { + "color": "#f74308", + "domains": [ + {"helix": 0, "forward": true, "start": 0, "end": 29} + ] + }, + { + "color": "#0066cc", + "domains": [ + {"helix": 0, "forward": false, "start": 0, "end": 29} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/56_helix_origami_rectangle.sc b/examples/output_designs/56_helix_origami_rectangle.sc index 21630ec..916c873 100644 --- a/examples/output_designs/56_helix_origami_rectangle.sc +++ b/examples/output_designs/56_helix_origami_rectangle.sc @@ -1,2080 +1,2080 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 160, "grid_position": [0, 0]}, - {"max_offset": 160, "grid_position": [0, 1]}, - {"max_offset": 160, "grid_position": [0, 2]}, - {"max_offset": 160, "grid_position": [0, 3]}, - {"max_offset": 160, "grid_position": [0, 4]}, - {"max_offset": 160, "grid_position": [0, 5]}, - {"max_offset": 160, "grid_position": [0, 6]}, - {"max_offset": 160, "grid_position": [0, 7]}, - {"max_offset": 160, "grid_position": [0, 8]}, - {"max_offset": 160, "grid_position": 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GTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGTCGTGTGACTGGTGAATCTGCCAATGTAAATAATCCATTTCAGACGATTGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCGGTAATATTGTTCTGGATATTACCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTGCTACAACGGTTAATTTGCGTGATGGACAGACTCTTTTACTCGGTGGCCTCACTGATTATAAAAACACTTCTCAGGATTCTGGCGTACCGTTCCTGTCTAAAATCCCTTTAATCGGCCTCCTGTTTAGCTCCCGCTCTGATTCTAACGAGGAAAGCACGTTATACGTGCTCGTCAAAGCAACCATAGTACGCGCCCTGTAGCGGCGCA", 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"TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGTCGTGTGACTGGTGAATCTGCCAATGTAAATAATCCATTTCAGACGATTGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCGGTAATATTGTTCTGGATATTACCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTGCTACAACGGTTAATTTGCGTGATGGACAGACTCTTTTACTCGGTGGCCTCACTGATTATAAAAACACTTCTCAGGATTCTGGCGTACCGTTCCTGTCTAAAATCCCTTTAATCGGCCTCCTGTTTAGCTCCCGCTCTGATTCTAACGAGGAAAGCACGTTATACGTGCTCGTCAAAGCAACCATAGTACGCGCCCTGTAGCGGCGCA", 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"end": 32} + ] + }, + { + "color": "#888888", + "sequence": "TCTTTTCATAATCAAATTATTAGCGTTTGCCA", + "domains": [ + {"helix": 5, "forward": true, "start": 16, "end": 32}, + {"helix": 4, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#32b86c", + "sequence": "GTCAGACGATTGGCCTCAGGAGGTTGAGGCAG", + "domains": [ + {"helix": 7, "forward": true, "start": 16, "end": 32}, + {"helix": 6, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#333333", + "sequence": "GTAACAGTGCCCGTATGGGGTCAGTGCCTTGA", + "domains": [ + {"helix": 9, "forward": true, "start": 16, "end": 32}, + {"helix": 8, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#320096", + "sequence": "TATAAGTATAGCCCGGCCGTCGAGAGGGTTGA", + "domains": [ + {"helix": 11, "forward": true, "start": 16, "end": 32}, + {"helix": 10, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#03b6a2", + "sequence": "GTCACCAGTACAAACTCGTAACACTGAGTTTC", + "domains": [ + {"helix": 13, "forward": true, "start": 16, "end": 32}, + {"helix": 12, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#7300de", + "sequence": "AAAGGAACAACTAAAGAGCGGAGTGAGAATAG", + "domains": [ + {"helix": 15, "forward": true, "start": 16, "end": 32}, + {"helix": 14, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#aaaa00", + "sequence": "ACAACCATCGCCCACGTGCGCCGACAATGACA", + "domains": [ + {"helix": 17, "forward": true, "start": 16, "end": 32}, + {"helix": 16, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#b8056c", + "sequence": "GGAAGTTTCCATTAAAAAAGACTTTTTCATGA", + "domains": [ + {"helix": 19, "forward": true, "start": 16, "end": 32}, + {"helix": 18, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#007200", + "sequence": "AAATTGTGTCGAAATCTGTATCATCGCCTGAT", + "domains": [ + {"helix": 21, "forward": true, "start": 16, "end": 32}, + {"helix": 20, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#cc0000", + 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GTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCT", 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"start": 16, "end": 32} - ] - }, - { - "color": "#7300de", - "sequence": "TAATGCAGATACATAAGAATACCACATTCAAC", - "domains": [ - {"helix": 15, "forward": true, "start": 16, "end": 32}, - {"helix": 14, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#aaaa00", - "sequence": "GCGAGAGGCTTTTGCAGATAAAAACCAAAATA", - "domains": [ - {"helix": 17, "forward": true, "start": 16, "end": 32}, - {"helix": 16, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#b8056c", - "sequence": "CATTGAATCCCCCTCAAATCGTCATAAATATT", - "domains": [ - {"helix": 19, "forward": true, "start": 16, "end": 32}, - {"helix": 18, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#007200", - "sequence": "AAAGCGGATTGCATCATATTATAGTCAGAAGC", - "domains": [ - {"helix": 21, "forward": true, "start": 16, "end": 32}, - {"helix": 20, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#cc0000", - "sequence": "CTCCAACAGGTCAGGACCAGACCGGAAGCAAA", - "domains": [ - {"helix": 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GTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCT", 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@@ -1,178 +1,178 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"grid_position": [0, 0]}, - {"grid_position": [0, 1]}, - {"grid_position": [0, 2]}, - {"grid_position": [0, 3]}, - {"grid_position": [0, 4]}, - {"grid_position": [0, 5]} - ], - "strands": [ - { - "color": "#0066cc", - "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCT", - "domains": [ - {"helix": 5, "forward": false, "start": 0, "end": 48}, - {"helix": 4, "forward": true, 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- }, - { - "color": "#7300de", - "sequence": "TGGACTCCACAAGAGTCCACTATTCGGGCAAC", - "domains": [ - {"helix": 2, "forward": false, "start": 32, "end": 40}, - {"helix": 1, "forward": true, "start": 32, "end": 56} - ] - }, - { - "color": "#aaaa00", - "sequence": "AGCTGATTCTTTTCACCAGTGAGAAAAGAACG", - "domains": [ - {"helix": 1, "forward": true, "start": 56, "end": 64}, - {"helix": 2, "forward": false, "start": 40, "end": 64} - ] - }, - { - "color": "#b8056c", - "sequence": "GTAAAGCACAAGTTTTTTGGGGTCCCTGTCGT", - "domains": [ - {"helix": 4, "forward": false, "start": 32, "end": 40}, - {"helix": 3, "forward": true, "start": 32, "end": 56} - ] - }, - { - "color": "#007200", - "sequence": "GCCAGCTGCTTTCCAGTCGGGAAAGAGGTGCC", - "domains": [ - {"helix": 3, "forward": true, "start": 56, "end": 64}, - {"helix": 4, "forward": false, "start": 40, "end": 64} - ] - }, - { - "color": "#cc0000", - "sequence": "GAACGTGGCGAGAAAGGAAGGGAAAGCCGGAA", - "domains": [ - {"helix": 5, "forward": true, "start": 24, 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"color": "#32b86c", - "sequence": "TGGTTTTTGCCCTTCACCGCCTGGGGTTTGCC", - "domains": [ - {"helix": 2, "forward": false, "start": 64, "end": 72}, - {"helix": 1, "forward": true, "start": 64, "end": 80}, - {"helix": 0, "forward": false, "start": 72, "end": 80} - ] - }, - { - "color": "#333333", - "sequence": "ACTGCCCGCATTAATGAATCGGCCCGCCAGGG", - "domains": [ - {"helix": 4, "forward": false, "start": 64, "end": 72}, - {"helix": 3, "forward": true, "start": 64, "end": 80}, - {"helix": 2, "forward": false, "start": 72, "end": 80} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]}, + {"grid_position": [0, 2]}, + {"grid_position": [0, 3]}, + {"grid_position": [0, 4]}, + {"grid_position": [0, 5]} + ], + "strands": [ + { + "color": "#0066cc", + "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCT", + "domains": [ + {"helix": 5, "forward": false, "start": 0, "end": 48}, + {"helix": 4, "forward": true, "start": 0, "end": 48}, + {"helix": 3, "forward": false, "start": 0, "end": 48}, + {"helix": 2, "forward": true, "start": 0, "end": 48}, + {"helix": 1, "forward": false, "start": 0, "end": 48}, + {"helix": 0, "forward": true, "start": 0, "end": 96}, + {"helix": 1, "forward": false, "start": 48, "end": 96}, + {"helix": 2, "forward": true, "start": 48, "end": 96}, + {"helix": 3, "forward": false, "start": 48, "end": 96}, + {"helix": 4, "forward": true, "start": 48, "end": 96}, + {"helix": 5, "forward": false, "start": 48, "end": 96} + ], + "is_scaffold": true + }, + { + "color": "#f74308", + "sequence": "CGAGATAGGGTTGAGTAATCAAAAGAATAGCC", + "domains": [ + {"helix": 1, "forward": true, "start": 0, "end": 16}, + {"helix": 0, "forward": false, "start": 0, "end": 16} + ] + }, + { + "color": "#57bb00", + "sequence": "CGATGGCCCACTACGTAAACCGTCTATCAGGG", + "domains": [ + {"helix": 3, "forward": true, "start": 0, "end": 16}, + {"helix": 2, "forward": false, "start": 0, "end": 16} + ] + }, + { + "color": "#888888", + "sequence": "TAGAGCTTGACGGGGAAAGGGAGCCCCCGATT", + "domains": [ + {"helix": 5, "forward": true, "start": 0, "end": 16}, + {"helix": 4, "forward": false, "start": 0, "end": 16} + ] + }, + { + "color": "#32b86c", + "sequence": "GCAAGCGGTCCACGCTCCCTGAGAGAGTTGCA", + "domains": [ + {"helix": 0, "forward": false, "start": 80, "end": 96}, + {"helix": 1, "forward": true, "start": 80, "end": 96} + ] + }, + { + "color": "#333333", + "sequence": "CGGTTTGCGTATTGGGAACGCGCGGGGAGAGG", + "domains": [ + {"helix": 2, "forward": false, "start": 80, "end": 96}, + {"helix": 3, "forward": true, "start": 80, "end": 96} + ] + }, + { + "color": "#320096", + "sequence": "ACTCACATTAATTGCGCCTAATGAGTGAGCTA", + "domains": [ + {"helix": 4, "forward": false, "start": 80, "end": 96}, + {"helix": 5, "forward": true, "start": 80, "end": 96} + ] + }, + { + "color": "#03b6a2", + "sequence": "CCAGCAGGCGAAAATCCTGTTTGATGGTGGTT", + "domains": [ + {"helix": 0, "forward": false, "start": 40, "end": 72} + ] + }, + { + "color": "#7300de", + "sequence": "TGGACTCCACAAGAGTCCACTATTCGGGCAAC", + "domains": [ + {"helix": 2, "forward": false, "start": 32, "end": 40}, + {"helix": 1, "forward": true, "start": 32, "end": 56} + ] + }, + { + "color": "#aaaa00", + "sequence": "AGCTGATTCTTTTCACCAGTGAGAAAAGAACG", + "domains": [ + {"helix": 1, "forward": true, "start": 56, "end": 64}, + {"helix": 2, "forward": false, "start": 40, "end": 64} + ] + }, + { + "color": "#b8056c", + "sequence": "GTAAAGCACAAGTTTTTTGGGGTCCCTGTCGT", + "domains": [ + {"helix": 4, "forward": false, "start": 32, "end": 40}, + {"helix": 3, "forward": true, "start": 32, "end": 56} + ] + }, + { + "color": "#007200", + "sequence": "GCCAGCTGCTTTCCAGTCGGGAAAGAGGTGCC", + "domains": [ + {"helix": 3, "forward": true, "start": 56, "end": 64}, + {"helix": 4, "forward": false, "start": 40, "end": 64} + ] + }, + { + "color": "#cc0000", + "sequence": "GAACGTGGCGAGAAAGGAAGGGAAAGCCGGAA", + "domains": [ + {"helix": 5, "forward": true, "start": 24, "end": 56} + ] + }, + { + "color": "#f7931e", + "sequence": "CCGAAATCGGCAAAATCCCTTATAGTTGTTCC", + "domains": [ + {"helix": 0, "forward": false, "start": 16, "end": 40}, + {"helix": 1, "forward": true, "start": 16, "end": 24} + ] + }, + { + "color": "#f74308", + "sequence": "AGTTTGGAAACGTCAAAGGGCGAAGAACCATC", + "domains": [ + {"helix": 1, "forward": true, "start": 24, "end": 32}, + {"helix": 2, "forward": false, "start": 16, "end": 32}, + {"helix": 3, "forward": true, "start": 16, "end": 24} + ] + }, + { + "color": "#57bb00", + "sequence": "ACCCAAATCTAAATCGGAACCCTAAAGCCGGC", + "domains": [ + {"helix": 3, "forward": true, "start": 24, "end": 32}, + {"helix": 4, "forward": false, "start": 16, "end": 32}, + {"helix": 5, "forward": true, "start": 16, "end": 24} + ] + }, + { + "color": "#888888", + "sequence": "GCATAAAGTGTAAAGCCTGGGGTGTTGCGCTC", + "domains": [ + {"helix": 5, "forward": true, "start": 56, "end": 80}, + {"helix": 4, "forward": false, "start": 72, "end": 80} + ] + }, + { + "color": "#32b86c", + "sequence": "TGGTTTTTGCCCTTCACCGCCTGGGGTTTGCC", + "domains": [ + {"helix": 2, "forward": false, "start": 64, "end": 72}, + {"helix": 1, "forward": true, "start": 64, "end": 80}, + {"helix": 0, "forward": false, "start": 72, "end": 80} + ] + }, + { + "color": "#333333", + "sequence": "ACTGCCCGCATTAATGAATCGGCCCGCCAGGG", + "domains": [ + {"helix": 4, "forward": false, "start": 64, "end": 72}, + {"helix": 3, "forward": true, "start": 64, "end": 80}, + {"helix": 2, "forward": false, "start": 72, "end": 80} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/6_helix_bundle_honeycomb.sc b/examples/output_designs/6_helix_bundle_honeycomb.sc index d68c5a8..bb72a9e 100644 --- a/examples/output_designs/6_helix_bundle_honeycomb.sc +++ b/examples/output_designs/6_helix_bundle_honeycomb.sc @@ -1,1870 +1,1870 @@ -{ - "version": "0.15.0", - "grid": "honeycomb", - "helices": [ - {"max_offset": 1295, "grid_position": [1, 1]}, - {"max_offset": 1295, "grid_position": [0, 1]}, - {"max_offset": 1295, "grid_position": [0, 2]}, - {"max_offset": 1295, "grid_position": [1, 2]}, - {"max_offset": 1295, "grid_position": [2, 2]}, - {"max_offset": 1295, "grid_position": [2, 1]} - ], - "strands": [ - { - "color": "#0066cc", - "sequence": "TGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCCGTCTTTATCGAGGTAACAAGCACCACGTAGCTTAAGCCCTGTTTACTCATTACACCAACCAGGAGGTCAGAGTTCGGAGAAATGATTTATGTGAAATGCGTCAGCCGATTCAAGGCCCCTATATTCGTGCCCACCGACGAGTTGCTTACAGATGGCAGGGCCGCACTGTCGGTATCATAGAGTCACTCCAGGGCGAGCGTAAATAGATTAGAAGCGGGGTTATTTTGGCGGGACATTGTCATAAGGTTGACAATTCAGCACTAAGGACACTTAAGTCGTGCGCATGAATTCACAACCACTTAGAAGAACATCCACCCTGGCTTCTCCTGAGAAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGTCGTGTGACTGGTGAATCTGCCAATGTAAATAATCCATTTCAGACGATTGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCGGTAATATTGTTCTGGATATTACCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTGCTACAACGGTTAATTTGCGTGATGGACAGACTCTTTTACTCGGTGGCCTCACTGATTATAAAAACACTTCTCAGGATTCTGGCGTACCGTTCCTGTCTAAAATCCCTTTAATCGGCCTCCTGTTTAGCTCCCGCTCTGATTCTAACGAGGAAAGCACGTTATACGTGCTCGTCAAAGCAACCATAGTACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCGCAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTTTCTTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCC", - "domains": [ - {"helix": 5, "forward": false, "start": 19, "end": 399}, - {"helix": 4, "forward": true, "start": 19, "end": 26}, - {"helix": 3, "forward": false, "start": 12, "end": 26}, - {"helix": 2, "forward": true, "start": 12, "end": 30}, - {"helix": 1, "forward": false, "start": 16, "end": 30}, - {"helix": 0, "forward": true, "start": 16, "end": 58}, - {"helix": 1, "forward": false, "start": 30, "end": 58}, - {"helix": 2, "forward": true, "start": 30, "end": 54}, - {"helix": 3, "forward": false, "start": 26, "end": 54}, - {"helix": 4, "forward": true, "start": 26, "end": 68}, - {"helix": 3, "forward": false, "start": 54, "end": 68}, - {"helix": 2, "forward": true, "start": 54, "end": 72}, - {"helix": 1, "forward": false, "start": 58, "end": 72}, - {"helix": 0, "forward": true, "start": 58, "end": 100}, - {"helix": 1, "forward": false, "start": 72, "end": 100}, - {"helix": 2, "forward": true, "start": 72, "end": 96}, - {"helix": 3, "forward": false, "start": 68, "end": 96}, - 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630, "end": 644}, - {"helix": 3, "forward": true, "start": 630, "end": 644} - ] - }, - { - "color": "#f74308", - "sequence": "ATAACGTACACTGAGCCCAATAGGAACCATCCTCAGAGCCAC", - "domains": [ - {"helix": 5, "forward": true, "start": 672, "end": 679}, - {"helix": 0, "forward": false, "start": 672, "end": 679}, - {"helix": 1, "forward": true, "start": 672, "end": 686}, - {"helix": 2, "forward": false, "start": 672, "end": 686} - ] - }, - { - "color": "#333333", - "sequence": "TACCGTAGCTTTCCCCGTACTCAGGAGGCAGAACCGCCACAA", - "domains": [ - {"helix": 0, "forward": false, "start": 679, "end": 686}, - {"helix": 5, "forward": true, "start": 679, "end": 686}, - {"helix": 4, "forward": false, "start": 672, "end": 686}, - {"helix": 3, "forward": true, "start": 672, "end": 686} - ] - }, - { - "color": "#888888", - "sequence": "GGAGGCCAGGATTATAAGAGGCTGAGACTGTATTTCGGAACC", - "domains": [ - {"helix": 5, "forward": true, "start": 714, "end": 721}, - {"helix": 0, "forward": false, "start": 714, "end": 721}, - {"helix": 1, "forward": true, "start": 714, "end": 728}, - {"helix": 2, "forward": false, "start": 714, "end": 728} - ] - }, - { - "color": "#03b6a2", - "sequence": "CAAGAGAGATTAAATTAACGGGGTCAGTATGCCCCCTGCCAT", - "domains": [ - {"helix": 0, "forward": false, "start": 721, "end": 728}, - {"helix": 5, "forward": true, "start": 721, "end": 728}, - {"helix": 4, "forward": false, "start": 714, "end": 728}, - {"helix": 3, "forward": true, "start": 714, "end": 728} - ] - }, - { - "color": "#333333", - "sequence": "AATCCTGGCCAGAACACAAACAAATAAAGCGAGGTTGAGGCA", - "domains": [ - {"helix": 5, "forward": true, "start": 756, "end": 763}, - {"helix": 0, "forward": false, "start": 756, "end": 763}, - {"helix": 1, "forward": true, "start": 756, "end": 770}, - {"helix": 2, "forward": false, "start": 756, "end": 770} - ] - }, - { - "color": "#aaaa00", - "sequence": "CATTAAAAGAAGTGCCACCACCCTCAGACAGCATTGACAGCA", - "domains": [ - {"helix": 0, "forward": false, "start": 763, "end": 770}, - {"helix": 5, "forward": true, "start": 763, "end": 770}, - {"helix": 4, "forward": false, "start": 756, "end": 770}, - {"helix": 3, "forward": true, "start": 756, "end": 770} - ] - }, - { - "color": "#03b6a2", - "sequence": "AAAGAGTCATCTTTTCATAGCCCCCTTAACCGTCAGACTGTA", - "domains": [ - {"helix": 5, "forward": true, "start": 798, "end": 805}, - {"helix": 0, "forward": false, "start": 798, "end": 805}, - {"helix": 1, "forward": true, "start": 798, "end": 812}, - {"helix": 2, "forward": false, "start": 798, "end": 812} - ] - }, - { - "color": "#007200", - "sequence": "CGTTTGCCTGTCCAATGAAACCATCGATGTTTGCCTTTAGCA", - "domains": [ - {"helix": 0, "forward": false, "start": 805, "end": 812}, - {"helix": 5, "forward": true, "start": 805, "end": 812}, - {"helix": 4, "forward": false, "start": 798, "end": 812}, - {"helix": 3, "forward": true, "start": 798, "end": 812} - ] - }, - { - "color": "#aaaa00", - "sequence": "TTCTTTGATCACCGGGAAATTATTCATTCGATTCAACCGATT", - "domains": [ - {"helix": 5, "forward": true, "start": 840, "end": 847}, - {"helix": 0, "forward": false, "start": 840, "end": 847}, - {"helix": 1, "forward": true, "start": 840, "end": 854}, - {"helix": 2, "forward": false, "start": 840, "end": 854} - ] - }, - { - "color": "#f7931e", - "sequence": "GTGAATTATTAGTATTGTCACAATCAATCAAAAGGGCGACCA", - "domains": [ - {"helix": 0, "forward": false, "start": 847, "end": 854}, - {"helix": 5, "forward": true, "start": 847, "end": 854}, - {"helix": 4, "forward": false, "start": 840, "end": 854}, - {"helix": 3, "forward": true, "start": 840, "end": 854} - ] - }, - { - "color": "#007200", - "sequence": "TCAAACTATTACGCAGAACTGGCATGATCAAAACCGAGGAAA", - "domains": [ - {"helix": 5, "forward": true, "start": 882, "end": 889}, - {"helix": 0, "forward": false, "start": 882, "end": 889}, - {"helix": 1, "forward": true, "start": 882, "end": 896}, - {"helix": 2, "forward": false, "start": 882, "end": 896} - ] - }, - { - "color": "#57bb00", - "sequence": "ACTCCTTATCGGCCCTTACCGAAGCCCTGTTACCAGAAGGAG", - "domains": [ - {"helix": 0, "forward": false, "start": 889, "end": 896}, - {"helix": 5, "forward": true, "start": 889, "end": 896}, - {"helix": 4, "forward": false, "start": 882, "end": 896}, - {"helix": 3, "forward": true, "start": 882, "end": 896} - ] - }, - { - "color": "#f7931e", - "sequence": "CGCCAGCGTAATTGTGAACACCCTGAACCATAAAAACAGGGA", - "domains": [ - {"helix": 5, "forward": true, "start": 924, "end": 931}, - {"helix": 0, "forward": false, "start": 924, "end": 931}, - {"helix": 1, "forward": true, "start": 924, "end": 938}, - {"helix": 2, "forward": false, "start": 924, "end": 938} - ] - }, - { - "color": "#32b86c", - "sequence": "TCAGAGGCATTGCAAACGATTTTTTGTTGAGAGAATAACATA", - "domains": [ - {"helix": 0, "forward": false, "start": 931, "end": 938}, - {"helix": 5, "forward": true, "start": 931, "end": 938}, - {"helix": 4, "forward": false, "start": 924, "end": 938}, - {"helix": 3, "forward": true, "start": 924, "end": 938} - ] - }, - { - "color": "#57bb00", - "sequence": "CATTTTGAATCTTATGCACCCAGCTACACCGGTTTTGAAGCC", - "domains": [ - {"helix": 5, "forward": true, "start": 966, "end": 973}, - {"helix": 0, "forward": false, "start": 966, "end": 973}, - {"helix": 1, "forward": true, "start": 966, "end": 980}, - {"helix": 2, "forward": false, "start": 966, "end": 980} - ] - }, - { - "color": "#320096", - "sequence": "TATCCTGACGCTCAGGCTTATCCGGTATCGACTTGCGGGACA", - "domains": [ - {"helix": 0, "forward": false, "start": 973, "end": 980}, - {"helix": 5, "forward": true, "start": 973, "end": 980}, - {"helix": 4, "forward": false, "start": 966, "end": 980}, - {"helix": 3, "forward": true, "start": 966, "end": 980} - ] - }, - { - "color": "#32b86c", - "sequence": "CAGATTCAGTACCGCATTCCAAGAACGGTTGTAGAAACCAAT", - "domains": [ - {"helix": 5, "forward": true, "start": 1008, "end": 1015}, - {"helix": 0, "forward": false, "start": 1008, "end": 1015}, - {"helix": 1, "forward": true, "start": 1008, "end": 1022}, - {"helix": 2, "forward": false, "start": 1008, "end": 1022} - ] - }, - { - "color": "#7300de", - "sequence": "TAAACCAACCAGTCTCAACAATAGATAAATTTACGAGCATCA", - "domains": [ - {"helix": 0, "forward": false, "start": 1015, "end": 1022}, - {"helix": 5, "forward": true, "start": 1015, "end": 1022}, - {"helix": 4, "forward": false, "start": 1008, "end": 1022}, - {"helix": 3, "forward": true, "start": 1008, "end": 1022} - ] - }, - { - "color": "#320096", - "sequence": "GGCCAACAGAATATGAGGCATTTTCGAGAGCGCCATATTTAA", - "domains": [ - {"helix": 5, "forward": true, "start": 1050, "end": 1057}, - {"helix": 0, "forward": false, "start": 1050, "end": 1057}, - {"helix": 1, "forward": true, "start": 1050, "end": 1064}, - {"helix": 2, "forward": false, "start": 1050, "end": 1064} - ] - }, - { - "color": "#b8056c", - "sequence": "TAATAAGAGAGATATTATACAAATTCTTTTAATTGAGAATAA", - "domains": [ - {"helix": 0, "forward": false, "start": 1057, "end": 1064}, - {"helix": 5, "forward": true, "start": 1057, "end": 1064}, - {"helix": 4, "forward": false, "start": 1050, "end": 1064}, - {"helix": 3, "forward": true, "start": 1050, "end": 1064} - ] - }, - { - "color": "#7300de", - "sequence": "TACGTGGGAAATACTCTTCTGACCTAAAGAGAGAAAACTTTT", - "domains": [ - {"helix": 5, "forward": true, "start": 1092, "end": 1099}, - {"helix": 0, "forward": false, "start": 1092, "end": 1099}, - {"helix": 1, "forward": true, "start": 1092, "end": 1106}, - {"helix": 2, "forward": false, "start": 1092, "end": 1106} - ] - }, - { - "color": "#cc0000", - "sequence": "ATGGTTTCACAGACTGGGTTATATAACTGACAAAGAACGCCT", - "domains": [ - {"helix": 0, "forward": false, "start": 1099, "end": 1106}, - {"helix": 5, "forward": true, "start": 1099, "end": 1106}, - {"helix": 4, "forward": false, "start": 1092, "end": 1106}, - {"helix": 3, "forward": true, "start": 1092, "end": 1106} - ] - }, - { - "color": "#b8056c", - "sequence": "ATGCGCGATAGCTTCCTTAGAATCCTTGACCTTGCTTCTGTA", - "domains": [ - {"helix": 5, "forward": true, "start": 1134, "end": 1141}, - {"helix": 0, "forward": false, "start": 1134, "end": 1141}, - {"helix": 1, "forward": true, "start": 1134, "end": 1148}, - {"helix": 2, "forward": false, "start": 1134, "end": 1148} - ] - }, - { - "color": "#f74308", - "sequence": "CATAGCGAACTGATTTTGAATTACCTTTTGAGTGAATAACAA", - "domains": [ - {"helix": 0, "forward": false, "start": 1141, "end": 1148}, - {"helix": 5, "forward": true, "start": 1141, "end": 1148}, - {"helix": 4, "forward": false, "start": 1134, "end": 1148}, - {"helix": 3, "forward": true, "start": 1134, "end": 1148} - ] - }, - { - "color": "#cc0000", - "sequence": "CGAACGAAGAGGCGTGAATACCAAGTTATTATCGGGAGAAAC", - "domains": [ - {"helix": 5, "forward": true, "start": 1176, "end": 1183}, - {"helix": 0, "forward": false, "start": 1176, "end": 1183}, - {"helix": 1, "forward": true, "start": 1176, "end": 1190}, - {"helix": 2, "forward": false, "start": 1176, "end": 1190} - ] - }, - { - "color": "#888888", - "sequence": "ATCGCGCACCACCAAATTGCGTAGATTTAGTACCTTTTACAT", - "domains": [ - {"helix": 0, "forward": false, "start": 1183, "end": 1190}, - {"helix": 5, "forward": true, "start": 1183, "end": 1190}, - {"helix": 4, "forward": false, "start": 1176, "end": 1190}, - {"helix": 3, "forward": true, "start": 1176, "end": 1190} - ] - }, - { - "color": "#f74308", - "sequence": "CAGTATTTAATCCTATCAGATGATGGCATCACCAGAAGGAGC", - "domains": [ - {"helix": 5, "forward": true, "start": 1218, "end": 1225}, - {"helix": 0, "forward": false, "start": 1218, "end": 1225}, - {"helix": 1, "forward": true, "start": 1218, "end": 1232}, - {"helix": 2, "forward": false, "start": 1218, "end": 1232} - ] - }, - { - "color": "#333333", - "sequence": "ATCAATAAACACCGGAACGTTATTAATTAACAAAGAAACCGA", - "domains": [ - {"helix": 0, "forward": false, "start": 1225, "end": 1232}, - {"helix": 5, "forward": true, "start": 1225, "end": 1232}, - {"helix": 4, "forward": false, "start": 1218, "end": 1232}, - {"helix": 3, "forward": true, "start": 1218, "end": 1232} - ] - } - ] +{ + "version": "0.19.0", + "grid": "honeycomb", + "helices": [ + 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"TGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCCGTCTTTATCGAGGTAACAAGCACCACGTAGCTTAAGCCCTGTTTACTCATTACACCAACCAGGAGGTCAGAGTTCGGAGAAATGATTTATGTGAAATGCGTCAGCCGATTCAAGGCCCCTATATTCGTGCCCACCGACGAGTTGCTTACAGATGGCAGGGCCGCACTGTCGGTATCATAGAGTCACTCCAGGGCGAGCGTAAATAGATTAGAAGCGGGGTTATTTTGGCGGGACATTGTCATAAGGTTGACAATTCAGCACTAAGGACACTTAAGTCGTGCGCATGAATTCACAACCACTTAGAAGAACATCCACCCTGGCTTCTCCTGAGAAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTT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1064}, + {"helix": 3, "forward": true, "start": 1050, "end": 1064} + ] + }, + { + "color": "#7300de", + "sequence": "TACGTGGGAAATACTCTTCTGACCTAAAGAGAGAAAACTTTT", + "domains": [ + {"helix": 5, "forward": true, "start": 1092, "end": 1099}, + {"helix": 0, "forward": false, "start": 1092, "end": 1099}, + {"helix": 1, "forward": true, "start": 1092, "end": 1106}, + {"helix": 2, "forward": false, "start": 1092, "end": 1106} + ] + }, + { + "color": "#cc0000", + "sequence": "ATGGTTTCACAGACTGGGTTATATAACTGACAAAGAACGCCT", + "domains": [ + {"helix": 0, "forward": false, "start": 1099, "end": 1106}, + {"helix": 5, "forward": true, "start": 1099, "end": 1106}, + {"helix": 4, "forward": false, "start": 1092, "end": 1106}, + {"helix": 3, "forward": true, "start": 1092, "end": 1106} + ] + }, + { + "color": "#b8056c", + "sequence": "ATGCGCGATAGCTTCCTTAGAATCCTTGACCTTGCTTCTGTA", + "domains": [ + {"helix": 5, "forward": true, "start": 1134, "end": 1141}, + {"helix": 0, "forward": false, "start": 1134, "end": 1141}, + {"helix": 1, "forward": true, "start": 1134, "end": 1148}, + {"helix": 2, "forward": false, "start": 1134, "end": 1148} + ] + }, + { + "color": "#f74308", + "sequence": "CATAGCGAACTGATTTTGAATTACCTTTTGAGTGAATAACAA", + "domains": [ + {"helix": 0, "forward": false, "start": 1141, "end": 1148}, + {"helix": 5, "forward": true, "start": 1141, "end": 1148}, + {"helix": 4, "forward": false, "start": 1134, "end": 1148}, + {"helix": 3, "forward": true, "start": 1134, "end": 1148} + ] + }, + { + "color": "#cc0000", + "sequence": "CGAACGAAGAGGCGTGAATACCAAGTTATTATCGGGAGAAAC", + "domains": [ + {"helix": 5, "forward": true, "start": 1176, "end": 1183}, + {"helix": 0, "forward": false, "start": 1176, "end": 1183}, + {"helix": 1, "forward": true, "start": 1176, "end": 1190}, + {"helix": 2, "forward": false, "start": 1176, "end": 1190} + ] + }, + { + "color": "#888888", + "sequence": "ATCGCGCACCACCAAATTGCGTAGATTTAGTACCTTTTACAT", + "domains": [ + {"helix": 0, "forward": false, "start": 1183, "end": 1190}, + {"helix": 5, "forward": true, "start": 1183, "end": 1190}, + {"helix": 4, "forward": false, "start": 1176, "end": 1190}, + {"helix": 3, "forward": true, "start": 1176, "end": 1190} + ] + }, + { + "color": "#f74308", + "sequence": "CAGTATTTAATCCTATCAGATGATGGCATCACCAGAAGGAGC", + "domains": [ + {"helix": 5, "forward": true, "start": 1218, "end": 1225}, + {"helix": 0, "forward": false, "start": 1218, "end": 1225}, + {"helix": 1, "forward": true, "start": 1218, "end": 1232}, + {"helix": 2, "forward": false, "start": 1218, "end": 1232} + ] + }, + { + "color": "#333333", + "sequence": "ATCAATAAACACCGGAACGTTATTAATTAACAAAGAAACCGA", + "domains": [ + {"helix": 0, "forward": false, "start": 1225, "end": 1232}, + {"helix": 5, "forward": true, "start": 1225, "end": 1232}, + {"helix": 4, "forward": false, "start": 1218, "end": 1232}, + {"helix": 3, "forward": true, "start": 1218, "end": 1232} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/6_helix_origami_rectangle.sc b/examples/output_designs/6_helix_origami_rectangle.sc index b490d28..29213f0 100644 --- a/examples/output_designs/6_helix_origami_rectangle.sc +++ b/examples/output_designs/6_helix_origami_rectangle.sc @@ -1,282 +1,282 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 192, "grid_position": [0, 0]}, - {"max_offset": 192, "grid_position": [0, 1]}, - {"max_offset": 192, "grid_position": [0, 2]}, - {"max_offset": 192, "grid_position": [0, 3]}, - {"max_offset": 192, "grid_position": [0, 4]}, - {"max_offset": 192, "grid_position": [0, 5]} - ], - "strands": [ - { - "color": "#0066cc", - "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGT", - "domains": [ - {"helix": 5, "forward": false, "start": 16, "end": 96, "deletions": [33, 81]}, - {"helix": 4, "forward": true, "start": 16, "end": 96, "deletions": [33, 81]}, - {"helix": 3, "forward": false, "start": 16, "end": 96, "deletions": [33, 81]}, - {"helix": 2, "forward": true, "start": 16, "end": 96, "deletions": [33, 81]}, - {"helix": 1, "forward": false, "start": 16, "end": 96, "deletions": [33, 81]}, - {"helix": 0, "forward": true, "start": 16, "end": 176, "deletions": [33, 81, 129]}, - {"helix": 1, "forward": false, "start": 96, "end": 176, "deletions": [129]}, - {"helix": 2, "forward": true, "start": 96, "end": 176, "deletions": [129]}, - {"helix": 3, "forward": false, "start": 96, "end": 176, "deletions": [129]}, - {"helix": 4, "forward": true, "start": 96, "end": 176, "deletions": [129]}, - {"helix": 5, "forward": false, "start": 96, "end": 176, "deletions": [129]} - ], - "is_scaffold": true - }, - { - "color": "#f74308", - "sequence": "GTGAGACGGGCAACAGGTTTTTCTTTTCACCA", - "domains": [ - {"helix": 1, "forward": true, "start": 16, "end": 32}, - {"helix": 0, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#57bb00", - "sequence": "AGGGTTGAGTGTTGTTAAGAATAGCCCGAGAT", - "domains": [ - {"helix": 3, "forward": true, "start": 16, "end": 32}, - {"helix": 2, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#888888", - "sequence": "AAATCGGAACCCTAAAGGTGCCGTAAAGCACT", - "domains": [ - {"helix": 5, "forward": true, "start": 16, "end": 32}, - {"helix": 4, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#32b86c", - "sequence": "GTGCCTAATGAGTGAGAAGTGTAAAGCCTGGG", - "domains": [ - {"helix": 0, "forward": false, "start": 160, "end": 176}, - {"helix": 1, "forward": true, "start": 160, "end": 176} - ] - }, - { - "color": "#333333", - "sequence": "AGTGCCAAGCTTGCATTTGTAAAACGACGGCC", - "domains": [ - {"helix": 2, "forward": false, "start": 160, "end": 176}, - {"helix": 3, "forward": true, "start": 160, "end": 176} - ] - }, - { - "color": "#320096", - "sequence": "AGCGCCATTCGCCATTGCCGGAAACCAGGCAA", - "domains": [ - {"helix": 4, "forward": false, "start": 160, "end": 176}, - {"helix": 5, "forward": true, "start": 160, "end": 176} - ] - }, - { - "color": "#03b6a2", - "sequence": "CCAGTCGGGAAACCTGTCGTGCCAGCTGCATT", - "domains": [ - {"helix": 0, "forward": false, "start": 88, "end": 120} - ] - }, - { - "color": "#7300de", - "sequence": "CGAAAATCCACGCTGGTTTGCCCTGTTTCC", - "domains": [ - {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, - {"helix": 1, "forward": true, "start": 80, "end": 104, "deletions": [81]} - ] - }, - { - "color": "#aaaa00", - "sequence": "TGTGTGAAGTAATCATGGTCATAGCCAGCAGG", - "domains": [ - {"helix": 1, "forward": true, "start": 104, "end": 112}, - {"helix": 2, "forward": false, "start": 88, "end": 112} - ] - }, - { - "color": "#b8056c", - "sequence": "AGGGCGACAAAGGGCGAAAAACGAAAGGGG", - "domains": [ - {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, - {"helix": 3, "forward": true, "start": 80, "end": 104, "deletions": [81]} - ] - }, - { - "color": "#007200", - "sequence": "GATGTGCTTATTACGCCAGCTGGCCGTCTATC", - "domains": [ - {"helix": 3, "forward": true, "start": 104, "end": 112}, - {"helix": 4, "forward": false, "start": 88, "end": 112} - ] - }, - { - "color": "#cc0000", - "sequence": "AACGTGGCGAGAAAGGAAGGGAAACGACGAC", - "domains": [ - {"helix": 5, "forward": true, "start": 72, "end": 104, "deletions": [81]} - ] - }, - { - "color": "#f7931e", - "sequence": "TTTGCGTATTGGGCGCCAGGGTGCTGATTG", - "domains": [ - {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, - {"helix": 1, "forward": true, "start": 32, "end": 40, "deletions": [33]} - ] - }, - { - "color": "#f74308", - "sequence": "CCCTTCACTCCCTTATAAATCAACCAGTTT", - "domains": [ - {"helix": 1, "forward": true, "start": 40, "end": 48}, - {"helix": 2, "forward": false, "start": 32, "end": 48, "deletions": [33]}, - {"helix": 3, "forward": true, "start": 32, "end": 40, "deletions": [33]} - ] - }, - { - "color": "#57bb00", - "sequence": "GGAACAAGGTTTTTTGGGGTCGAGGGAGCC", - "domains": [ - {"helix": 3, "forward": true, "start": 40, "end": 48}, - {"helix": 4, "forward": false, "start": 32, "end": 48, "deletions": [33]}, - {"helix": 5, "forward": true, "start": 32, "end": 40, "deletions": [33]} - ] - }, - { - "color": "#888888", - "sequence": "CCCGATTTAGAGCTTGACGGGGAACCATCACC", - "domains": [ - {"helix": 5, "forward": true, "start": 40, "end": 64}, - {"helix": 4, "forward": false, "start": 56, "end": 64} - ] - }, - { - "color": "#32b86c", - "sequence": "CGGCAAAACGCCTGGCCCTGAGAGAGAGGCGG", - "domains": [ - {"helix": 2, "forward": false, "start": 48, "end": 56}, - {"helix": 1, "forward": true, "start": 48, "end": 64}, - {"helix": 0, "forward": false, "start": 56, "end": 64} - ] - }, - { - "color": "#333333", - "sequence": "CAAATCAAAGTCCACTATTAAAGATCCGAAAT", - "domains": [ - {"helix": 4, "forward": false, "start": 48, "end": 56}, - {"helix": 3, "forward": true, "start": 48, "end": 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{"helix": 4, "forward": false, "start": 120, "end": 128} - ] - }, - { - "color": "#b8056c", - "sequence": "TCGAATTCATTGTTATCCGCTCACCCCGCTTT", - "domains": [ - {"helix": 2, "forward": false, "start": 112, "end": 120}, - {"helix": 1, "forward": true, "start": 112, "end": 128}, - {"helix": 0, "forward": false, "start": 120, "end": 128} - ] - }, - { - "color": "#007200", - "sequence": "CTCTTCGCGCAAGGCGATTAAGTTTACCGAGC", - "domains": [ - {"helix": 4, "forward": false, "start": 112, "end": 120}, - {"helix": 3, "forward": true, "start": 112, "end": 128}, - {"helix": 2, "forward": false, "start": 120, "end": 128} - ] - }, - { - "color": "#cc0000", - "sequence": "CATTAATTGCGTTGCGCTCACTGAATTCCA", - "domains": [ - {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, - {"helix": 1, "forward": true, "start": 128, "end": 136, "deletions": [129]} - ] - }, - { - "color": "#f7931e", - "sequence": "CACAACATTAGAGGATCCCCGGGGGGTAAC", - "domains": [ - {"helix": 1, "forward": true, 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- }, - { - "color": "#32b86c", - "sequence": "GCAACTGTTTTCCCAGTCACGACGGCCTGCAG", - "domains": [ - {"helix": 4, "forward": false, "start": 144, "end": 152}, - {"helix": 3, "forward": true, "start": 144, "end": 160}, - {"helix": 2, "forward": false, "start": 152, "end": 160} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"max_offset": 192, "grid_position": [0, 0]}, + {"max_offset": 192, "grid_position": [0, 1]}, + {"max_offset": 192, "grid_position": [0, 2]}, + {"max_offset": 192, "grid_position": [0, 3]}, + {"max_offset": 192, "grid_position": [0, 4]}, + {"max_offset": 192, "grid_position": [0, 5]} + ], + "strands": [ + { + "color": "#0066cc", + "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGT", + "domains": [ + {"helix": 5, "forward": false, "start": 16, "end": 96, "deletions": [33, 81]}, + {"helix": 4, "forward": true, "start": 16, "end": 96, "deletions": [33, 81]}, + {"helix": 3, "forward": false, "start": 16, "end": 96, "deletions": [33, 81]}, + {"helix": 2, "forward": true, "start": 16, "end": 96, "deletions": [33, 81]}, + {"helix": 1, "forward": false, "start": 16, "end": 96, "deletions": [33, 81]}, + {"helix": 0, "forward": true, "start": 16, "end": 176, "deletions": [33, 81, 129]}, + {"helix": 1, "forward": false, "start": 96, "end": 176, "deletions": [129]}, + {"helix": 2, "forward": true, "start": 96, "end": 176, "deletions": [129]}, + {"helix": 3, "forward": false, "start": 96, "end": 176, "deletions": [129]}, + {"helix": 4, "forward": true, "start": 96, "end": 176, "deletions": [129]}, + {"helix": 5, "forward": false, "start": 96, "end": 176, "deletions": [129]} + ], + "is_scaffold": true + }, + { + "color": "#f74308", + "sequence": "GTGAGACGGGCAACAGGTTTTTCTTTTCACCA", + "domains": [ + {"helix": 1, "forward": true, "start": 16, "end": 32}, + {"helix": 0, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#57bb00", + "sequence": "AGGGTTGAGTGTTGTTAAGAATAGCCCGAGAT", + "domains": [ + {"helix": 3, "forward": true, "start": 16, "end": 32}, + {"helix": 2, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#888888", + "sequence": "AAATCGGAACCCTAAAGGTGCCGTAAAGCACT", + "domains": [ + {"helix": 5, "forward": true, "start": 16, "end": 32}, + {"helix": 4, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#32b86c", + "sequence": "GTGCCTAATGAGTGAGAAGTGTAAAGCCTGGG", + "domains": [ + {"helix": 0, "forward": false, "start": 160, "end": 176}, + {"helix": 1, "forward": true, "start": 160, "end": 176} + ] + }, + { + "color": "#333333", + "sequence": "AGTGCCAAGCTTGCATTTGTAAAACGACGGCC", + "domains": [ + {"helix": 2, "forward": false, "start": 160, "end": 176}, + {"helix": 3, "forward": true, "start": 160, "end": 176} + ] + }, + { + "color": "#320096", + "sequence": "AGCGCCATTCGCCATTGCCGGAAACCAGGCAA", + "domains": [ + {"helix": 4, "forward": false, "start": 160, "end": 176}, + {"helix": 5, "forward": true, "start": 160, "end": 176} + ] + }, + { + "color": "#03b6a2", + "sequence": "CCAGTCGGGAAACCTGTCGTGCCAGCTGCATT", + "domains": [ + {"helix": 0, "forward": false, "start": 88, "end": 120} + ] + }, + { + "color": "#7300de", + "sequence": "CGAAAATCCACGCTGGTTTGCCCTGTTTCC", + "domains": [ + {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, + {"helix": 1, "forward": true, "start": 80, "end": 104, "deletions": [81]} + ] + }, + { + "color": "#aaaa00", + "sequence": "TGTGTGAAGTAATCATGGTCATAGCCAGCAGG", + "domains": [ + {"helix": 1, "forward": true, "start": 104, "end": 112}, + {"helix": 2, "forward": false, "start": 88, "end": 112} + ] + }, + { + "color": "#b8056c", + "sequence": "AGGGCGACAAAGGGCGAAAAACGAAAGGGG", + "domains": [ + {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, + {"helix": 3, "forward": true, "start": 80, "end": 104, "deletions": [81]} + ] + }, + { + "color": "#007200", + "sequence": "GATGTGCTTATTACGCCAGCTGGCCGTCTATC", + "domains": [ + {"helix": 3, "forward": true, "start": 104, "end": 112}, + {"helix": 4, "forward": false, "start": 88, "end": 112} + ] + }, + { + "color": "#cc0000", + "sequence": "AACGTGGCGAGAAAGGAAGGGAAACGACGAC", + "domains": [ + {"helix": 5, "forward": true, "start": 72, "end": 104, "deletions": [81]} + ] + }, + { + "color": "#f7931e", + "sequence": "TTTGCGTATTGGGCGCCAGGGTGCTGATTG", + "domains": [ + {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, + {"helix": 1, "forward": true, "start": 32, "end": 40, "deletions": [33]} + ] + }, + { + "color": "#f74308", + "sequence": "CCCTTCACTCCCTTATAAATCAACCAGTTT", + "domains": [ + {"helix": 1, "forward": true, "start": 40, "end": 48}, + {"helix": 2, "forward": false, "start": 32, "end": 48, "deletions": [33]}, + {"helix": 3, "forward": true, "start": 32, "end": 40, "deletions": [33]} + ] + }, + { + "color": "#57bb00", + "sequence": "GGAACAAGGTTTTTTGGGGTCGAGGGAGCC", + "domains": [ + {"helix": 3, "forward": true, "start": 40, "end": 48}, + {"helix": 4, "forward": false, "start": 32, "end": 48, "deletions": [33]}, + {"helix": 5, "forward": true, "start": 32, "end": 40, "deletions": [33]} + ] + }, + { + "color": "#888888", + "sequence": "CCCGATTTAGAGCTTGACGGGGAACCATCACC", + "domains": [ + {"helix": 5, "forward": true, "start": 40, "end": 64}, + {"helix": 4, "forward": false, "start": 56, "end": 64} + ] + }, + { + "color": "#32b86c", + "sequence": "CGGCAAAACGCCTGGCCCTGAGAGAGAGGCGG", + "domains": [ + {"helix": 2, "forward": false, "start": 48, "end": 56}, + {"helix": 1, "forward": true, "start": 48, "end": 64}, + {"helix": 0, "forward": false, "start": 56, "end": 64} + ] + }, + { + "color": "#333333", + "sequence": "CAAATCAAAGTCCACTATTAAAGATCCGAAAT", + "domains": [ + {"helix": 4, "forward": false, "start": 48, "end": 56}, + {"helix": 3, "forward": true, "start": 48, "end": 64}, + {"helix": 2, "forward": false, "start": 56, "end": 64} + ] + }, + { + "color": "#320096", + "sequence": "AATGAATCGGCCAACGCGCGGGGAGTTGCAG", + "domains": [ + {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, + {"helix": 1, "forward": true, "start": 64, "end": 72} + ] + }, + { + "color": "#03b6a2", + "sequence": "CAAGCGGTCCTGTTTGATGGTGGTACGTGGAC", + "domains": [ + {"helix": 1, "forward": true, "start": 72, "end": 80}, + {"helix": 2, "forward": false, "start": 64, "end": 80}, + {"helix": 3, "forward": true, "start": 64, "end": 72} + ] + }, + { + "color": "#7300de", + "sequence": "TCCAACGTTGGCCCACTACGTGAAAGCCGGCG", + "domains": [ + {"helix": 3, "forward": true, "start": 72, "end": 80}, + {"helix": 4, "forward": false, "start": 64, "end": 80}, + {"helix": 5, "forward": true, "start": 64, "end": 72} + ] + }, + { + "color": "#aaaa00", + "sequence": "AGTATCGGCCTCAGGAAGATCGCAGTGCGGGC", + "domains": [ + {"helix": 5, "forward": true, "start": 104, "end": 128}, + {"helix": 4, "forward": false, "start": 120, "end": 128} + ] + }, + { + "color": "#b8056c", + "sequence": "TCGAATTCATTGTTATCCGCTCACCCCGCTTT", + "domains": [ + {"helix": 2, "forward": false, "start": 112, "end": 120}, + {"helix": 1, "forward": true, "start": 112, "end": 128}, + {"helix": 0, "forward": false, "start": 120, "end": 128} + ] + }, + { + "color": "#007200", + "sequence": "CTCTTCGCGCAAGGCGATTAAGTTTACCGAGC", + "domains": [ + {"helix": 4, "forward": false, "start": 112, "end": 120}, + {"helix": 3, "forward": true, "start": 112, "end": 128}, + {"helix": 2, "forward": false, "start": 120, "end": 128} + ] + }, + { + "color": "#cc0000", + "sequence": "CATTAATTGCGTTGCGCTCACTGAATTCCA", + "domains": [ + {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, + {"helix": 1, "forward": true, "start": 128, "end": 136, "deletions": [129]} + ] + }, + { + "color": "#f7931e", + "sequence": "CACAACATTAGAGGATCCCCGGGGGGTAAC", + "domains": [ + {"helix": 1, "forward": true, "start": 136, "end": 144}, + {"helix": 2, "forward": false, "start": 128, "end": 144, "deletions": [129]}, + {"helix": 3, "forward": true, "start": 128, "end": 136, "deletions": [129]} + ] + }, + { + "color": "#f74308", + "sequence": "GCCAGGGTTGGGAAGGGCGATCGCTCCAGC", + "domains": [ + {"helix": 3, "forward": true, "start": 136, "end": 144}, + {"helix": 4, "forward": false, "start": 128, "end": 144, "deletions": [129]}, + {"helix": 5, "forward": true, "start": 128, "end": 136, "deletions": [129]} + ] + }, + { + "color": "#57bb00", + "sequence": "CAGCTTTCCGGCACCGCTTCTGGTCAGGCTGC", + "domains": [ + {"helix": 5, "forward": true, "start": 136, "end": 160}, + {"helix": 4, "forward": false, "start": 152, "end": 160} + ] + }, + { + "color": "#888888", + "sequence": "GTCGACTCACGAGCCGGAAGCATACTAACTCA", + "domains": [ + {"helix": 2, "forward": false, "start": 144, "end": 152}, + {"helix": 1, "forward": true, "start": 144, "end": 160}, + {"helix": 0, "forward": false, "start": 152, "end": 160} + ] + }, + { + "color": "#32b86c", + "sequence": "GCAACTGTTTTCCCAGTCACGACGGCCTGCAG", + "domains": [ + {"helix": 4, "forward": false, "start": 144, "end": 152}, + {"helix": 3, "forward": true, "start": 144, "end": 160}, + {"helix": 2, "forward": false, "start": 152, "end": 160} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.sc b/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.sc index 960730a..6e280c5 100644 --- a/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.sc +++ b/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.sc @@ -1,283 +1,283 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 192, "grid_position": [0, 0]}, - {"max_offset": 192, "grid_position": [0, 1]}, - {"max_offset": 192, "grid_position": [0, 2]}, - {"max_offset": 192, "grid_position": [0, 3]}, - {"max_offset": 192, "grid_position": [0, 4]}, - {"max_offset": 192, "grid_position": [0, 5]} - ], - "helices_view_order": [5, 4, 3, 2, 1, 0], - "strands": [ - { - "color": "#0066cc", - "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGT", - "domains": [ - {"helix": 5, "forward": false, "start": 16, "end": 96, "deletions": [33, 81]}, - {"helix": 4, "forward": true, "start": 16, "end": 96, "deletions": [33, 81]}, - {"helix": 3, "forward": false, "start": 16, "end": 96, "deletions": [33, 81]}, - {"helix": 2, "forward": true, "start": 16, "end": 96, "deletions": [33, 81]}, - {"helix": 1, "forward": false, "start": 16, "end": 96, "deletions": [33, 81]}, - {"helix": 0, "forward": true, "start": 16, "end": 176, "deletions": [33, 81, 129]}, - {"helix": 1, "forward": false, "start": 96, "end": 176, "deletions": [129]}, - {"helix": 2, "forward": true, "start": 96, "end": 176, "deletions": [129]}, - {"helix": 3, "forward": false, "start": 96, "end": 176, "deletions": [129]}, - {"helix": 4, "forward": true, "start": 96, "end": 176, "deletions": [129]}, - {"helix": 5, "forward": false, "start": 96, "end": 176, "deletions": [129]} - ], - "is_scaffold": true - }, - { - "color": "#f74308", - "sequence": "GTGAGACGGGCAACAGGTTTTTCTTTTCACCA", - "domains": [ - {"helix": 1, "forward": true, "start": 16, "end": 32}, - {"helix": 0, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#57bb00", - "sequence": "AGGGTTGAGTGTTGTTAAGAATAGCCCGAGAT", - "domains": [ - {"helix": 3, "forward": true, "start": 16, "end": 32}, - {"helix": 2, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#888888", - "sequence": "AAATCGGAACCCTAAAGGTGCCGTAAAGCACT", - "domains": [ - {"helix": 5, "forward": true, "start": 16, "end": 32}, - {"helix": 4, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#32b86c", - "sequence": "GTGCCTAATGAGTGAGAAGTGTAAAGCCTGGG", - "domains": [ - {"helix": 0, "forward": false, "start": 160, "end": 176}, - {"helix": 1, "forward": true, "start": 160, "end": 176} - ] - }, - { - "color": "#333333", - "sequence": "AGTGCCAAGCTTGCATTTGTAAAACGACGGCC", - "domains": [ - {"helix": 2, "forward": false, "start": 160, "end": 176}, - {"helix": 3, "forward": true, "start": 160, "end": 176} - ] - }, - { - "color": "#320096", - "sequence": "AGCGCCATTCGCCATTGCCGGAAACCAGGCAA", - "domains": [ - {"helix": 4, "forward": false, "start": 160, "end": 176}, - {"helix": 5, "forward": true, "start": 160, "end": 176} - ] - }, - { - "color": "#03b6a2", - "sequence": "CCAGTCGGGAAACCTGTCGTGCCAGCTGCATT", - "domains": [ - {"helix": 0, "forward": false, "start": 88, "end": 120} - ] - }, - { - "color": "#7300de", - "sequence": "CGAAAATCCACGCTGGTTTGCCCTGTTTCC", - "domains": [ - {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, - {"helix": 1, "forward": true, "start": 80, "end": 104, "deletions": [81]} - ] - }, - { - "color": "#aaaa00", - "sequence": "TGTGTGAAGTAATCATGGTCATAGCCAGCAGG", - "domains": [ - {"helix": 1, "forward": true, "start": 104, "end": 112}, - {"helix": 2, "forward": false, "start": 88, "end": 112} - ] - }, - { - "color": "#b8056c", - "sequence": "AGGGCGACAAAGGGCGAAAAACGAAAGGGG", - "domains": [ - {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, - {"helix": 3, "forward": true, "start": 80, "end": 104, "deletions": [81]} - ] - }, - { - "color": "#007200", - "sequence": "GATGTGCTTATTACGCCAGCTGGCCGTCTATC", - "domains": [ - {"helix": 3, "forward": true, "start": 104, "end": 112}, - {"helix": 4, "forward": false, "start": 88, "end": 112} - ] - }, - { - "color": "#cc0000", - "sequence": "AACGTGGCGAGAAAGGAAGGGAAACGACGAC", - "domains": [ - {"helix": 5, "forward": true, "start": 72, "end": 104, "deletions": [81]} - ] - }, - { - "color": "#f7931e", - "sequence": "TTTGCGTATTGGGCGCCAGGGTGCTGATTG", - "domains": [ - {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, - {"helix": 1, "forward": true, "start": 32, "end": 40, "deletions": [33]} - ] - }, - { - "color": "#f74308", - "sequence": "CCCTTCACTCCCTTATAAATCAACCAGTTT", - "domains": [ - {"helix": 1, "forward": true, "start": 40, "end": 48}, - {"helix": 2, "forward": false, "start": 32, "end": 48, "deletions": [33]}, - {"helix": 3, "forward": true, "start": 32, "end": 40, "deletions": [33]} - ] - }, - { - "color": "#57bb00", - "sequence": "GGAACAAGGTTTTTTGGGGTCGAGGGAGCC", - "domains": [ - {"helix": 3, "forward": true, "start": 40, "end": 48}, - {"helix": 4, "forward": false, "start": 32, "end": 48, "deletions": [33]}, - {"helix": 5, "forward": true, "start": 32, "end": 40, "deletions": [33]} - ] - }, - { - "color": "#888888", - "sequence": "CCCGATTTAGAGCTTGACGGGGAACCATCACC", - "domains": [ - {"helix": 5, "forward": true, "start": 40, "end": 64}, - {"helix": 4, "forward": false, "start": 56, "end": 64} - ] - }, - { - "color": "#32b86c", - "sequence": "CGGCAAAACGCCTGGCCCTGAGAGAGAGGCGG", - "domains": [ - {"helix": 2, "forward": false, "start": 48, "end": 56}, - {"helix": 1, "forward": true, "start": 48, "end": 64}, - {"helix": 0, "forward": false, "start": 56, "end": 64} - ] - }, - { - "color": "#333333", - "sequence": "CAAATCAAAGTCCACTATTAAAGATCCGAAAT", - "domains": [ - {"helix": 4, "forward": false, "start": 48, "end": 56}, - {"helix": 3, "forward": true, "start": 48, "end": 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- }, - { - "color": "#32b86c", - "sequence": "GCAACTGTTTTCCCAGTCACGACGGCCTGCAG", - "domains": [ - {"helix": 4, "forward": false, "start": 144, "end": 152}, - {"helix": 3, "forward": true, "start": 144, "end": 160}, - {"helix": 2, "forward": false, "start": 152, "end": 160} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"max_offset": 192, "grid_position": [0, 0]}, + {"max_offset": 192, "grid_position": [0, 1]}, + {"max_offset": 192, "grid_position": [0, 2]}, + {"max_offset": 192, "grid_position": [0, 3]}, + {"max_offset": 192, "grid_position": [0, 4]}, + {"max_offset": 192, "grid_position": [0, 5]} + ], + "helices_view_order": [5, 4, 3, 2, 1, 0], + "strands": [ + { + "color": "#0066cc", + "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGT", + "domains": [ + {"helix": 5, "forward": false, 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true, "start": 16, "end": 32}, + {"helix": 0, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#57bb00", + "sequence": "AGGGTTGAGTGTTGTTAAGAATAGCCCGAGAT", + "domains": [ + {"helix": 3, "forward": true, "start": 16, "end": 32}, + {"helix": 2, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#888888", + "sequence": "AAATCGGAACCCTAAAGGTGCCGTAAAGCACT", + "domains": [ + {"helix": 5, "forward": true, "start": 16, "end": 32}, + {"helix": 4, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#32b86c", + "sequence": "GTGCCTAATGAGTGAGAAGTGTAAAGCCTGGG", + "domains": [ + {"helix": 0, "forward": false, "start": 160, "end": 176}, + {"helix": 1, "forward": true, "start": 160, "end": 176} + ] + }, + { + "color": "#333333", + "sequence": "AGTGCCAAGCTTGCATTTGTAAAACGACGGCC", + "domains": [ + {"helix": 2, "forward": false, "start": 160, "end": 176}, + {"helix": 3, "forward": true, "start": 160, "end": 176} + ] + }, + { + "color": "#320096", + "sequence": "AGCGCCATTCGCCATTGCCGGAAACCAGGCAA", + "domains": [ + {"helix": 4, "forward": false, "start": 160, "end": 176}, + {"helix": 5, "forward": true, "start": 160, "end": 176} + ] + }, + { + "color": "#03b6a2", + "sequence": "CCAGTCGGGAAACCTGTCGTGCCAGCTGCATT", + "domains": [ + {"helix": 0, "forward": false, "start": 88, "end": 120} + ] + }, + { + "color": "#7300de", + "sequence": "CGAAAATCCACGCTGGTTTGCCCTGTTTCC", + "domains": [ + {"helix": 2, "forward": false, "start": 80, "end": 88, "deletions": [81]}, + {"helix": 1, "forward": true, "start": 80, "end": 104, "deletions": [81]} + ] + }, + { + "color": "#aaaa00", + "sequence": "TGTGTGAAGTAATCATGGTCATAGCCAGCAGG", + "domains": [ + {"helix": 1, "forward": true, "start": 104, "end": 112}, + {"helix": 2, "forward": false, "start": 88, "end": 112} + ] + }, + { + "color": "#b8056c", + "sequence": "AGGGCGACAAAGGGCGAAAAACGAAAGGGG", + "domains": [ + {"helix": 4, "forward": false, "start": 80, "end": 88, "deletions": [81]}, + {"helix": 3, "forward": true, "start": 80, "end": 104, "deletions": [81]} + ] + }, + { + "color": "#007200", + "sequence": "GATGTGCTTATTACGCCAGCTGGCCGTCTATC", + "domains": [ + {"helix": 3, "forward": true, "start": 104, "end": 112}, + {"helix": 4, "forward": false, "start": 88, "end": 112} + ] + }, + { + "color": "#cc0000", + "sequence": "AACGTGGCGAGAAAGGAAGGGAAACGACGAC", + "domains": [ + {"helix": 5, "forward": true, "start": 72, "end": 104, "deletions": [81]} + ] + }, + { + "color": "#f7931e", + "sequence": "TTTGCGTATTGGGCGCCAGGGTGCTGATTG", + "domains": [ + {"helix": 0, "forward": false, "start": 32, "end": 56, "deletions": [33]}, + {"helix": 1, "forward": true, "start": 32, "end": 40, "deletions": [33]} + ] + }, + { + "color": "#f74308", + "sequence": "CCCTTCACTCCCTTATAAATCAACCAGTTT", + "domains": [ + {"helix": 1, "forward": true, "start": 40, "end": 48}, + {"helix": 2, "forward": false, "start": 32, "end": 48, "deletions": [33]}, + {"helix": 3, "forward": true, "start": 32, "end": 40, "deletions": [33]} + ] + }, + { + "color": "#57bb00", + "sequence": "GGAACAAGGTTTTTTGGGGTCGAGGGAGCC", + "domains": [ + {"helix": 3, "forward": true, "start": 40, "end": 48}, + {"helix": 4, "forward": false, "start": 32, "end": 48, "deletions": [33]}, + {"helix": 5, "forward": true, "start": 32, "end": 40, "deletions": [33]} + ] + }, + { + "color": "#888888", + "sequence": "CCCGATTTAGAGCTTGACGGGGAACCATCACC", + "domains": [ + {"helix": 5, "forward": true, "start": 40, "end": 64}, + {"helix": 4, "forward": false, "start": 56, "end": 64} + ] + }, + { + "color": "#32b86c", + "sequence": "CGGCAAAACGCCTGGCCCTGAGAGAGAGGCGG", + "domains": [ + {"helix": 2, "forward": false, "start": 48, "end": 56}, + {"helix": 1, "forward": true, "start": 48, "end": 64}, + {"helix": 0, "forward": false, "start": 56, "end": 64} + ] + }, + { + "color": "#333333", + "sequence": "CAAATCAAAGTCCACTATTAAAGATCCGAAAT", + "domains": [ + {"helix": 4, "forward": false, "start": 48, "end": 56}, + {"helix": 3, "forward": true, "start": 48, "end": 64}, + {"helix": 2, "forward": false, "start": 56, "end": 64} + ] + }, + { + "color": "#320096", + "sequence": "AATGAATCGGCCAACGCGCGGGGAGTTGCAG", + "domains": [ + {"helix": 0, "forward": false, "start": 64, "end": 88, "deletions": [81]}, + {"helix": 1, "forward": true, "start": 64, "end": 72} + ] + }, + { + "color": "#03b6a2", + "sequence": "CAAGCGGTCCTGTTTGATGGTGGTACGTGGAC", + "domains": [ + {"helix": 1, "forward": true, "start": 72, "end": 80}, + {"helix": 2, "forward": false, "start": 64, "end": 80}, + {"helix": 3, "forward": true, "start": 64, "end": 72} + ] + }, + { + "color": "#7300de", + "sequence": "TCCAACGTTGGCCCACTACGTGAAAGCCGGCG", + "domains": [ + {"helix": 3, "forward": true, "start": 72, "end": 80}, + {"helix": 4, "forward": false, "start": 64, "end": 80}, + {"helix": 5, "forward": true, "start": 64, "end": 72} + ] + }, + { + "color": "#aaaa00", + "sequence": "AGTATCGGCCTCAGGAAGATCGCAGTGCGGGC", + "domains": [ + {"helix": 5, "forward": true, "start": 104, "end": 128}, + {"helix": 4, "forward": false, "start": 120, "end": 128} + ] + }, + { + "color": "#b8056c", + "sequence": "TCGAATTCATTGTTATCCGCTCACCCCGCTTT", + "domains": [ + {"helix": 2, "forward": false, "start": 112, "end": 120}, + {"helix": 1, "forward": true, "start": 112, "end": 128}, + {"helix": 0, "forward": false, "start": 120, "end": 128} + ] + }, + { + "color": "#007200", + "sequence": "CTCTTCGCGCAAGGCGATTAAGTTTACCGAGC", + "domains": [ + {"helix": 4, "forward": false, "start": 112, "end": 120}, + {"helix": 3, "forward": true, "start": 112, "end": 128}, + {"helix": 2, "forward": false, "start": 120, "end": 128} + ] + }, + { + "color": "#cc0000", + "sequence": "CATTAATTGCGTTGCGCTCACTGAATTCCA", + "domains": [ + {"helix": 0, "forward": false, "start": 128, "end": 152, "deletions": [129]}, + {"helix": 1, "forward": true, "start": 128, "end": 136, "deletions": [129]} + ] + }, + { + "color": "#f7931e", + "sequence": "CACAACATTAGAGGATCCCCGGGGGGTAAC", + "domains": [ + {"helix": 1, "forward": true, "start": 136, "end": 144}, + {"helix": 2, "forward": false, "start": 128, "end": 144, "deletions": [129]}, + {"helix": 3, "forward": true, "start": 128, "end": 136, "deletions": [129]} + ] + }, + { + "color": "#f74308", + "sequence": "GCCAGGGTTGGGAAGGGCGATCGCTCCAGC", + "domains": [ + {"helix": 3, "forward": true, "start": 136, "end": 144}, + {"helix": 4, "forward": false, "start": 128, "end": 144, "deletions": [129]}, + {"helix": 5, "forward": true, "start": 128, "end": 136, "deletions": [129]} + ] + }, + { + "color": "#57bb00", + "sequence": "CAGCTTTCCGGCACCGCTTCTGGTCAGGCTGC", + "domains": [ + {"helix": 5, "forward": true, "start": 136, "end": 160}, + {"helix": 4, "forward": false, "start": 152, "end": 160} + ] + }, + { + "color": "#888888", + "sequence": "GTCGACTCACGAGCCGGAAGCATACTAACTCA", + "domains": [ + {"helix": 2, "forward": false, "start": 144, "end": 152}, + {"helix": 1, "forward": true, "start": 144, "end": 160}, + {"helix": 0, "forward": false, "start": 152, "end": 160} + ] + }, + { + "color": "#32b86c", + "sequence": "GCAACTGTTTTCCCAGTCACGACGGCCTGCAG", + "domains": [ + {"helix": 4, "forward": false, "start": 144, "end": 152}, + {"helix": 3, "forward": true, "start": 144, "end": 160}, + {"helix": 2, "forward": false, "start": 152, "end": 160} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/circular.sc b/examples/output_designs/circular.sc index d5fae32..96e14a0 100644 --- a/examples/output_designs/circular.sc +++ b/examples/output_designs/circular.sc @@ -1,34 +1,34 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"grid_position": [0, 0]}, - {"grid_position": [0, 1]} - ], - "strands": [ - { - "circular": true, - "color": "#f74308", - "domains": [ - {"helix": 0, "forward": true, "start": 0, "end": 8}, - {"helix": 1, "forward": false, "start": 0, "end": 8} - ] - }, - { - "circular": true, - "color": "#57bb00", - "domains": [ - {"helix": 0, "forward": true, "start": 8, "end": 16}, - {"loopout": 5}, - {"helix": 1, "forward": false, "start": 8, "end": 16} - ] - }, - { - "color": "#888888", - "domains": [ - {"helix": 0, "forward": true, "start": 16, "end": 24}, - {"helix": 1, "forward": false, "start": 16, "end": 24} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]} + ], + "strands": [ + { + "circular": true, + "color": "#f74308", + "domains": [ + {"helix": 0, "forward": true, "start": 0, "end": 8}, + {"helix": 1, "forward": false, "start": 0, "end": 8} + ] + }, + { + "circular": true, + "color": "#57bb00", + "domains": [ + {"helix": 0, "forward": true, "start": 8, "end": 16}, + {"loopout": 5}, + {"helix": 1, "forward": false, "start": 8, "end": 16} + ] + }, + { + "color": "#888888", + "domains": [ + {"helix": 0, "forward": true, "start": 16, "end": 24}, + {"helix": 1, "forward": false, "start": 16, "end": 24} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/consecutive_domains.sc b/examples/output_designs/consecutive_domains.sc index 15fe538..4d3647f 100644 --- a/examples/output_designs/consecutive_domains.sc +++ b/examples/output_designs/consecutive_domains.sc @@ -1,24 +1,24 @@ -{ - "version": "0.17.3", - "grid": "square", - "helices": [ - {"max_offset": 100, "grid_position": [0, 0]}, - {"max_offset": 100, "grid_position": [0, 1]} - ], - "strands": [ - { - "color": "#f74308", - "domains": [ - {"helix": 0, "forward": true, "start": 0, "end": 8}, - {"helix": 0, "forward": true, "start": 8, "end": 16} - ] - }, - { - "color": "#57bb00", - "domains": [ - {"helix": 1, "forward": false, "start": 8, "end": 16}, - {"helix": 1, "forward": false, "start": 0, "end": 8} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"max_offset": 100, "grid_position": [0, 0]}, + {"max_offset": 100, "grid_position": [0, 1]} + ], + "strands": [ + { + "color": "#f74308", + "domains": [ + {"helix": 0, "forward": true, "start": 0, "end": 8}, + {"helix": 0, "forward": true, "start": 8, "end": 16} + ] + }, + { + "color": "#57bb00", + "domains": [ + {"helix": 1, "forward": false, "start": 8, "end": 16}, + {"helix": 1, "forward": false, "start": 0, "end": 8} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/domain_colors.sc b/examples/output_designs/domain_colors.sc index c7a36c3..c8b9b4b 100644 --- a/examples/output_designs/domain_colors.sc +++ b/examples/output_designs/domain_colors.sc @@ -1,5 +1,5 @@ { - "version": "0.17.8", + "version": "0.19.0", "grid": "square", "helices": [ {"max_offset": 100, "grid_position": [0, 0]}, diff --git a/examples/output_designs/draw_strand_move_negative.sc b/examples/output_designs/draw_strand_move_negative.sc index 6915678..dd9a2cc 100644 --- a/examples/output_designs/draw_strand_move_negative.sc +++ b/examples/output_designs/draw_strand_move_negative.sc @@ -1,11 +1,10 @@ { - "version": "0.18.2", + "version": "0.19.0", "grid": "square", "helices": [ { "max_offset": 20, "grid_position": [0, 0], - "roll": 282.857142857, "major_ticks": [0, 5, 10, 15, 20] } ], diff --git a/examples/output_designs/empty.sc b/examples/output_designs/empty.sc index b5828bf..49d093e 100644 --- a/examples/output_designs/empty.sc +++ b/examples/output_designs/empty.sc @@ -1,6 +1,6 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [], - "strands": [] +{ + "version": "0.19.0", + "grid": "square", + "helices": [], + "strands": [] } \ No newline at end of file diff --git a/examples/output_designs/extension_and_loopout_oxdna_export.sc b/examples/output_designs/extension_and_loopout_oxdna_export.sc index d8dbb93..45f079a 100644 --- a/examples/output_designs/extension_and_loopout_oxdna_export.sc +++ b/examples/output_designs/extension_and_loopout_oxdna_export.sc @@ -1,22 +1,22 @@ -{ - "version": "0.17.6", - "grid": "square", - "helices": [ - {"max_offset": 32, "grid_position": [0, 0], "roll": 210}, - {"max_offset": 32, "grid_position": [0, 1], "roll": 20}, - {"max_offset": 32, "grid_position": [0, 2], "roll": 210} - ], - "strands": [ - { - "color": "#f74308", - "domains": [ - {"extension_num_bases": 5}, - {"helix": 0, "forward": true, "start": 0, "end": 21}, - {"helix": 1, "forward": false, "start": 0, "end": 21}, - {"loopout": 32}, - {"helix": 2, "forward": true, "start": 0, "end": 21}, - {"extension_num_bases": 7} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"max_offset": 32, "grid_position": [0, 0], "roll": 210}, + {"max_offset": 32, "grid_position": [0, 1], "roll": 20}, + {"max_offset": 32, "grid_position": [0, 2], "roll": 210} + ], + "strands": [ + { + "color": "#f74308", + "domains": [ + {"extension_num_bases": 5}, + {"helix": 0, "forward": true, "start": 0, "end": 21}, + {"helix": 1, "forward": false, "start": 0, "end": 21}, + {"loopout": 32}, + {"helix": 2, "forward": true, "start": 0, "end": 21}, + {"extension_num_bases": 7} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/extensions.sc b/examples/output_designs/extensions.sc index 8525dc6..0619005 100644 --- a/examples/output_designs/extensions.sc +++ b/examples/output_designs/extensions.sc @@ -1,53 +1,53 @@ -{ - "version": "0.17.5", - "grid": "square", - "helices": [ - {"max_offset": 32, "grid_position": [0, 0]}, - {"max_offset": 32, "grid_position": [0, 1]}, - {"max_offset": 32, "grid_position": [0, 2], "roll": 30} - ], - "modifications_in_design": { - "/3Cy3Sp/": { - "display_text": "Cy3", - "idt_text": "/3Cy3Sp/", - "display_connector": false, - "location": "3'" - }, - "/5Cy5/": { - "display_text": "Cy5", - "idt_text": "/5Cy5/", - "display_connector": false, - "location": "5'" - } - }, - "strands": [ - { - "name": "strand1", - "color": "#f74308", - "sequence": "TATTTGGGGGGGGCCCCCCCCTTTGGGGGGGGATAAAAA", - "domains": [ - {"extension_num_bases": 5, "display_length": 2.5, "name": "ext_5p 1"}, - {"name": "domain 1", "helix": 0, "forward": true, "start": 0, "end": 8}, - {"helix": 1, "forward": false, "start": 0, "end": 8}, - {"loopout": 3, "name": "loopout 1"}, - {"helix": 2, "forward": true, "start": 0, "end": 8}, - {"extension_num_bases": 7, "name": "ext_3p 1"} - ], - "5prime_modification": "/5Cy5/", - "3prime_modification": "/3Cy3Sp/" - }, - { - "name": "strand2", - "color": "#57bb00", - "sequence": "ATAAACCCCCCCCGGGGGGGGAAACCCCCCCCTATTTTT", - "domains": [ - {"extension_num_bases": 5, "display_length": 3.5, "display_angle": 60, "name": "ext_5p 2"}, - {"helix": 0, "forward": false, "start": 16, "end": 24}, - {"helix": 1, "forward": true, "start": 16, "end": 24}, - {"loopout": 3}, - {"helix": 2, "forward": false, "start": 16, "end": 24}, - {"extension_num_bases": 7, "name": "ext_3p 2"} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"max_offset": 32, "grid_position": [0, 0]}, + {"max_offset": 32, "grid_position": [0, 1]}, + {"max_offset": 32, "grid_position": [0, 2], "roll": 30} + ], + "modifications_in_design": { + "/3Cy3Sp/": { + "display_text": "Cy3", + "vendor_code": "/3Cy3Sp/", + "display_connector": false, + "location": "3'" + }, + "/5Cy5/": { + "display_text": "Cy5", + "vendor_code": "/5Cy5/", + "display_connector": false, + "location": "5'" + } + }, + "strands": [ + { + "name": "strand1", + "color": "#f74308", + "sequence": "TATTTGGGGGGGGCCCCCCCCTTTGGGGGGGGATAAAAA", + "domains": [ + {"extension_num_bases": 5, "display_length": 2.5, "display_angle": 45, "name": "ext_5p 1"}, + {"name": "domain 1", "helix": 0, "forward": true, "start": 0, "end": 8}, + {"helix": 1, "forward": false, "start": 0, "end": 8}, + {"loopout": 3, "name": "loopout 1"}, + {"helix": 2, "forward": true, "start": 0, "end": 8}, + {"extension_num_bases": 7, "name": "ext_3p 1"} + ], + "5prime_modification": "/5Cy5/", + "3prime_modification": "/3Cy3Sp/" + }, + { + "name": "strand2", + "color": "#57bb00", + "sequence": "ATAAACCCCCCCCGGGGGGGGAAACCCCCCCCTATTTTT", + "domains": [ + {"extension_num_bases": 5, "display_length": 3.5, "display_angle": 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b/examples/output_designs/idt-plates-explicit.sc @@ -1,5 +1,5 @@ { - "version": "0.18.1", + "version": "0.19.0", "grid": "square", "helices": [ {"grid_position": [0, 0]}, @@ -10,7 +10,7 @@ "name": "staple1", "color": "#f74308", "sequence": "TATTATAGTCTTACCCTGAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A1"}, "domains": [ {"helix": 0, "forward": true, "start": 0, "end": 10}, {"helix": 1, "forward": false, "start": 0, "end": 10} @@ -20,7 +20,7 @@ "name": "staple2", "color": "#57bb00", "sequence": "AGAAGCAAAGAATCAGGTCT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B1"}, "domains": [ {"helix": 0, "forward": true, "start": 10, "end": 20}, {"helix": 1, "forward": false, "start": 10, "end": 20} @@ -30,7 +30,7 @@ "name": "staple3", "color": "#888888", "sequence": "CGGATTGCATATAAATCAAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C1"}, "domains": [ {"helix": 0, "forward": true, "start": 20, "end": 30}, {"helix": 1, "forward": false, "start": 20, "end": 30} @@ -40,7 +40,7 @@ "name": "staple4", "color": "#32b86c", "sequence": "CAAAAAGATTGAGAATGACC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D1"}, "domains": [ {"helix": 0, "forward": true, "start": 30, "end": 40}, {"helix": 1, "forward": false, "start": 30, "end": 40} @@ -50,7 +50,7 @@ "name": "staple5", "color": "#333333", "sequence": "AAGAGGAAGCTTCAGAAAAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E1"}, "domains": [ {"helix": 0, "forward": true, "start": 40, "end": 50}, {"helix": 1, "forward": false, "start": 40, "end": 50} @@ -60,7 +60,7 @@ "name": "staple6", "color": "#320096", "sequence": "CCGAAAGACTCTTTAAACAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F1"}, "domains": [ {"helix": 0, "forward": true, "start": 50, "end": 60}, {"helix": 1, "forward": false, "start": 50, "end": 60} @@ -70,7 +70,7 @@ "name": "staple7", "color": "#03b6a2", "sequence": "TCAAATATCGCCCTCAAATG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G1"}, "domains": [ {"helix": 0, "forward": true, "start": 60, "end": 70}, {"helix": 1, "forward": false, "start": 60, "end": 70} @@ -80,7 +80,7 @@ "name": "staple8", "color": "#7300de", "sequence": "CGTTTTAATTCATTGAATCC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H1"}, "domains": [ {"helix": 0, "forward": true, "start": 70, "end": 80}, {"helix": 1, "forward": false, "start": 70, "end": 80} @@ -90,7 +90,7 @@ "name": "staple9", "color": "#aaaa00", "sequence": "CGAGCTTCAACATAAATATT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A2"}, "domains": [ {"helix": 0, "forward": true, "start": 80, "end": 90}, {"helix": 1, "forward": false, "start": 80, "end": 90} @@ -100,7 +100,7 @@ "name": "staple10", "color": "#b8056c", "sequence": "AGCGAACCAGGCGGAATCGT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B2"}, "domains": [ {"helix": 0, "forward": true, "start": 90, "end": 100}, {"helix": 1, "forward": false, "start": 90, "end": 100} @@ -110,7 +110,7 @@ "name": "staple11", "color": "#007200", "sequence": "ACCGGAAGCAGTCCAATACT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C2"}, "domains": [ {"helix": 0, "forward": true, "start": 100, "end": 110}, {"helix": 1, "forward": false, "start": 100, "end": 110} @@ -120,7 +120,7 @@ "name": "staple12", "color": "#cc0000", "sequence": "AACTCCAACAACTGGATAGC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D2"}, "domains": [ {"helix": 0, "forward": true, "start": 110, "end": 120}, {"helix": 1, "forward": false, "start": 110, "end": 120} @@ -130,7 +130,7 @@ "name": "staple13", "color": "#f7931e", "sequence": "GGTCAGGATTAAATGTTTAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E2"}, "domains": [ {"helix": 0, "forward": true, "start": 120, "end": 130}, {"helix": 1, "forward": false, "start": 120, "end": 130} @@ -140,7 +140,7 @@ "name": "staple14", "color": "#f74308", "sequence": "AGAGAGTACCGGTAATAGTA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F2"}, "domains": [ {"helix": 0, "forward": true, "start": 130, "end": 140}, {"helix": 1, "forward": false, "start": 130, "end": 140} @@ -150,7 +150,7 @@ "name": "staple15", "color": "#57bb00", "sequence": "TTTAATTGCTTGCCAGAGGG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G2"}, "domains": [ {"helix": 0, "forward": true, "start": 140, "end": 150}, {"helix": 1, "forward": false, "start": 140, "end": 150} @@ -160,7 +160,7 @@ "name": "staple16", "color": "#888888", "sequence": "CCTTTTGATAAAAGAAGTTT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H2"}, "domains": [ {"helix": 0, "forward": true, "start": 150, "end": 160}, {"helix": 1, "forward": false, "start": 150, "end": 160} @@ -170,7 +170,7 @@ "name": "staple17", "color": "#32b86c", "sequence": "AGAGGTCATTGGCTTTTGCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A3"}, "domains": [ {"helix": 0, "forward": true, "start": 160, "end": 170}, {"helix": 1, "forward": false, "start": 160, "end": 170} @@ -180,7 +180,7 @@ "name": "staple18", "color": "#333333", "sequence": "TTTGCGGATGAATAGCGAGA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B3"}, "domains": [ {"helix": 0, "forward": true, "start": 170, "end": 180}, {"helix": 1, "forward": false, "start": 170, "end": 180} @@ -190,7 +190,7 @@ "name": "staple19", "color": "#320096", "sequence": "GCTTAGAGCTTAAAAACCAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C3"}, "domains": [ {"helix": 0, "forward": true, "start": 180, "end": 190}, {"helix": 1, "forward": false, "start": 180, "end": 190} @@ -200,7 +200,7 @@ "name": "staple20", "color": "#03b6a2", "sequence": "TAATTGCTGACAGACGACGA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D3"}, "domains": [ {"helix": 0, "forward": true, "start": 190, "end": 200}, {"helix": 1, "forward": false, "start": 190, "end": 200} @@ -210,7 +210,7 @@ "name": "staple21", "color": "#7300de", "sequence": "ATATAATGCTCCTCGTTTAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E3"}, "domains": [ {"helix": 0, "forward": true, "start": 200, "end": 210}, {"helix": 1, "forward": false, "start": 200, "end": 210} @@ -220,7 +220,7 @@ "name": "staple22", "color": "#aaaa00", "sequence": "GTAGCTCAACCTATCATAAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F3"}, "domains": [ {"helix": 0, "forward": true, "start": 210, "end": 220}, {"helix": 1, "forward": false, "start": 210, "end": 220} @@ -230,7 +230,7 @@ "name": "staple23", "color": "#b8056c", "sequence": "ATGTTTTAAAAAGAGCAACA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G3"}, "domains": [ {"helix": 0, "forward": true, "start": 220, "end": 230}, {"helix": 1, "forward": false, "start": 220, "end": 230} @@ -240,7 +240,7 @@ "name": "staple24", "color": "#007200", "sequence": "TATGCAACTAGAGGCATAGT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H3"}, "domains": [ {"helix": 0, "forward": true, "start": 230, "end": 240}, {"helix": 1, "forward": false, "start": 230, "end": 240} @@ -250,7 +250,7 @@ "name": "staple25", "color": "#cc0000", "sequence": "AAGTACGGTGAAGGAATTAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A4"}, "domains": [ {"helix": 0, "forward": true, "start": 240, "end": 250}, {"helix": 1, "forward": false, "start": 240, "end": 250} @@ -260,7 +260,7 @@ "name": "staple26", "color": "#f7931e", "sequence": "TCTGGAAGTTATAACGCCAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B4"}, "domains": [ {"helix": 0, "forward": true, "start": 250, "end": 260}, {"helix": 1, "forward": false, "start": 250, "end": 260} @@ -270,7 +270,7 @@ "name": "staple27", "color": "#f74308", "sequence": "TCATTCCATAATGCAGATAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C4"}, "domains": [ {"helix": 0, "forward": true, "start": 260, "end": 270}, {"helix": 1, "forward": false, "start": 260, "end": 270} @@ -280,7 +280,7 @@ "name": "staple28", "color": "#57bb00", "sequence": "TAACAGTTGACATTCAACTA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D4"}, "domains": [ {"helix": 0, "forward": true, "start": 270, "end": 280}, {"helix": 1, "forward": false, "start": 270, "end": 280} @@ -290,7 +290,7 @@ "name": "staple29", "color": "#888888", "sequence": "TTCCCAATTCAGGAATACCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E4"}, "domains": [ {"helix": 0, "forward": true, "start": 280, "end": 290}, {"helix": 1, "forward": false, "start": 280, "end": 290} @@ -300,7 +300,7 @@ "name": "staple30", "color": "#32b86c", "sequence": "TGCGAACGAGGTTGAGATTT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F4"}, "domains": [ {"helix": 0, "forward": true, "start": 290, "end": 300}, {"helix": 1, "forward": false, "start": 290, "end": 300} @@ -310,7 +310,7 @@ "name": "staple31", "color": "#333333", "sequence": "TAGATTTAGTAGATTCATCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G4"}, "domains": [ {"helix": 0, "forward": true, "start": 300, "end": 310}, {"helix": 1, "forward": false, "start": 300, "end": 310} @@ -320,7 +320,7 @@ "name": "staple32", "color": "#320096", "sequence": "TTGACCATTAACAGGTAGAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H4"}, "domains": [ {"helix": 0, "forward": true, "start": 310, "end": 320}, {"helix": 1, "forward": false, "start": 310, "end": 320} @@ -330,7 +330,7 @@ "name": "staple33", "color": "#03b6a2", "sequence": "GATACATTTCCAACATTATT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A5"}, "domains": [ {"helix": 0, "forward": true, "start": 320, "end": 330}, {"helix": 1, "forward": false, "start": 320, "end": 330} @@ -340,7 +340,7 @@ "name": "staple34", "color": "#7300de", "sequence": "GCAAATGGTCACTAACGGAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B5"}, "domains": [ {"helix": 0, "forward": true, "start": 330, "end": 340}, {"helix": 1, "forward": false, "start": 330, "end": 340} @@ -350,7 +350,7 @@ "name": "staple35", "color": "#aaaa00", "sequence": "AATAACCTGTAATAAAACGA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C5"}, "domains": [ {"helix": 0, "forward": true, "start": 340, "end": 350}, {"helix": 1, "forward": false, "start": 340, "end": 350} @@ -360,7 +360,7 @@ "name": "staple36", "color": "#b8056c", "sequence": "TTAGCTATATAATCTACGTT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D5"}, "domains": [ {"helix": 0, "forward": true, "start": 350, "end": 360}, {"helix": 1, "forward": false, "start": 350, "end": 360} @@ -370,7 +370,7 @@ "name": "staple37", "color": "#007200", "sequence": "TTTCATTTGGTGGGAAGAAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E5"}, "domains": [ {"helix": 0, "forward": true, "start": 360, "end": 370}, {"helix": 1, "forward": false, "start": 360, "end": 370} @@ -380,7 +380,7 @@ "name": "staple38", "color": "#cc0000", "sequence": "GGCGCGAGCTGTCAGGACGT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F5"}, "domains": [ {"helix": 0, "forward": true, "start": 370, "end": 380}, {"helix": 1, "forward": false, "start": 370, "end": 380} @@ -390,7 +390,7 @@ "name": "staple39", "color": "#f7931e", "sequence": "GAAAAGGTGGCATTATACCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G5"}, "domains": [ {"helix": 0, "forward": true, "start": 380, "end": 390}, {"helix": 1, "forward": false, "start": 380, "end": 390} @@ -400,7 +400,7 @@ "name": "staple40", "color": "#f74308", "sequence": "CATCAATTCTAGAACTGGCT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H5"}, "domains": [ {"helix": 0, "forward": true, "start": 390, "end": 400}, {"helix": 1, "forward": false, "start": 390, "end": 400} @@ -410,7 +410,7 @@ "name": "staple41", "color": "#57bb00", "sequence": "ACTAATAGTATGCGATTTTA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A6"}, "domains": [ {"helix": 0, "forward": true, "start": 400, "end": 410}, {"helix": 1, "forward": false, "start": 400, "end": 410} @@ -420,7 +420,7 @@ "name": "staple42", "color": "#888888", "sequence": "GTAGCATTAAAATTACCTTA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B6"}, "domains": [ {"helix": 0, "forward": true, "start": 410, "end": 420}, {"helix": 1, "forward": false, "start": 410, "end": 420} @@ -430,7 +430,7 @@ "name": "staple43", "color": "#32b86c", "sequence": "CATCCAATAAAATCATTGTG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C6"}, "domains": [ {"helix": 0, "forward": true, "start": 420, "end": 430}, {"helix": 1, "forward": false, "start": 420, "end": 430} @@ -440,7 +440,7 @@ "name": "staple44", "color": "#333333", "sequence": "ATCATACAGGTTTCAACTTT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D6"}, "domains": [ {"helix": 0, "forward": true, "start": 430, "end": 440}, {"helix": 1, "forward": false, "start": 430, "end": 440} @@ -450,7 +450,7 @@ "name": "staple45", "color": "#320096", "sequence": "CAAGGCAAAGGATGGTTTAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E6"}, "domains": [ {"helix": 0, "forward": true, "start": 440, "end": 450}, {"helix": 1, "forward": false, "start": 440, "end": 450} @@ -460,7 +460,7 @@ "name": "staple46", "color": "#03b6a2", "sequence": "AATTAGCAAATTGGGCTTGA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F6"}, "domains": [ {"helix": 0, "forward": true, "start": 450, "end": 460}, {"helix": 1, "forward": false, "start": 450, "end": 460} @@ -470,7 +470,7 @@ "name": "staple47", "color": "#7300de", "sequence": "ATTAAGCAATGAGTAGTAAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G6"}, "domains": [ {"helix": 0, "forward": true, "start": 460, "end": 470}, {"helix": 1, "forward": false, "start": 460, "end": 470} @@ -480,7 +480,7 @@ "name": "staple48", "color": "#aaaa00", "sequence": "AAAGCCTCAGACACCAGAAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H6"}, "domains": [ {"helix": 0, "forward": true, "start": 470, "end": 480}, {"helix": 1, "forward": false, "start": 470, "end": 480} @@ -490,7 +490,7 @@ "name": "staple49", "color": "#b8056c", "sequence": "AGCATAAAGCCTGACGAGAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A7"}, "domains": [ {"helix": 0, "forward": true, "start": 480, "end": 490}, {"helix": 1, "forward": false, "start": 480, "end": 490} @@ -500,7 +500,7 @@ "name": "staple50", "color": "#007200", "sequence": "TAAATCGGTTAAGGCTTGCC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B7"}, "domains": [ {"helix": 0, "forward": true, "start": 490, "end": 500}, {"helix": 1, "forward": false, "start": 490, "end": 500} @@ -510,7 +510,7 @@ "name": "staple51", "color": "#cc0000", "sequence": "GTACCAAAAATTCAGTGAAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C7"}, "domains": [ {"helix": 0, "forward": true, "start": 500, "end": 510}, {"helix": 1, "forward": false, "start": 500, "end": 510} @@ -520,7 +520,7 @@ "name": "staple52", "color": "#f7931e", "sequence": "CATTATGACCAAGCTGCTCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D7"}, "domains": [ {"helix": 0, "forward": true, "start": 510, "end": 520}, {"helix": 1, "forward": false, "start": 510, "end": 520} @@ -530,7 +530,7 @@ "name": "staple53", "color": "#f74308", "sequence": "CTGTAATACTCAACGTAACA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E7"}, "domains": [ {"helix": 0, "forward": true, "start": 520, "end": 530}, {"helix": 1, "forward": false, "start": 520, "end": 530} @@ -540,7 +540,7 @@ "name": "staple54", "color": "#57bb00", "sequence": "TTTGCGGGAGTTACCCAAAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F7"}, "domains": [ {"helix": 0, "forward": true, "start": 530, "end": 540}, {"helix": 1, "forward": false, "start": 530, "end": 540} @@ -550,7 +550,7 @@ "name": "staple55", "color": "#888888", "sequence": "AAGCCTTTATCGGATATTCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G7"}, "domains": [ {"helix": 0, "forward": true, "start": 540, "end": 550}, {"helix": 1, "forward": false, "start": 540, "end": 550} @@ -560,7 +560,7 @@ "name": "staple56", "color": "#32b86c", "sequence": "TTCAACGCAATGACAAGAAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H7"}, "domains": [ {"helix": 0, "forward": true, "start": 550, "end": 560}, {"helix": 1, "forward": false, "start": 550, "end": 560} @@ -570,7 +570,7 @@ "name": "staple57", "color": "#333333", "sequence": "GGATAAAAATAGAGTAATCT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A8"}, "domains": [ {"helix": 0, "forward": true, "start": 560, "end": 570}, {"helix": 1, "forward": false, "start": 560, "end": 570} @@ -580,7 +580,7 @@ "name": "staple58", "color": "#320096", "sequence": "TTTTAGAACCACCTTCATCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B8"}, "domains": [ {"helix": 0, "forward": true, "start": 570, "end": 580}, {"helix": 1, "forward": false, "start": 570, "end": 580} @@ -590,7 +590,7 @@ "name": "staple59", "color": "#03b6a2", "sequence": "CTCATATATTAGGCTGGCTG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C8"}, "domains": [ {"helix": 0, "forward": true, "start": 580, "end": 590}, {"helix": 1, "forward": false, "start": 580, "end": 590} @@ -600,7 +600,7 @@ "name": "staple60", "color": "#7300de", "sequence": "TTAAATGCAACCAGGCGCAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D8"}, "domains": [ {"helix": 0, "forward": true, "start": 590, "end": 600}, {"helix": 1, "forward": false, "start": 590, "end": 600} @@ -610,7 +610,7 @@ "name": "staple61", "color": "#aaaa00", "sequence": "TGCCTGAGTAGGTGTACAGA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E8"}, "domains": [ {"helix": 0, "forward": true, "start": 600, "end": 610}, {"helix": 1, "forward": false, "start": 600, "end": 610} @@ -620,7 +620,7 @@ "name": "staple62", "color": "#b8056c", "sequence": "ATGTGTAGGTACAGATGAAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F8"}, "domains": [ {"helix": 0, "forward": true, "start": 610, "end": 620}, {"helix": 1, "forward": false, "start": 610, "end": 620} @@ -630,7 +630,7 @@ "name": "staple63", "color": "#007200", "sequence": "AAAGATTCAATTGAAAGAGG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G8"}, "domains": [ {"helix": 0, "forward": true, "start": 620, "end": 630}, {"helix": 1, "forward": false, "start": 620, "end": 630} @@ -640,7 +640,7 @@ "name": "staple64", "color": "#cc0000", "sequence": "AAGGGTGAGACTGACCAACT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H8"}, "domains": [ {"helix": 0, "forward": true, "start": 630, "end": 640}, {"helix": 1, "forward": false, "start": 630, "end": 640} @@ -650,7 +650,7 @@ "name": "staple65", "color": "#f7931e", "sequence": "AAGGCCGGAGGGGAACCGAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A9"}, "domains": [ {"helix": 0, "forward": true, "start": 640, "end": 650}, {"helix": 1, "forward": false, "start": 640, "end": 650} @@ -660,7 +660,7 @@ "name": "staple66", "color": "#f74308", "sequence": "ACAGTCAAATTCAATCATAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B9"}, "domains": [ {"helix": 0, "forward": true, "start": 650, "end": 660}, {"helix": 1, "forward": false, "start": 650, "end": 660} @@ -670,7 +670,7 @@ "name": "staple67", "color": "#57bb00", "sequence": "CACCATCAATGCGCAGACGG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C9"}, "domains": [ {"helix": 0, "forward": true, "start": 660, "end": 670}, {"helix": 1, "forward": false, "start": 660, "end": 670} @@ -680,7 +680,7 @@ "name": "staple68", "color": "#888888", "sequence": "ATGATATTCACCGGAACGAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D9"}, "domains": [ {"helix": 0, "forward": true, "start": 670, "end": 680}, {"helix": 1, "forward": false, "start": 670, "end": 680} @@ -690,7 +690,7 @@ "name": "staple69", "color": "#32b86c", "sequence": "ACCGTTCTAGTGTTACTTAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E9"}, "domains": [ {"helix": 0, "forward": true, "start": 680, "end": 690}, {"helix": 1, "forward": false, "start": 680, "end": 690} @@ -700,7 +700,7 @@ "name": "staple70", "color": "#333333", "sequence": "CTGATAAATTACCTGCTCCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F9"}, "domains": [ {"helix": 0, "forward": true, "start": 690, "end": 700}, {"helix": 1, "forward": false, "start": 690, "end": 700} @@ -710,7 +710,7 @@ "name": "staple71", "color": "#320096", "sequence": "AATGCCGGAGGAAATCCGCG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G9"}, "domains": [ {"helix": 0, "forward": true, "start": 700, "end": 710}, {"helix": 1, "forward": false, "start": 700, "end": 710} @@ -720,7 +720,7 @@ "name": "staple72", "color": "#03b6a2", "sequence": "AGGGTAGCTAAAATTGTGTC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H9"}, "domains": [ {"helix": 0, "forward": true, "start": 710, "end": 720}, {"helix": 1, "forward": false, "start": 710, "end": 720} @@ -730,7 +730,7 @@ "name": "staple73", "color": "#7300de", "sequence": "TTTTTGAGAGATCGCCTGAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A10"}, "domains": [ {"helix": 0, "forward": true, "start": 720, "end": 730}, {"helix": 1, "forward": false, "start": 720, "end": 730} @@ -740,7 +740,7 @@ "name": "staple74", "color": "#aaaa00", "sequence": "ATCTACAAAGGATTTGTATC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B10"}, "domains": [ {"helix": 0, "forward": true, "start": 730, "end": 740}, {"helix": 1, "forward": false, "start": 730, "end": 740} @@ -750,7 +750,7 @@ "name": "staple75", "color": "#b8056c", "sequence": "GCTATCAGGTGTACAACGGA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C10"}, "domains": [ {"helix": 0, "forward": true, "start": 740, "end": 750}, {"helix": 1, "forward": false, "start": 740, "end": 750} @@ -760,7 +760,7 @@ "name": "staple76", "color": "#007200", "sequence": "CATTGCCTGAGCGAAACAAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D10"}, "domains": [ {"helix": 0, "forward": true, "start": 750, "end": 760}, {"helix": 1, "forward": false, "start": 750, "end": 760} @@ -770,7 +770,7 @@ "name": "staple77", "color": "#cc0000", "sequence": "GAGTCTGGAGTATACCAAGC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E10"}, "domains": [ {"helix": 0, "forward": true, "start": 760, "end": 770}, {"helix": 1, "forward": false, "start": 760, "end": 770} @@ -780,7 +780,7 @@ "name": "staple78", "color": "#f7931e", "sequence": "CAAACAAGAGCCCCAGCGAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F10"}, "domains": [ {"helix": 0, "forward": true, "start": 770, "end": 780}, {"helix": 1, "forward": false, "start": 770, "end": 780} @@ -790,7 +790,7 @@ "name": "staple79", "color": "#f74308", "sequence": "AATCGATGAACATCTTTGAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G10"}, "domains": [ {"helix": 0, "forward": true, "start": 780, "end": 790}, {"helix": 1, "forward": false, "start": 780, "end": 790} @@ -800,7 +800,7 @@ "name": "staple80", "color": "#57bb00", "sequence": "CGGTAATCGTCTAAAACACT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H10"}, "domains": [ {"helix": 0, "forward": true, "start": 790, "end": 800}, {"helix": 1, "forward": false, "start": 790, "end": 800} @@ -810,7 +810,7 @@ "name": "staple81", "color": "#888888", "sequence": "AAAACTAGCAAAAGAATACA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A11"}, "domains": [ {"helix": 0, "forward": true, "start": 800, "end": 810}, {"helix": 1, "forward": false, "start": 800, "end": 810} @@ -820,7 +820,7 @@ "name": "staple82", "color": "#32b86c", "sequence": "TGTCAATCATGAAAGAGGCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B11"}, "domains": [ {"helix": 0, "forward": true, "start": 810, "end": 820}, {"helix": 1, "forward": false, "start": 810, "end": 820} @@ -830,7 +830,7 @@ "name": "staple83", "color": "#333333", "sequence": "ATGTACCCCGAACCTAAAAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C11"}, "domains": [ {"helix": 0, "forward": true, "start": 820, "end": 830}, {"helix": 1, "forward": false, "start": 820, "end": 830} @@ -840,7 +840,7 @@ "name": "staple84", "color": "#320096", "sequence": "GTTGATAATCCGAAGGCACC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D11"}, "domains": [ {"helix": 0, "forward": true, "start": 830, "end": 840}, {"helix": 1, "forward": false, "start": 830, "end": 840} @@ -850,7 +850,7 @@ "name": "staple85", "color": "#03b6a2", "sequence": "AGAAAAGCCCAATGCCACTA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E11"}, "domains": [ {"helix": 0, "forward": true, "start": 840, "end": 850}, {"helix": 1, "forward": false, "start": 840, "end": 850} @@ -860,7 +860,7 @@ "name": "staple86", "color": "#7300de", "sequence": "CAAAAACAGGTAAAATACGT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F11"}, "domains": [ {"helix": 0, "forward": true, "start": 850, "end": 860}, {"helix": 1, "forward": false, "start": 850, "end": 860} @@ -870,7 +870,7 @@ "name": "staple87", "color": "#aaaa00", "sequence": "AAGATTGTATATTAAACGGG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G11"}, "domains": [ {"helix": 0, "forward": true, "start": 860, "end": 870}, {"helix": 1, "forward": false, "start": 860, "end": 870} @@ -880,7 +880,7 @@ "name": "staple88", "color": "#b8056c", "sequence": "AAGCAAATATGGAAGTTTCC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H11"}, "domains": [ {"helix": 0, "forward": true, "start": 870, "end": 880}, {"helix": 1, "forward": false, "start": 870, "end": 880} @@ -890,7 +890,7 @@ "name": "staple89", "color": "#007200", "sequence": "TTAAATTGTATTTTTCATGA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "A12"}, "domains": [ {"helix": 0, "forward": true, "start": 880, "end": 890}, {"helix": 1, "forward": false, "start": 880, "end": 890} @@ -900,7 +900,7 @@ "name": "staple90", "color": "#cc0000", "sequence": "AACGTTAATAGACTAAAGAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "B12"}, "domains": [ {"helix": 0, "forward": true, "start": 890, "end": 900}, {"helix": 1, "forward": false, "start": 890, "end": 900} @@ -910,7 +910,7 @@ "name": "staple91", "color": "#f7931e", "sequence": "TTTTGTTAAAAGGCTTTGAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "C12"}, "domains": [ {"helix": 0, "forward": true, "start": 900, "end": 910}, {"helix": 1, "forward": false, "start": 900, "end": 910} @@ -920,7 +920,7 @@ "name": "staple92", "color": "#f74308", "sequence": "ATTCGCATTAACGGCTACAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "D12"}, "domains": [ {"helix": 0, "forward": true, "start": 910, "end": 920}, {"helix": 1, "forward": false, "start": 910, "end": 920} @@ -930,7 +930,7 @@ "name": "staple93", "color": "#57bb00", "sequence": "AATTTTTGTTGAGGGTAGCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "E12"}, "domains": [ {"helix": 0, "forward": true, "start": 920, "end": 930}, {"helix": 1, "forward": false, "start": 920, "end": 930} @@ -940,7 +940,7 @@ "name": "staple94", "color": "#888888", "sequence": "AAATCAGCTCGCATCGGAAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "F12"}, "domains": [ {"helix": 0, "forward": true, "start": 930, "end": 940}, {"helix": 1, "forward": false, "start": 930, "end": 940} @@ -950,7 +950,7 @@ "name": "staple95", "color": "#32b86c", "sequence": "ATTTTTTAACGCGAAAGACA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "G12"}, "domains": [ {"helix": 0, "forward": true, "start": 940, "end": 950}, {"helix": 1, "forward": false, "start": 940, "end": 950} @@ -960,7 +960,7 @@ "name": "staple96", "color": "#333333", "sequence": "CAATAGGAACACCCTCAGCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate1", "well": "H12"}, "domains": [ {"helix": 0, "forward": true, "start": 950, "end": 960}, {"helix": 1, "forward": false, "start": 950, "end": 960} @@ -970,7 +970,7 @@ "name": "staple97", "color": "#320096", "sequence": "GCCATCAAAACGGGATCGTC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A1"}, "domains": [ {"helix": 0, "forward": true, "start": 960, "end": 970}, {"helix": 1, "forward": false, "start": 960, "end": 970} @@ -980,7 +980,7 @@ "name": "staple98", "color": "#03b6a2", "sequence": "ATAATTCGCGGCCGCTTTTG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B1"}, "domains": [ {"helix": 0, "forward": true, "start": 970, "end": 980}, {"helix": 1, "forward": false, "start": 970, "end": 980} @@ -990,7 +990,7 @@ "name": "staple99", "color": "#7300de", "sequence": "TCTGGCCTTCGGAGTTAAAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C1"}, "domains": [ {"helix": 0, "forward": true, "start": 980, "end": 990}, {"helix": 1, "forward": false, "start": 980, "end": 990} @@ -1000,7 +1000,7 @@ "name": "staple100", "color": "#aaaa00", "sequence": "CTGTAGCCAGAGGCTTGCAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D1"}, "domains": [ {"helix": 0, "forward": true, "start": 990, "end": 1000}, {"helix": 1, "forward": false, "start": 990, "end": 1000} @@ -1010,7 +1010,7 @@ "name": "staple101", "color": "#b8056c", "sequence": "CTTTCATCAATCGGTCGCTG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E1"}, "domains": [ {"helix": 0, "forward": true, "start": 1000, "end": 1010}, {"helix": 1, "forward": false, "start": 1000, "end": 1010} @@ -1020,7 +1020,7 @@ "name": "staple102", "color": "#007200", "sequence": "CATTAAATGTACCGATATAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F1"}, "domains": [ {"helix": 0, "forward": true, "start": 1010, "end": 1020}, {"helix": 1, "forward": false, "start": 1010, "end": 1020} @@ -1030,7 +1030,7 @@ "name": "staple103", "color": "#cc0000", "sequence": "GAGCGAGTAACCCACGCATA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G1"}, "domains": [ {"helix": 0, "forward": true, "start": 1020, "end": 1030}, {"helix": 1, "forward": false, "start": 1020, "end": 1030} @@ -1040,7 +1040,7 @@ "name": "staple104", "color": "#f7931e", "sequence": "CAACCCGTCGACAACCATCG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H1"}, "domains": [ {"helix": 0, "forward": true, "start": 1030, "end": 1040}, {"helix": 1, "forward": false, "start": 1030, "end": 1040} @@ -1050,7 +1050,7 @@ "name": "staple105", "color": "#f74308", "sequence": "GATTCTCCGTGACAATGACA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A2"}, "domains": [ {"helix": 0, "forward": true, "start": 1040, "end": 1050}, {"helix": 1, "forward": false, "start": 1040, "end": 1050} @@ -1060,7 +1060,7 @@ "name": "staple106", "color": "#57bb00", "sequence": "GGGAACAAACTAGTTGCGCC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B2"}, "domains": [ {"helix": 0, "forward": true, "start": 1050, "end": 1060}, {"helix": 1, "forward": false, "start": 1050, "end": 1060} @@ -1070,7 +1070,7 @@ "name": "staple107", "color": "#888888", "sequence": "GGCGGATTGATTGATACCGA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C2"}, "domains": [ {"helix": 0, "forward": true, "start": 1060, "end": 1070}, {"helix": 1, "forward": false, "start": 1060, "end": 1070} @@ -1080,7 +1080,7 @@ "name": "staple108", "color": "#32b86c", "sequence": "CCGTAATGGGCTTAAACAGC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D2"}, "domains": [ {"helix": 0, "forward": true, "start": 1070, "end": 1080}, {"helix": 1, "forward": false, "start": 1070, "end": 1080} @@ -1090,7 +1090,7 @@ "name": "staple109", "color": "#333333", "sequence": "ATAGGTCACGAGGTGAATTT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E2"}, "domains": [ {"helix": 0, "forward": true, "start": 1080, "end": 1090}, {"helix": 1, "forward": false, "start": 1080, "end": 1090} @@ -1100,7 +1100,7 @@ "name": "staple110", "color": "#320096", "sequence": "TTGGTGTAGACTTGCTTTCG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F2"}, "domains": [ {"helix": 0, "forward": true, "start": 1090, "end": 1100}, {"helix": 1, "forward": false, "start": 1090, "end": 1100} @@ -1110,7 +1110,7 @@ "name": "staple111", "color": "#03b6a2", "sequence": "TGGGCGCATCGGTTTATCAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G2"}, "domains": [ {"helix": 0, "forward": true, "start": 1100, "end": 1110}, {"helix": 1, "forward": false, "start": 1100, "end": 1110} @@ -1120,7 +1120,7 @@ "name": "staple112", "color": "#7300de", "sequence": "GTAACCGTGCTAATTGTATC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H2"}, "domains": [ {"helix": 0, "forward": true, "start": 1110, "end": 1120}, {"helix": 1, "forward": false, "start": 1110, "end": 1120} @@ -1130,7 +1130,7 @@ "name": "staple113", "color": "#aaaa00", "sequence": "ATCTGCCAGTAAGGAGCCTT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A3"}, "domains": [ {"helix": 0, "forward": true, "start": 1120, "end": 1130}, {"helix": 1, "forward": false, "start": 1120, "end": 1130} @@ -1140,7 +1140,7 @@ "name": "staple114", "color": "#b8056c", "sequence": "TTGAGGGGACAAGGCTCCAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B3"}, "domains": [ {"helix": 0, "forward": true, "start": 1130, "end": 1140}, {"helix": 1, "forward": false, "start": 1130, "end": 1140} @@ -1150,7 +1150,7 @@ "name": "staple115", "color": "#007200", "sequence": "GACGACAGTACTCCAAAAAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C3"}, "domains": [ {"helix": 0, "forward": true, "start": 1140, "end": 1150}, {"helix": 1, "forward": false, "start": 1140, "end": 1150} @@ -1160,7 +1160,7 @@ "name": "staple116", "color": "#cc0000", "sequence": "TCGGCCTCAGCGTTGAAAAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D3"}, "domains": [ {"helix": 0, "forward": true, "start": 1150, "end": 1160}, {"helix": 1, "forward": false, "start": 1150, "end": 1160} @@ -1170,7 +1170,7 @@ "name": "staple117", "color": "#f7931e", "sequence": "GAAGATCGCAAATTTTTTCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E3"}, "domains": [ {"helix": 0, "forward": true, "start": 1160, "end": 1170}, {"helix": 1, "forward": false, "start": 1160, "end": 1170} @@ -1180,7 +1180,7 @@ "name": "staple118", "color": "#f74308", "sequence": "CTCCAGCCAGTGCGAATAAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F3"}, "domains": [ {"helix": 0, "forward": true, "start": 1170, "end": 1180}, {"helix": 1, "forward": false, "start": 1170, "end": 1180} @@ -1190,7 +1190,7 @@ "name": "staple119", "color": "#57bb00", "sequence": "CTTTCCGGCACTAAAGGAAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G3"}, "domains": [ {"helix": 0, "forward": true, "start": 1180, "end": 1190}, {"helix": 1, "forward": false, "start": 1180, "end": 1190} @@ -1200,7 +1200,7 @@ "name": "staple120", "color": "#888888", "sequence": "CCGCTTCTGGAAAGGAACAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H3"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H3"}, "domains": [ {"helix": 0, "forward": true, "start": 1190, "end": 1200}, {"helix": 1, "forward": false, "start": 1190, "end": 1200} @@ -1210,7 +1210,7 @@ "name": "staple121", "color": "#32b86c", "sequence": "TGCCGGAAACGTGAGAATAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A4"}, "domains": [ {"helix": 0, "forward": true, "start": 1200, "end": 1210}, {"helix": 1, "forward": false, "start": 1200, "end": 1210} @@ -1220,7 +1220,7 @@ "name": "staple122", "color": "#333333", "sequence": "CAGGCAAAGCTTTCAGCGGA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B4"}, "domains": [ {"helix": 0, "forward": true, "start": 1210, "end": 1220}, {"helix": 1, "forward": false, "start": 1210, "end": 1220} @@ -1230,7 +1230,7 @@ "name": "staple123", "color": "#320096", "sequence": "GCCATTCGCCCTTTCAACAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C4"}, "domains": [ {"helix": 0, "forward": true, "start": 1220, "end": 1230}, {"helix": 1, "forward": false, "start": 1220, "end": 1230} @@ -1240,7 +1240,7 @@ "name": "staple124", "color": "#03b6a2", "sequence": "ATTCAGGCTGTGCTAAACAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D4"}, "domains": [ {"helix": 0, "forward": true, "start": 1230, "end": 1240}, {"helix": 1, "forward": false, "start": 1230, "end": 1240} @@ -1250,7 +1250,7 @@ "name": "staple125", "color": "#7300de", "sequence": "CGCAACTGTTTATGGGATTT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E4"}, "domains": [ {"helix": 0, "forward": true, "start": 1240, "end": 1250}, {"helix": 1, "forward": false, "start": 1240, "end": 1250} @@ -1260,7 +1260,7 @@ "name": "staple126", "color": "#aaaa00", "sequence": "GGGAAGGGCGGAATTTTCTG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F4"}, "domains": [ {"helix": 0, "forward": true, "start": 1250, "end": 1260}, {"helix": 1, "forward": false, "start": 1250, "end": 1260} @@ -1270,7 +1270,7 @@ "name": "staple127", "color": "#b8056c", "sequence": "ATCGGTGCGGGTTAGTAAAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G4"}, "domains": [ {"helix": 0, "forward": true, "start": 1260, "end": 1270}, {"helix": 1, "forward": false, "start": 1260, "end": 1270} @@ -1280,7 +1280,7 @@ "name": "staple128", "color": "#007200", "sequence": "GCCTCTTCGCCTTTCCAGAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H4"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H4"}, "domains": [ {"helix": 0, "forward": true, "start": 1270, "end": 1280}, {"helix": 1, "forward": false, "start": 1270, "end": 1280} @@ -1290,7 +1290,7 @@ "name": "staple129", "color": "#cc0000", "sequence": "TATTACGCCAGTTTTGTCGT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A5"}, "domains": [ {"helix": 0, "forward": true, "start": 1280, "end": 1290}, {"helix": 1, "forward": false, "start": 1280, "end": 1290} @@ -1300,7 +1300,7 @@ "name": "staple130", "color": "#f7931e", "sequence": "GCTGGCGAAAACGATCTAAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B5"}, "domains": [ {"helix": 0, "forward": true, "start": 1290, "end": 1300}, {"helix": 1, "forward": false, "start": 1290, "end": 1300} @@ -1310,7 +1310,7 @@ "name": "staple131", "color": "#f74308", "sequence": "GGGGGATGTGAGTTAGCGTA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C5"}, "domains": [ {"helix": 0, "forward": true, "start": 1300, "end": 1310}, {"helix": 1, "forward": false, "start": 1300, "end": 1310} @@ -1320,7 +1320,7 @@ "name": "staple132", "color": "#57bb00", "sequence": "CTGCAAGGCGCAGCCCTCAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D5"}, "domains": [ {"helix": 0, "forward": true, "start": 1310, "end": 1320}, {"helix": 1, "forward": false, "start": 1310, "end": 1320} @@ -1330,7 +1330,7 @@ "name": "staple133", "color": "#888888", "sequence": "ATTAAGTTGGATTCCACAGA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E5"}, "domains": [ {"helix": 0, "forward": true, "start": 1320, "end": 1330}, {"helix": 1, "forward": false, "start": 1320, "end": 1330} @@ -1340,7 +1340,7 @@ "name": "staple134", "color": "#32b86c", "sequence": "GTAACGCCAGCGCCTGTAGC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F5"}, "domains": [ {"helix": 0, "forward": true, "start": 1330, "end": 1340}, {"helix": 1, "forward": false, "start": 1330, "end": 1340} @@ -1350,7 +1350,7 @@ "name": "staple135", "color": "#333333", "sequence": "GGTTTTCCCACAAACTACAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G5"}, "domains": [ {"helix": 0, "forward": true, "start": 1340, "end": 1350}, {"helix": 1, "forward": false, "start": 1340, "end": 1350} @@ -1360,7 +1360,7 @@ "name": "staple136", "color": "#320096", "sequence": "GTCACGACGTGTCACCAGTA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H5"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H5"}, "domains": [ {"helix": 0, "forward": true, "start": 1350, "end": 1360}, {"helix": 1, "forward": false, "start": 1350, "end": 1360} @@ -1370,7 +1370,7 @@ "name": "staple137", "color": "#03b6a2", "sequence": "TGTAAAACGAACTGAGTTTC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A6"}, "domains": [ {"helix": 0, "forward": true, "start": 1360, "end": 1370}, {"helix": 1, "forward": false, "start": 1360, "end": 1370} @@ -1380,7 +1380,7 @@ "name": "staple138", "color": "#7300de", "sequence": "CGGCCAGTGCGTACCGTAAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B6"}, "domains": [ {"helix": 0, "forward": true, "start": 1370, "end": 1380}, {"helix": 1, "forward": false, "start": 1370, "end": 1380} @@ -1390,7 +1390,7 @@ "name": "staple139", "color": "#aaaa00", "sequence": "CAAGCTTGCAAGGAACCCAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C6"}, "domains": [ {"helix": 0, "forward": true, "start": 1380, "end": 1390}, {"helix": 1, "forward": false, "start": 1380, "end": 1390} @@ -1400,7 +1400,7 @@ "name": "staple140", "color": "#b8056c", "sequence": "TGCCTGCAGGCAAGCCCAAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D6"}, "domains": [ {"helix": 0, "forward": true, "start": 1390, "end": 1400}, {"helix": 1, "forward": false, "start": 1390, "end": 1400} @@ -1410,7 +1410,7 @@ "name": "staple141", "color": "#007200", "sequence": "TCGACTCTAGTCAGGGATAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E6"}, "domains": [ {"helix": 0, "forward": true, "start": 1400, "end": 1410}, {"helix": 1, "forward": false, "start": 1400, "end": 1410} @@ -1420,7 +1420,7 @@ "name": "staple142", "color": "#cc0000", "sequence": "AGGATCCCCGACCCTCATTT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F6"}, "domains": [ {"helix": 0, "forward": true, "start": 1410, "end": 1420}, {"helix": 1, "forward": false, "start": 1410, "end": 1420} @@ -1430,7 +1430,7 @@ "name": "staple143", "color": "#f7931e", "sequence": "GGTACCGAGCCAGAGCCACC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G6"}, "domains": [ {"helix": 0, "forward": true, "start": 1420, "end": 1430}, {"helix": 1, "forward": false, "start": 1420, "end": 1430} @@ -1440,7 +1440,7 @@ "name": "staple144", "color": "#f74308", "sequence": "TCGAATTCGTCCGCCACCCT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H6"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H6"}, "domains": [ {"helix": 0, "forward": true, "start": 1430, "end": 1440}, {"helix": 1, "forward": false, "start": 1430, "end": 1440} @@ -1450,7 +1450,7 @@ "name": "staple145", "color": "#57bb00", "sequence": "AATCATGGTCACCCTCAGAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A7"}, "domains": [ {"helix": 0, "forward": true, "start": 1440, "end": 1450}, {"helix": 1, "forward": false, "start": 1440, "end": 1450} @@ -1460,7 +1460,7 @@ "name": "staple146", "color": "#888888", "sequence": "ATAGCTGTTTCAGAACCGCC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B7"}, "domains": [ {"helix": 0, "forward": true, "start": 1450, "end": 1460}, {"helix": 1, "forward": false, "start": 1450, "end": 1460} @@ -1470,7 +1470,7 @@ "name": "staple147", "color": "#32b86c", "sequence": "CCTGTGTGAACCGCCACCCT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C7"}, "domains": [ {"helix": 0, "forward": true, "start": 1460, "end": 1470}, {"helix": 1, "forward": false, "start": 1460, "end": 1470} @@ -1480,7 +1480,7 @@ "name": "staple148", "color": "#333333", "sequence": "ATTGTTATCCAGGTTTAGTA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D7"}, "domains": [ {"helix": 0, "forward": true, "start": 1470, "end": 1480}, {"helix": 1, "forward": false, "start": 1470, "end": 1480} @@ -1490,7 +1490,7 @@ "name": "staple149", "color": "#320096", "sequence": "GCTCACAATTCGTACTCAGG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E7"}, "domains": [ {"helix": 0, "forward": true, "start": 1480, "end": 1490}, {"helix": 1, "forward": false, "start": 1480, "end": 1490} @@ -1500,7 +1500,7 @@ "name": "staple150", "color": "#03b6a2", "sequence": "CCACACAACAGGTGTATCAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F7"}, "domains": [ {"helix": 0, "forward": true, "start": 1490, "end": 1500}, {"helix": 1, "forward": false, "start": 1490, "end": 1500} @@ -1510,7 +1510,7 @@ "name": "staple151", "color": "#7300de", "sequence": "TACGAGCCGGGCCCGGAATA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G7"}, "domains": [ {"helix": 0, "forward": true, "start": 1500, "end": 1510}, {"helix": 1, "forward": false, "start": 1500, "end": 1510} @@ -1520,7 +1520,7 @@ "name": "staple152", "color": "#aaaa00", "sequence": "AAGCATAAAGTATAAGTATA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H7"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H7"}, "domains": [ {"helix": 0, "forward": true, "start": 1510, "end": 1520}, {"helix": 1, "forward": false, "start": 1510, "end": 1520} @@ -1530,7 +1530,7 @@ "name": "staple153", "color": "#b8056c", "sequence": "TGTAAAGCCTAGAGGGTTGA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A8"}, "domains": [ {"helix": 0, "forward": true, "start": 1520, "end": 1530}, {"helix": 1, "forward": false, "start": 1520, "end": 1530} @@ -1540,7 +1540,7 @@ "name": "staple154", "color": "#007200", "sequence": "GGGGTGCCTAAGTGCCGTCG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B8"}, "domains": [ {"helix": 0, "forward": true, "start": 1530, "end": 1540}, {"helix": 1, "forward": false, "start": 1530, "end": 1540} @@ -1550,7 +1550,7 @@ "name": "staple155", "color": "#cc0000", "sequence": "ATGAGTGAGCCAGGCGGATA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C8"}, "domains": [ {"helix": 0, "forward": true, "start": 1540, "end": 1550}, {"helix": 1, "forward": false, "start": 1540, "end": 1550} @@ -1560,7 +1560,7 @@ "name": "staple156", "color": "#f7931e", "sequence": "TAACTCACATTGCTCAGTAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D8"}, "domains": [ {"helix": 0, "forward": true, "start": 1550, "end": 1560}, {"helix": 1, "forward": false, "start": 1550, "end": 1560} @@ -1570,7 +1570,7 @@ "name": "staple157", "color": "#f74308", "sequence": "TAATTGCGTTAGCGGGGTTT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E8"}, "domains": [ {"helix": 0, "forward": true, "start": 1560, "end": 1570}, {"helix": 1, "forward": false, "start": 1560, "end": 1570} @@ -1580,7 +1580,7 @@ "name": "staple158", "color": "#57bb00", "sequence": "GCGCTCACTGGATTAGGATT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F8"}, "domains": [ {"helix": 0, "forward": true, "start": 1570, "end": 1580}, {"helix": 1, "forward": false, "start": 1570, "end": 1580} @@ -1590,7 +1590,7 @@ "name": "staple159", "color": "#888888", "sequence": "CCCGCTTTCCTCAAGAGAAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G8"}, "domains": [ {"helix": 0, "forward": true, "start": 1580, "end": 1590}, {"helix": 1, "forward": false, "start": 1580, "end": 1590} @@ -1600,7 +1600,7 @@ "name": "staple160", "color": "#32b86c", "sequence": "AGTCGGGAAACTGAGACTCC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H8"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H8"}, "domains": [ {"helix": 0, "forward": true, "start": 1590, "end": 1600}, {"helix": 1, "forward": false, "start": 1590, "end": 1600} @@ -1610,7 +1610,7 @@ "name": "staple161", "color": "#333333", "sequence": "CCTGTCGTGCTATTAAGAGG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A9"}, "domains": [ {"helix": 0, "forward": true, "start": 1600, "end": 1610}, {"helix": 1, "forward": false, "start": 1600, "end": 1610} @@ -1620,7 +1620,7 @@ "name": "staple162", "color": "#320096", "sequence": "CAGCTGCATTAACATGAAAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B9"}, "domains": [ {"helix": 0, "forward": true, "start": 1610, "end": 1620}, {"helix": 1, "forward": false, "start": 1610, "end": 1620} @@ -1630,7 +1630,7 @@ "name": "staple163", "color": "#03b6a2", "sequence": "AATGAATCGGATTATTCTGA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C9"}, "domains": [ {"helix": 0, "forward": true, "start": 1620, "end": 1630}, {"helix": 1, "forward": false, "start": 1620, "end": 1630} @@ -1640,7 +1640,7 @@ "name": "staple164", "color": "#7300de", "sequence": "CCAACGCGCGTTCGGAACCT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D9"}, "domains": [ {"helix": 0, "forward": true, "start": 1630, "end": 1640}, {"helix": 1, "forward": false, "start": 1630, "end": 1640} @@ -1650,7 +1650,7 @@ "name": "staple165", "color": "#aaaa00", "sequence": "GGGAGAGGCGCCCTGCCTAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E9"}, "domains": [ {"helix": 0, "forward": true, "start": 1640, "end": 1650}, {"helix": 1, "forward": false, "start": 1640, "end": 1650} @@ -1660,7 +1660,7 @@ "name": "staple166", "color": "#b8056c", "sequence": "GTTTGCGTATAGTTAATGCC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F9"}, "domains": [ {"helix": 0, "forward": true, "start": 1650, "end": 1660}, {"helix": 1, "forward": false, "start": 1650, "end": 1660} @@ -1670,7 +1670,7 @@ "name": "staple167", "color": "#007200", "sequence": "TGGGCGCCAGCCGTATAAAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G9"}, "domains": [ {"helix": 0, "forward": true, "start": 1660, "end": 1670}, {"helix": 1, "forward": false, "start": 1660, "end": 1670} @@ -1680,7 +1680,7 @@ "name": "staple168", "color": "#cc0000", "sequence": "GGTGGTTTTTGTAACAGTGC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H9"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H9"}, "domains": [ {"helix": 0, "forward": true, "start": 1670, "end": 1680}, {"helix": 1, "forward": false, "start": 1670, "end": 1680} @@ -1690,7 +1690,7 @@ "name": "staple169", "color": "#f7931e", "sequence": "CTTTTCACCAAGTGCCTTGA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A10"}, "domains": [ {"helix": 0, "forward": true, "start": 1680, "end": 1690}, {"helix": 1, "forward": false, "start": 1680, "end": 1690} @@ -1700,7 +1700,7 @@ "name": "staple170", "color": "#f74308", "sequence": "GTGAGACGGGTAACGGGGTC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B10"}, "domains": [ {"helix": 0, "forward": true, "start": 1690, "end": 1700}, {"helix": 1, "forward": false, "start": 1690, "end": 1700} @@ -1710,7 +1710,7 @@ "name": "staple171", "color": "#57bb00", "sequence": "CAACAGCTGATAATAAGTTT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C10"}, "domains": [ {"helix": 0, "forward": true, "start": 1700, "end": 1710}, {"helix": 1, "forward": false, "start": 1700, "end": 1710} @@ -1720,7 +1720,7 @@ "name": "staple172", "color": "#888888", "sequence": "TTGCCCTTCAAGTGTACTGG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D10"}, "domains": [ {"helix": 0, "forward": true, "start": 1710, "end": 1720}, {"helix": 1, "forward": false, "start": 1710, "end": 1720} @@ -1730,7 +1730,7 @@ "name": "staple173", "color": "#32b86c", "sequence": "CCGCCTGGCCATGATACAGG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E10"}, "domains": [ {"helix": 0, "forward": true, "start": 1720, "end": 1730}, {"helix": 1, "forward": false, "start": 1720, "end": 1730} @@ -1740,7 +1740,7 @@ "name": "staple174", "color": "#333333", "sequence": "CTGAGAGAGTATGGCTTTTG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F10"}, "domains": [ {"helix": 0, "forward": true, "start": 1730, "end": 1740}, {"helix": 1, "forward": false, "start": 1730, "end": 1740} @@ -1750,7 +1750,7 @@ "name": "staple175", "color": "#320096", "sequence": "TGCAGCAAGCAGCGTCATAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G10"}, "domains": [ {"helix": 0, "forward": true, "start": 1740, "end": 1750}, {"helix": 1, "forward": false, "start": 1740, "end": 1750} @@ -1760,7 +1760,7 @@ "name": "staple176", "color": "#03b6a2", "sequence": "GGTCCACGCTCGTTCCAGTA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H10"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H10"}, "domains": [ {"helix": 0, "forward": true, "start": 1750, "end": 1760}, {"helix": 1, "forward": false, "start": 1750, "end": 1760} @@ -1770,7 +1770,7 @@ "name": "staple177", "color": "#7300de", "sequence": "GGTTTGCCCCCTGAATTTAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A11"}, "domains": [ {"helix": 0, "forward": true, "start": 1760, "end": 1770}, {"helix": 1, "forward": false, "start": 1760, "end": 1770} @@ -1780,7 +1780,7 @@ "name": "staple178", "color": "#aaaa00", "sequence": "AGCAGGCGAAAGCGCAGTCT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B11"}, "domains": [ {"helix": 0, "forward": true, "start": 1770, "end": 1780}, {"helix": 1, "forward": false, "start": 1770, "end": 1780} @@ -1790,7 +1790,7 @@ "name": "staple179", "color": "#b8056c", "sequence": "AATCCTGTTTCAGAATGGAA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C11"}, "domains": [ {"helix": 0, "forward": true, "start": 1780, "end": 1790}, {"helix": 1, "forward": false, "start": 1780, "end": 1790} @@ -1800,7 +1800,7 @@ "name": "staple180", "color": "#007200", "sequence": "GATGGTGGTTTCATTAAAGC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D11"}, "domains": [ {"helix": 0, "forward": true, "start": 1790, "end": 1800}, {"helix": 1, "forward": false, "start": 1790, "end": 1800} @@ -1810,7 +1810,7 @@ "name": "staple181", "color": "#cc0000", "sequence": "CCGAAATCGGAAATAAATCC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E11"}, "domains": [ {"helix": 0, "forward": true, "start": 1800, "end": 1810}, {"helix": 1, "forward": false, "start": 1800, "end": 1810} @@ -1820,7 +1820,7 @@ "name": "staple182", "color": "#f7931e", "sequence": "CAAAATCCCTATTCACAAAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F11"}, "domains": [ {"helix": 0, "forward": true, "start": 1810, "end": 1820}, {"helix": 1, "forward": false, "start": 1810, "end": 1820} @@ -1830,7 +1830,7 @@ "name": "staple183", "color": "#f74308", "sequence": "TATAAATCAATGGCCTTGAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G11"}, "domains": [ {"helix": 0, "forward": true, "start": 1820, "end": 1830}, {"helix": 1, "forward": false, "start": 1820, "end": 1830} @@ -1840,7 +1840,7 @@ "name": "staple184", "color": "#57bb00", "sequence": "AAGAATAGCCGTCAGACGAT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H11"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H11"}, "domains": [ {"helix": 0, "forward": true, "start": 1830, "end": 1840}, {"helix": 1, "forward": false, "start": 1830, "end": 1840} @@ -1850,7 +1850,7 @@ "name": "staple185", "color": "#888888", "sequence": "CGAGATAGGGGTTGAGGCAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "A12"}, "domains": [ {"helix": 0, "forward": true, "start": 1840, "end": 1850}, {"helix": 1, "forward": false, "start": 1840, "end": 1850} @@ -1860,7 +1860,7 @@ "name": "staple186", "color": "#32b86c", "sequence": "TTGAGTGTTGTTGACAGGAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "B12"}, "domains": [ {"helix": 0, "forward": true, "start": 1850, "end": 1860}, {"helix": 1, "forward": false, "start": 1850, "end": 1860} @@ -1870,7 +1870,7 @@ "name": "staple187", "color": "#333333", "sequence": "TTCCAGTTTGGCCGCCAGCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "C12"}, "domains": [ {"helix": 0, "forward": true, "start": 1860, "end": 1870}, {"helix": 1, "forward": false, "start": 1860, "end": 1870} @@ -1880,7 +1880,7 @@ "name": "staple188", "color": "#320096", "sequence": "GAACAAGAGTCACCAGAGCC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "D12"}, "domains": [ {"helix": 0, "forward": true, "start": 1870, "end": 1880}, {"helix": 1, "forward": false, "start": 1870, "end": 1880} @@ -1890,7 +1890,7 @@ "name": "staple189", "color": "#03b6a2", "sequence": "CCACTATTAACCAGAACCAC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "E12"}, "domains": [ {"helix": 0, "forward": true, "start": 1880, "end": 1890}, {"helix": 1, "forward": false, "start": 1880, "end": 1890} @@ -1900,7 +1900,7 @@ "name": "staple190", "color": "#7300de", "sequence": "AGAACGTGGAAGAGCCGCCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "F12"}, "domains": [ {"helix": 0, "forward": true, "start": 1890, "end": 1900}, {"helix": 1, "forward": false, "start": 1890, "end": 1900} @@ -1910,7 +1910,7 @@ "name": "staple191", "color": "#aaaa00", "sequence": "CTCCAACGTCCACCACCCTC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "G12"}, "domains": [ {"helix": 0, "forward": true, "start": 1900, "end": 1910}, {"helix": 1, "forward": false, "start": 1900, "end": 1910} @@ -1920,7 +1920,7 @@ "name": "staple192", "color": "#b8056c", "sequence": "AAAGGGCGAACCCTCAGAGC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H12"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate2", "well": "H12"}, "domains": [ {"helix": 0, "forward": true, "start": 1910, "end": 1920}, {"helix": 1, "forward": false, "start": 1910, "end": 1920} @@ -1930,7 +1930,7 @@ "name": "staple193", "color": "#007200", "sequence": "AAACCGTCTAAGAACCGCCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "A1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "A1"}, "domains": [ {"helix": 0, "forward": true, "start": 1920, "end": 1930}, {"helix": 1, "forward": false, "start": 1920, "end": 1930} @@ -1940,7 +1940,7 @@ "name": "staple194", "color": "#cc0000", "sequence": "TCAGGGCGATCGCCACCCTC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "B1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "B1"}, "domains": [ {"helix": 0, "forward": true, "start": 1930, "end": 1940}, {"helix": 1, "forward": false, "start": 1930, "end": 1940} @@ -1950,7 +1950,7 @@ "name": "staple195", "color": "#f7931e", "sequence": "GGCCCACTACCCCTCAGAGC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "C1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "C1"}, "domains": [ {"helix": 0, "forward": true, "start": 1940, "end": 1950}, {"helix": 1, "forward": false, "start": 1940, "end": 1950} @@ -1960,7 +1960,7 @@ "name": "staple196", "color": "#f74308", "sequence": "GTGAACCATCGGAACCGCCT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "D1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "D1"}, "domains": [ {"helix": 0, "forward": true, "start": 1950, "end": 1960}, {"helix": 1, "forward": false, "start": 1950, "end": 1960} @@ -1970,7 +1970,7 @@ "name": "staple197", "color": "#57bb00", "sequence": "ACCCAAATCAAGCCACCACC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "E1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "E1"}, "domains": [ {"helix": 0, "forward": true, "start": 1960, "end": 1970}, {"helix": 1, "forward": false, "start": 1960, "end": 1970} @@ -1980,7 +1980,7 @@ "name": "staple198", "color": "#888888", "sequence": "AGTTTTTTGGCCGGAACCAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "F1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "F1"}, "domains": [ {"helix": 0, "forward": true, "start": 1970, "end": 1980}, {"helix": 1, "forward": false, "start": 1970, "end": 1980} @@ -1990,7 +1990,7 @@ "name": "staple199", "color": "#32b86c", "sequence": "GGTCGAGGTGATCAAAATCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "G1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "G1"}, "domains": [ {"helix": 0, "forward": true, "start": 1980, "end": 1990}, {"helix": 1, "forward": false, "start": 1980, "end": 1990} @@ -2000,7 +2000,7 @@ "name": "staple200", "color": "#333333", "sequence": "CCGTAAAGCATCTTTTCATA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "H1"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "H1"}, "domains": [ {"helix": 0, "forward": true, "start": 1990, "end": 2000}, {"helix": 1, "forward": false, "start": 1990, "end": 2000} @@ -2010,7 +2010,7 @@ "name": "staple201", "color": "#320096", "sequence": "CTAAATCGGAGCGTTTGCCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "A2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "A2"}, "domains": [ {"helix": 0, "forward": true, "start": 2000, "end": 2010}, {"helix": 1, "forward": false, "start": 2000, "end": 2010} @@ -2020,7 +2020,7 @@ "name": "staple202", "color": "#03b6a2", "sequence": "ACCCTAAAGGCCCCTTATTA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "B2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "B2"}, "domains": [ {"helix": 0, "forward": true, "start": 2010, "end": 2020}, {"helix": 1, "forward": false, "start": 2010, "end": 2020} @@ -2030,7 +2030,7 @@ "name": "staple203", "color": "#7300de", "sequence": "GAGCCCCCGACGGTCATAGC", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "C2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "C2"}, "domains": [ {"helix": 0, "forward": true, "start": 2020, "end": 2030}, {"helix": 1, "forward": false, "start": 2020, "end": 2030} @@ -2040,7 +2040,7 @@ "name": "staple204", "color": "#aaaa00", "sequence": "TTTAGAGCTTTCGGCATTTT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "D2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "D2"}, "domains": [ {"helix": 0, "forward": true, "start": 2030, "end": 2040}, {"helix": 1, "forward": false, "start": 2030, "end": 2040} @@ -2050,7 +2050,7 @@ "name": "staple205", "color": "#b8056c", "sequence": "GACGGGGAAACGCGTTTTCA", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "E2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "E2"}, "domains": [ {"helix": 0, "forward": true, "start": 2040, "end": 2050}, {"helix": 1, "forward": false, "start": 2040, "end": 2050} @@ -2060,7 +2060,7 @@ "name": "staple206", "color": "#007200", "sequence": "GCCGGCGAACCAGACTGTAG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "F2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "F2"}, "domains": [ {"helix": 0, "forward": true, "start": 2050, "end": 2060}, {"helix": 1, "forward": false, "start": 2050, "end": 2060} @@ -2070,7 +2070,7 @@ "name": "staple207", "color": "#cc0000", "sequence": "GTGGCGAGAACCTTTAGCGT", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "G2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "G2"}, "domains": [ {"helix": 0, "forward": true, "start": 2060, "end": 2070}, {"helix": 1, "forward": false, "start": 2060, "end": 2070} @@ -2080,7 +2080,7 @@ "name": "staple208", "color": "#f7931e", "sequence": "AGGAAGGGAAATCAAGTTTG", - "idt": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "H2"}, + "vendor": {"scale": "25nm", "purification": "STD", "plate": "plate3", "well": "H2"}, "domains": [ {"helix": 0, "forward": true, "start": 2070, "end": 2080}, {"helix": 1, "forward": false, "start": 2070, "end": 2080} diff --git a/examples/output_designs/long_range_crossovers.sc b/examples/output_designs/long_range_crossovers.sc index 6dca13b..8a30f8f 100644 --- a/examples/output_designs/long_range_crossovers.sc +++ b/examples/output_designs/long_range_crossovers.sc @@ -1,192 +1,192 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"grid_position": [0, 0]}, - {"grid_position": [0, 1]}, - {"grid_position": [0, 2]}, - {"grid_position": [0, 3]}, - {"grid_position": [0, 4]}, - {"grid_position": [0, 5]}, - {"grid_position": [0, 6]}, - {"grid_position": [0, 7]}, - {"grid_position": [0, 8]}, - {"grid_position": [0, 9]}, - {"grid_position": [0, 10]}, - {"grid_position": [0, 11]}, - {"grid_position": [0, 12]}, - {"grid_position": [0, 13]}, - {"grid_position": [0, 14]}, - {"grid_position": [0, 15]} - ], - "strands": [ - { - "color": "#f74308", - "domains": [ - {"helix": 0, "forward": false, "start": 0, "end": 16}, - {"helix": 15, "forward": true, "start": 0, "end": 16} - ] - }, - { - "color": "#57bb00", - "domains": [ - {"helix": 15, "forward": true, "start": 16, "end": 32}, - {"helix": 0, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#888888", - "domains": [ - {"helix": 0, "forward": false, "start": 32, "end": 48}, - {"helix": 15, "forward": true, "start": 32, "end": 48} - ] - }, - { - "color": "#32b86c", - "domains": [ - {"helix": 1, "forward": false, "start": 0, "end": 16}, - {"helix": 14, "forward": true, "start": 0, "end": 16} - ] - }, - { - "color": "#333333", - "domains": [ - {"helix": 14, "forward": true, "start": 16, "end": 32}, - {"helix": 1, "forward": false, "start": 16, "end": 32} - ] - }, - { - "color": "#320096", - "domains": [ - {"helix": 1, "forward": false, "start": 32, "end": 48}, - {"helix": 14, "forward": true, 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"version": "0.19.0", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]}, + {"grid_position": [0, 2]}, + {"grid_position": [0, 3]}, + {"grid_position": [0, 4]}, + {"grid_position": [0, 5]}, + {"grid_position": [0, 6]}, + {"grid_position": [0, 7]}, + {"grid_position": [0, 8]}, + {"grid_position": [0, 9]}, + {"grid_position": [0, 10]}, + {"grid_position": [0, 11]}, + {"grid_position": [0, 12]}, + {"grid_position": [0, 13]}, + {"grid_position": [0, 14]}, + {"grid_position": [0, 15]} + ], + "strands": [ + { + "color": "#f74308", + "domains": [ + {"helix": 0, "forward": false, "start": 0, "end": 16}, + {"helix": 15, "forward": true, "start": 0, "end": 16} + ] + }, + { + "color": "#57bb00", + "domains": [ + {"helix": 15, "forward": true, "start": 16, "end": 32}, + {"helix": 0, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#888888", + "domains": [ + {"helix": 0, "forward": false, "start": 32, "end": 48}, + {"helix": 15, "forward": true, "start": 32, "end": 48} + ] + }, + { + "color": "#32b86c", + "domains": [ + {"helix": 1, "forward": false, "start": 0, "end": 16}, + {"helix": 14, "forward": true, "start": 0, "end": 16} + ] + }, + { + "color": "#333333", + "domains": [ + {"helix": 14, "forward": true, "start": 16, "end": 32}, + {"helix": 1, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#320096", + "domains": [ + {"helix": 1, "forward": false, "start": 32, "end": 48}, + {"helix": 14, "forward": true, "start": 32, "end": 48} + ] + }, + { + "color": "#03b6a2", + "domains": [ + {"helix": 2, "forward": false, "start": 0, "end": 16}, + {"helix": 13, "forward": true, "start": 0, "end": 16} + ] + }, + { + "color": "#7300de", + "domains": [ + {"helix": 13, "forward": true, "start": 16, "end": 32}, + {"helix": 2, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#aaaa00", + "domains": [ + {"helix": 2, "forward": false, "start": 32, "end": 48}, + {"helix": 13, "forward": true, "start": 32, "end": 48} + ] + }, + { + "color": "#b8056c", + "domains": [ + {"helix": 3, "forward": false, "start": 0, "end": 16}, + {"helix": 12, "forward": true, "start": 0, "end": 16} + ] + }, + { + "color": "#007200", + "domains": [ + {"helix": 12, "forward": true, "start": 16, "end": 32}, + {"helix": 3, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#cc0000", + "domains": [ + {"helix": 3, "forward": false, "start": 32, "end": 48}, + {"helix": 12, "forward": true, "start": 32, "end": 48} + ] + }, + { + "color": "#f7931e", + "domains": [ + {"helix": 4, "forward": false, "start": 0, "end": 16}, + {"helix": 11, "forward": true, "start": 0, "end": 16} + ] + }, + { + "color": "#f74308", + "domains": [ + {"helix": 11, "forward": true, "start": 16, "end": 32}, + {"helix": 4, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#57bb00", + "domains": [ + {"helix": 4, "forward": false, "start": 32, "end": 48}, + {"helix": 11, "forward": true, "start": 32, "end": 48} + ] + }, + { + "color": "#888888", + "domains": [ + {"helix": 5, "forward": false, "start": 0, "end": 16}, + {"helix": 10, "forward": true, "start": 0, "end": 16} + ] + }, + { + "color": "#32b86c", + "domains": [ + {"helix": 10, "forward": true, "start": 16, "end": 32}, + {"helix": 5, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#333333", + "domains": [ + {"helix": 5, "forward": false, "start": 32, "end": 48}, + {"helix": 10, "forward": true, "start": 32, "end": 48} + ] + }, + { + "color": "#320096", + "domains": [ + {"helix": 6, "forward": false, "start": 0, "end": 16}, + {"helix": 9, "forward": true, "start": 0, "end": 16} + ] + }, + { + "color": "#03b6a2", + "domains": [ + {"helix": 9, "forward": true, "start": 16, "end": 32}, + {"helix": 6, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#7300de", + "domains": [ + {"helix": 6, "forward": false, "start": 32, "end": 48}, + {"helix": 9, "forward": true, "start": 32, "end": 48} + ] + }, + { + "color": "#aaaa00", + "domains": [ + {"helix": 7, "forward": false, "start": 0, "end": 16}, + {"helix": 8, "forward": true, "start": 0, "end": 16} + ] + }, + { + "color": "#b8056c", + "domains": [ + {"helix": 8, "forward": true, "start": 16, "end": 32}, + {"helix": 7, "forward": false, "start": 16, "end": 32} + ] + }, + { + "color": "#007200", + "domains": [ + {"helix": 7, "forward": false, "start": 32, "end": 48}, + {"helix": 8, "forward": true, "start": 32, "end": 48} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/loopouts_all_types.sc b/examples/output_designs/loopouts_all_types.sc index 51dfce2..eb0d710 100644 --- a/examples/output_designs/loopouts_all_types.sc +++ b/examples/output_designs/loopouts_all_types.sc @@ -1,28 +1,28 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 8, "grid_position": [0, 0]}, - {"max_offset": 8, "grid_position": [0, 1]}, - {"grid_position": [0, 2]} - ], - "strands": [ - { - "color": "#f74308", - "sequence": "ACGACGACTTTACGTCGTCGTTTTACGACGACGATTTACTTACGCACGACGATTTTTTTTTTACGTTGCAGGTCGTCGTGACGACGACTGTCGTCGT", - "domains": [ - {"helix": 0, "forward": true, "start": 0, "end": 8}, - {"loopout": 5}, - {"helix": 0, "forward": false, "start": 0, "end": 8}, - {"loopout": 5}, - {"helix": 1, "forward": true, "start": 0, "end": 8}, - {"loopout": 10}, - {"helix": 2, "forward": false, "start": 16, "end": 24}, - {"loopout": 20}, - {"helix": 2, "forward": true, "start": 16, "end": 32}, - {"loopout": 1}, - {"helix": 2, "forward": false, "start": 24, "end": 32} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"max_offset": 8, "grid_position": [0, 0]}, + {"max_offset": 8, "grid_position": [0, 1]}, + {"grid_position": [0, 2]} + ], + "strands": [ + { + "color": "#f74308", + "sequence": "ACGACGACTTTACGTCGTCGTTTTACGACGACGATTTACTTACGCACGACGATTTTTTTTTTACGTTGCAGGTCGTCGTGACGACGACTGTCGTCGT", + "domains": [ + {"helix": 0, "forward": true, "start": 0, "end": 8}, + {"loopout": 5}, + {"helix": 0, "forward": false, "start": 0, "end": 8}, + {"loopout": 5}, + {"helix": 1, "forward": true, "start": 0, "end": 8}, + {"loopout": 10}, + {"helix": 2, "forward": false, "start": 16, "end": 24}, + {"loopout": 20}, + {"helix": 2, "forward": true, "start": 16, "end": 32}, + {"loopout": 1}, + {"helix": 2, "forward": false, "start": 24, "end": 32} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/many_big_helices.sc b/examples/output_designs/many_big_helices.sc index 5c80fda..56ee8e8 100644 --- a/examples/output_designs/many_big_helices.sc +++ b/examples/output_designs/many_big_helices.sc @@ -1,37 +1,37 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 2000, "grid_position": [0, 0]}, - {"max_offset": 2000, "grid_position": [0, 1]}, - {"max_offset": 2000, "grid_position": [0, 2]}, - {"max_offset": 2000, "grid_position": [0, 3]}, - {"max_offset": 2000, "grid_position": [0, 4]}, - {"max_offset": 2000, "grid_position": [0, 5]}, - {"max_offset": 2000, "grid_position": [0, 6]}, - {"max_offset": 2000, "grid_position": [0, 7]}, - {"max_offset": 2000, "grid_position": [0, 8]}, - {"max_offset": 2000, "grid_position": [0, 9]}, - {"max_offset": 2000, "grid_position": [0, 10]}, - {"max_offset": 2000, "grid_position": [0, 11]}, - {"max_offset": 2000, "grid_position": [0, 12]}, - {"max_offset": 2000, "grid_position": [0, 13]}, - {"max_offset": 2000, "grid_position": [0, 14]}, - {"max_offset": 2000, "grid_position": [0, 15]}, - {"max_offset": 2000, "grid_position": [0, 16]}, - {"max_offset": 2000, "grid_position": [0, 17]}, - {"max_offset": 2000, "grid_position": [0, 18]}, - {"max_offset": 2000, "grid_position": [0, 19]}, - {"max_offset": 2000, "grid_position": [0, 20]}, - {"max_offset": 2000, "grid_position": [0, 21]}, - {"max_offset": 2000, "grid_position": [0, 22]}, - {"max_offset": 2000, "grid_position": [0, 23]}, - {"max_offset": 2000, "grid_position": [0, 24]}, - {"max_offset": 2000, "grid_position": [0, 25]}, - {"max_offset": 2000, "grid_position": [0, 26]}, - {"max_offset": 2000, "grid_position": [0, 27]}, - {"max_offset": 2000, "grid_position": [0, 28]}, - {"max_offset": 2000, "grid_position": [0, 29]} - ], - "strands": [] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"max_offset": 2000, "grid_position": [0, 0]}, + {"max_offset": 2000, "grid_position": [0, 1]}, + {"max_offset": 2000, "grid_position": [0, 2]}, + {"max_offset": 2000, "grid_position": [0, 3]}, + {"max_offset": 2000, "grid_position": [0, 4]}, + {"max_offset": 2000, "grid_position": [0, 5]}, + {"max_offset": 2000, "grid_position": [0, 6]}, + {"max_offset": 2000, "grid_position": [0, 7]}, + {"max_offset": 2000, "grid_position": [0, 8]}, + {"max_offset": 2000, "grid_position": [0, 9]}, + {"max_offset": 2000, "grid_position": [0, 10]}, + {"max_offset": 2000, "grid_position": [0, 11]}, + {"max_offset": 2000, "grid_position": [0, 12]}, + {"max_offset": 2000, "grid_position": [0, 13]}, + {"max_offset": 2000, "grid_position": [0, 14]}, + {"max_offset": 2000, "grid_position": [0, 15]}, + {"max_offset": 2000, "grid_position": [0, 16]}, + {"max_offset": 2000, "grid_position": [0, 17]}, + {"max_offset": 2000, "grid_position": [0, 18]}, + {"max_offset": 2000, "grid_position": [0, 19]}, + {"max_offset": 2000, "grid_position": [0, 20]}, + {"max_offset": 2000, "grid_position": [0, 21]}, + {"max_offset": 2000, "grid_position": [0, 22]}, + {"max_offset": 2000, "grid_position": [0, 23]}, + {"max_offset": 2000, "grid_position": [0, 24]}, + {"max_offset": 2000, "grid_position": [0, 25]}, + {"max_offset": 2000, "grid_position": [0, 26]}, + {"max_offset": 2000, "grid_position": [0, 27]}, + {"max_offset": 2000, "grid_position": [0, 28]}, + {"max_offset": 2000, "grid_position": [0, 29]} + ], + "strands": [] } \ No newline at end of file diff --git a/examples/output_designs/many_helices_modifications.sc b/examples/output_designs/many_helices_modifications.sc index 2d10c37..c7cb424 100644 --- a/examples/output_designs/many_helices_modifications.sc +++ b/examples/output_designs/many_helices_modifications.sc @@ -1,60 +1,60 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"grid_position": [0, 0]}, - {"grid_position": [0, 1]}, - {"grid_position": [0, 2]}, - {"grid_position": [0, 3]}, - {"grid_position": [0, 4]}, - {"grid_position": [0, 5]}, - {"grid_position": [0, 6]}, - {"grid_position": [0, 7]} - ], - "modifications_in_design": { - "/3Cy3Sp/": { - "display_text": "Cy3", - "idt_text": "/3Cy3Sp/", - "display_connector": false, - "location": "3'" - }, - "/iBiodT/": { - "display_text": "B", - "idt_text": "/iBiodT/", - "display_connector": false, - "location": "internal", - "allowed_bases": ["T"] - }, - "/5Biosg/": { - "display_text": "B", - "idt_text": "/5Biosg/", - "display_connector": false, - "location": "5'" - }, - "/iCy3/": { - "display_text": "Cy3", - "idt_text": "/iCy3/", - "display_connector": false, - "location": "internal" - } - }, - "strands": [ - { - "color": "#f74308", - "sequence": "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT", - "domains": [ - {"helix": 0, "forward": true, "start": 0, "end": 16, "deletions": [11, 12]}, - {"helix": 1, "forward": false, "start": 0, "end": 16, "deletions": [12], "insertions": [[4, 1]]}, - {"helix": 2, "forward": true, "start": 0, "end": 16}, - {"helix": 3, "forward": false, "start": 0, "end": 16}, - {"helix": 4, "forward": true, "start": 0, "end": 16}, - {"helix": 5, "forward": false, "start": 0, "end": 16}, - {"helix": 6, "forward": true, "start": 0, "end": 16}, - {"helix": 7, "forward": false, "start": 0, "end": 16} - ], - "5prime_modification": "/5Biosg/", - "3prime_modification": "/3Cy3Sp/", - "internal_modifications": {"5": "/iCy3/", "10": "/iBiodT/", "21": "/iCy3/", "26": "/iBiodT/", "37": "/iCy3/", "42": "/iBiodT/", "53": "/iCy3/", "58": "/iBiodT/", "69": "/iCy3/", "74": "/iBiodT/", "85": "/iCy3/", "90": "/iBiodT/", "101": "/iCy3/", "106": "/iBiodT/", "117": "/iCy3/", "122": "/iBiodT/"} - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]}, + {"grid_position": [0, 1]}, + {"grid_position": [0, 2]}, + {"grid_position": [0, 3]}, + {"grid_position": [0, 4]}, + {"grid_position": [0, 5]}, + {"grid_position": [0, 6]}, + {"grid_position": [0, 7]} + ], + "modifications_in_design": { + "/5Biosg/": { + "display_text": "B", + "vendor_code": "/5Biosg/", + "display_connector": false, + "location": "5'" + }, + "/iBiodT/": { + "display_text": "B", + "vendor_code": "/iBiodT/", + "display_connector": false, + "location": "internal", + "allowed_bases": ["T"] + }, + "/3Cy3Sp/": { + "display_text": "Cy3", + "vendor_code": "/3Cy3Sp/", + "display_connector": false, + "location": "3'" + }, + "/iCy3/": { + "display_text": "Cy3", + "vendor_code": "/iCy3/", + "display_connector": false, + "location": "internal" + } + }, + "strands": [ + { + "color": "#f74308", + "sequence": "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT", + "domains": [ + {"helix": 0, "forward": true, "start": 0, "end": 16, "deletions": [11, 12]}, + {"helix": 1, "forward": false, "start": 0, "end": 16, "deletions": [12], "insertions": [[4, 1]]}, + {"helix": 2, "forward": true, "start": 0, "end": 16}, + {"helix": 3, "forward": false, "start": 0, "end": 16}, + {"helix": 4, "forward": true, "start": 0, "end": 16}, + {"helix": 5, "forward": false, "start": 0, "end": 16}, + {"helix": 6, "forward": true, "start": 0, "end": 16}, + {"helix": 7, "forward": false, "start": 0, "end": 16} + ], + "5prime_modification": "/5Biosg/", + "3prime_modification": "/3Cy3Sp/", + "internal_modifications": {"5": "/iCy3/", "10": "/iBiodT/", "21": "/iCy3/", "26": "/iBiodT/", "37": "/iCy3/", "42": "/iBiodT/", "53": "/iCy3/", "58": "/iBiodT/", "69": "/iCy3/", "74": "/iBiodT/", "85": "/iCy3/", "90": "/iBiodT/", "101": "/iCy3/", "106": "/iBiodT/", "117": "/iCy3/", "122": "/iBiodT/"} + } + ] } \ No newline at end of file diff --git a/examples/output_designs/names_domains_strands.sc b/examples/output_designs/names_domains_strands.sc index 950828e..30616ea 100644 --- a/examples/output_designs/names_domains_strands.sc +++ b/examples/output_designs/names_domains_strands.sc @@ -1,72 +1,72 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"grid_position": [0, 0]} - ], - "strands": [ - { - "name": "bottom strand", - "color": "#f74308", - "domains": [ - {"name": "domain 8*", "helix": 0, "forward": false, "start": 56, "end": 64}, - {"name": "domain 7*", "helix": 0, "forward": false, "start": 48, "end": 56}, - {"name": "domain 6*", "helix": 0, "forward": false, "start": 40, "end": 48}, - {"name": "domain 5*", "helix": 0, "forward": false, "start": 32, "end": 40}, - {"name": "domain 4*", "helix": 0, "forward": false, "start": 24, "end": 32}, - {"name": "domain 3*", "helix": 0, "forward": false, "start": 16, "end": 24}, - {"name": "domain 2*", "helix": 0, "forward": false, "start": 8, "end": 16}, - {"name": "domain 1*", "helix": 0, "forward": false, "start": 0, "end": 8} - ] - }, - { - "name": "top strand 1", - "color": "#57bb00", - "domains": [ - {"name": "domain 1", "helix": 0, "forward": true, "start": 0, "end": 8} - ] - }, - { - "name": "top strand 2", - "color": "#888888", - "domains": [ - {"name": "domain 50", "helix": 0, "forward": true, "start": 8, "end": 16} - ] - }, - { - "name": "top strand 3", - "color": "#32b86c", - "domains": [ - {"name": "domain 3", "helix": 0, "forward": true, "start": 16, "end": 24} - ] - }, - { - "name": "top strand 4", - "color": "#333333", - "domains": [ - {"name": "domain 4*", "helix": 0, "forward": true, "start": 24, "end": 32} - ] - }, - { - "name": "top strand 5", - "color": "#320096", - "domains": [ - {"name": "domain 5", "helix": 0, "forward": true, "start": 32, "end": 41} - ] - }, - { - "name": "top strand 7", - "color": "#03b6a2", - "domains": [ - {"name": "domain 7", "helix": 0, "forward": true, "start": 48, "end": 55} - ] - }, - { - "name": "top strand 9", - "color": "#7300de", - "domains": [ - {"name": "domain 9", "helix": 0, "forward": true, "start": 64, "end": 72} - ] - } - ] +{ + "version": "0.19.0", + "grid": "square", + "helices": [ + {"grid_position": [0, 0]} + ], + "strands": [ + { + "name": "bottom strand", + "color": "#f74308", + "domains": [ + {"name": "domain 8*", "helix": 0, "forward": false, "start": 56, "end": 64}, + {"name": "domain 7*", "helix": 0, "forward": false, "start": 48, "end": 56}, + {"name": "domain 6*", "helix": 0, "forward": false, "start": 40, "end": 48}, + {"name": "domain 5*", "helix": 0, "forward": false, "start": 32, "end": 40}, + {"name": "domain 4*", "helix": 0, "forward": false, "start": 24, "end": 32}, + {"name": "domain 3*", "helix": 0, "forward": false, "start": 16, "end": 24}, + {"name": "domain 2*", "helix": 0, "forward": false, "start": 8, "end": 16}, + {"name": "domain 1*", "helix": 0, "forward": false, "start": 0, "end": 8} + ] + }, + { + "name": "top strand 1", + "color": "#57bb00", + "domains": [ + {"name": "domain 1", "helix": 0, "forward": true, "start": 0, "end": 8} + ] + }, + { + "name": "top strand 2", + "color": "#888888", + "domains": [ + {"name": "domain 50", "helix": 0, "forward": true, "start": 8, "end": 16} + ] + }, + { + "name": "top strand 3", + "color": "#32b86c", + "domains": [ + {"name": "domain 3", "helix": 0, "forward": true, "start": 16, "end": 24} + ] + }, + { + "name": "top strand 4", + "color": "#333333", + "domains": [ + {"name": "domain 4*", "helix": 0, "forward": true, "start": 24, "end": 32} + ] + }, + { + "name": "top strand 5", + "color": "#320096", + "domains": [ + {"name": "domain 5", "helix": 0, "forward": true, "start": 32, "end": 41} + ] + }, + { + "name": "top strand 7", + "color": "#03b6a2", + "domains": [ + {"name": "domain 7", "helix": 0, "forward": true, "start": 48, "end": 55} + ] + }, + { + "name": "top strand 9", + "color": "#7300de", + "domains": [ + {"name": "domain 9", "helix": 0, "forward": true, "start": 64, "end": 72} + ] + } + ] } \ No newline at end of file diff --git a/examples/output_designs/oxdna_export_with_pitch.sc b/examples/output_designs/oxdna_export_with_pitch.sc index 984c6e9..44ebb83 100644 --- a/examples/output_designs/oxdna_export_with_pitch.sc +++ b/examples/output_designs/oxdna_export_with_pitch.sc @@ -1,12 +1,6 @@ { - "version": "0.17.8", - "groups": { - "default_group": { - "position": {"x": 0, "y": 0, "z": 0}, - "pitch": 45, - "grid": "square" - } - }, + "version": "0.19.0", + "grid": "square", "helices": [ {"max_offset": 100, "grid_position": [0, 0]}, {"max_offset": 100, "grid_position": [0, 1]} diff --git a/examples/output_designs/proposal.sc b/examples/output_designs/proposal.sc index a20ea4e..2390fed 100644 --- a/examples/output_designs/proposal.sc +++ b/examples/output_designs/proposal.sc @@ -1,1919 +1,1919 @@ -{ - "version": "0.15.0", - "grid": "none", - "helices": [ - {"max_offset": 512, "position": {"x": 0, "y": 0, "z": 0}}, - {"max_offset": 512, "position": {"x": 0, "y": 0.0, "z": 2.5}}, - {"max_offset": 512, "position": {"x": 0, "y": 0.9567085809127245, "z": 4.809698831278217}}, - {"max_offset": 512, "position": {"x": 0, "y": 2.7244755338790934, "z": 6.577465784244586}}, - {"max_offset": 512, "position": {"x": 0, "y": 5.034174365157311, "z": 7.534174365157311}}, - {"max_offset": 512, "position": {"x": 0, "y": 7.534174365157311, "z": 7.534174365157311}}, - {"max_offset": 512, "position": {"x": 0, "y": 9.843873196435528, "z": 6.577465784244587}}, - {"max_offset": 512, "position": {"x": 0, "y": 11.611640149401897, "z": 4.809698831278218}}, - {"max_offset": 512, "position": {"x": 0, "y": 12.568348730314622, "z": 2.500000000000001}}, - {"max_offset": 512, "position": {"x": 0, "y": 12.568348730314622, "z": 8.881784197001252e-16}}, - {"max_offset": 512, "position": {"x": 0, "y": 11.611640149401897, "z": -2.309698831278216}}, - {"max_offset": 512, "position": {"x": 0, "y": 9.843873196435528, "z": -4.077465784244586}}, - {"max_offset": 512, "position": {"x": 0, "y": 7.534174365157312, "z": -5.034174365157312}}, - {"max_offset": 512, "position": {"x": 0, "y": 5.034174365157312, "z": -5.0341743651573125}}, - {"max_offset": 512, "position": {"x": 0, "y": 2.724475533879095, "z": -4.077465784244588}}, - {"max_offset": 512, "position": {"x": 0, "y": 0.9567085809127276, "z": -2.309698831278218}} - ], - "helices_view_order": [15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0], - "strands": [ - { - "color": "#0066cc", - "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGTCGTGTGACTGGTGAATCTGCCAATGTAAATAATCCATTTCAGACGATTGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCGGTAATATTGTTCTGGATATTACCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTGCTACAACGGTTAATTTGCGTGATGGACAGACTCTTTTACTCGGTGGCCTCACTGATTATAAAA", - "domains": [ - {"helix": 15, "forward": false, "start": 32, "end": 102, "deletions": [68]}, - {"helix": 14, "forward": true, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 59, 91, 123, 155, 187, 219], "insertions": [[75, 1], [107, 1], [139, 1], [171, 1], [203, 1], [235, 1]]}, - {"helix": 13, "forward": false, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 75, 107, 139, 171, 203, 235], "insertions": [[59, 1], [91, 1], [123, 1], [155, 1], [187, 1], [219, 1]]}, - {"helix": 12, "forward": true, "start": 32, "end": 240, "deletions": [68, 115, 163, 212]}, - {"helix": 11, "forward": false, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 75, 107, 139, 171, 203, 235], "insertions": [[59, 1], [91, 1], [123, 1], [155, 1], [187, 1], [219, 1]]}, - {"helix": 10, "forward": true, "start": 32, "end": 240, "deletions": [68, 115, 163, 212, 59, 91, 123, 155, 187, 219], "insertions": [[75, 1], [107, 1], [139, 1], [171, 1], [203, 1], [235, 1]]}, - {"helix": 9, "forward": 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"TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGTCGTGTGACTGGTGAATCTGCCAATGTAAATAATCCATTTCAGACGATTGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCGGTAATATTGTTCTGGATATTACCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTGCTACAACGGTTAATTTGCGTGATGGACAGACTCTTTTACTCGGTGGCCTCACTGATTATAAAA", 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"forward": false, "start": 224, "end": 232}, + {"helix": 3, "forward": true, "start": 224, "end": 248} + ] + }, + { + "color": "#333333", + "sequence": "ACCGGAACGCCATCTTTTCATAAAGTAAGAGC", + "domains": [ + {"helix": 3, "forward": true, "start": 248, "end": 256}, + {"helix": 4, "forward": false, "start": 232, "end": 256, "deletions": [251], "insertions": [[235, 1]]} + ] + }, + { + "color": "#320096", + "sequence": "TAGAGCTTAGAGGTCATTTTTGCGGAATACC", + "domains": [ + {"helix": 6, "forward": false, "start": 224, "end": 232}, + {"helix": 5, "forward": true, "start": 224, "end": 248, "deletions": [235]} + ] + }, + { + "color": "#03b6a2", + "sequence": "CAAAAGAACGAAACGCAATAATAACGGATGGCT", + "domains": [ + {"helix": 5, "forward": true, "start": 248, "end": 256, "insertions": [[251, 1]]}, + {"helix": 6, "forward": false, "start": 232, "end": 256} + ] + }, + { + "color": "#7300de", + "sequence": "AAATGCAAATTTTTAGAACCCTCTTTAGCGA", + "domains": [ + {"helix": 8, "forward": false, "start": 224, "end": 232}, + {"helix": 7, "forward": true, "start": 224, "end": 248, "deletions": [235]} + ] + }, + { + "color": "#aaaa00", + "sequence": "ACCTCCCGAAAGAACGCGAGGCGTATATATTTT", + "domains": [ + {"helix": 7, "forward": true, "start": 248, "end": 256, "insertions": [[251, 1]]}, + {"helix": 8, "forward": false, "start": 232, "end": 256, "deletions": [251], "insertions": [[235, 1]]} + ] + }, + { + "color": "#b8056c", + "sequence": "CTTTCATCTCGCGTCTGGCCTTCCTGTTTAGT", + "domains": [ + {"helix": 10, "forward": false, "start": 224, "end": 232}, + {"helix": 9, "forward": true, "start": 224, "end": 248} + ] + }, + { + "color": "#007200", + "sequence": "ATCATATGTTACTAGAAAAAGCCTGTAGCCAG", + "domains": [ + {"helix": 9, "forward": true, "start": 248, "end": 256}, + {"helix": 10, "forward": false, "start": 232, "end": 256, "deletions": [251], "insertions": [[235, 1]]} + ] + }, + { + "color": "#cc0000", + "sequence": "TAGAGGATCTTGCATGCCTGCAGTACCTGAG", + "domains": [ + {"helix": 12, "forward": false, 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a/examples/output_designs/relax_helix_rolls.sc b/examples/output_designs/relax_helix_rolls.sc index 29d63c4..7fc6189 100644 --- a/examples/output_designs/relax_helix_rolls.sc +++ b/examples/output_designs/relax_helix_rolls.sc @@ -1,5 +1,5 @@ { - "version": "0.18.2", + "version": "0.19.0", "grid": "square", "helices": [ { diff --git a/examples/output_designs/sst-motif-3_2.sc b/examples/output_designs/sst-motif-3_2.sc index fd9e294..7ea1742 100644 --- a/examples/output_designs/sst-motif-3_2.sc +++ b/examples/output_designs/sst-motif-3_2.sc @@ -1,465 +1,465 @@ -{ - "version": "0.15.0", - "grid": "square", - "helices": [ - {"max_offset": 160, "grid_position": [0, 0], "major_tick_distance": 10}, - {"max_offset": 180, "grid_position": [0, 1], "major_tick_distance": 10}, - {"grid_position": [0, 2], "major_tick_distance": 10}, - {"max_offset": 180, "grid_position": [0, 3], "major_tick_distance": 10}, - {"grid_position": [0, 4], "major_tick_distance": 10}, - {"max_offset": 180, "grid_position": 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- {"max_offset": 672, "grid_position": [0, 25]}, - {"max_offset": 672, "grid_position": [0, 26]}, - {"max_offset": 672, "grid_position": [0, 27]}, - {"max_offset": 672, "grid_position": [0, 28]}, - {"max_offset": 672, "grid_position": [0, 29]}, - {"max_offset": 672, "grid_position": [0, 30]}, - {"max_offset": 672, "grid_position": [0, 31]}, - {"max_offset": 672, "grid_position": [0, 32]}, - {"max_offset": 672, "grid_position": [0, 33]}, - {"max_offset": 672, "grid_position": [0, 34]}, - {"max_offset": 672, "grid_position": [0, 35]}, - {"max_offset": 672, "grid_position": [0, 36]}, - {"max_offset": 672, "grid_position": [0, 37]}, - {"max_offset": 672, "grid_position": [0, 38]}, - {"max_offset": 672, "grid_position": [0, 39]} - ], - "strands": [ - { - "color": "#0066cc", - "sequence": "TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGTCGTGTGACTGGTGAATCTGCCAATGTAAATAATCCATTTCAGACGATTGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCGGTAATATTGTTCTGGATATTACCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTGCTACAACGGTTAATTTGCGTGATGGACAGACTCTTTTACTCGGTGGCCTCACTGATTATAAAAACACTTCTCAGGATTCTGGCGTACCGTTCCTGTCTAAAATCCCTTTAATCGGCCTCCTGTTTAGCTCCCGCTCTGATTCTAACGAGGAAAGCACGTTATACGTGCTCGTCAAAGCAACCATAGTACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCGCAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTTTC??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????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"TTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCGGAACCACCATCAAACAGGATTTTCGCCTGCTGGGGCAAACCAGCGTGGACCGCTTGCTGCAACTCTCTCAGGGCCAGGCGGTGAAGGGCAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAAAGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCCGGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATACTGTCGTCGTCCCCTCAAACTGGCAGATGCACGGTTACGATGCGCCCATCTACACCAACGTGACCTATCCCATTACGGTCAATCCGCCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCGAATTTTAACAAAATATTAACGTTTACAATTTAAATATTTGCTTATACAATCTTCCTGTTTTTGGGGCTTTTCTGATTATCAACCGGGGTACATATGATTGACATGCTAGTTTTACGATTACCGTTCATCGATTCTCTTGTTTGCTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTTTGAATCTTTACCTACACATTACTCAGGCATTGCATTTAAAATATATGAGGGTTCTAAAAATTTTTATCCTTGCGTTGAAATAAAGGCTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAGCTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGCTACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTATTGACCATTTGCGAAATGTATCTAATGGTCAAACTAAATCTACTCGTTCGCAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTAGTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAATCCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTTGCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTCGTTTTCTGAACTGTTTAAAGCATTTGAGGGGGATTCAATGAATATTTATGACGATTCCGCAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTAGTTGAATGTGGTATTCCTAAATCTCAACTGATGAATCTTTCTACCTGTAATAATGTTGTTCCGTTAGTTCGTTTTATTAACGTAGATTTTTCTTCCCAACGTCCTGACTGGTATAATGAGCCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATTTGGGTAATGAATATCCGGTTCTTGTCAAGATTACTCTTGATGAAGGTCAGCCAGCCTATGCGCCTGGTCTGTACACCGTTCATCTGTCCTCTTTCAAAGTTGGTCAGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCGTTTTAGGTTGGTGCCTTCGTAGTGGCATTACGTATTTTACCCGTTTAATGGAAACTTCCTCATGAAAAAGTCTTTAGTCCTCAAAGCCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTGACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCGATACAATTAAAGGCTCCTTTTGGAGCCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAGTTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCCCATACAGAAAATTCATTTACTAACGTCTGGAAAGACGACAAAACTTTAGATCGTTACGCTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTTACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCCGGGCTATACTTATATCAACCCTCTCGACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAGCCTCTTAATACTTTCATGTTTCAGAATAATAGGTTCCGAAATAGGCAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTTAAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTAATGAGGATTTATTTGTTTGTGAATATCAAGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGGCGGCTCTGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGTGGCGGCTCTGAGGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGTGATTTTGATTATGAAAAGATGGCAAACGCTAATAAGGGGGCTATGACCGAAAATGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGCTATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGGCTCTAATTCCCAAATGGCTCAAGTCGGTGACGGTGATAATTCACCTTTAATGAATAATTTCCGTCAATATTTACCTTCCCTCCCTCAATCGGTTGAATGTCGCCCTTTTGTCTTTGGCGCTGGTAAACCATATGAATTTTCTATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATGTTGCCACCTTTATGTATGTATTTTCTACGTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTGCGTTTCCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATCTGCTTACTTTTCTTAAAAAGGGCTTCGGTAAGATAGCTATTGCTATTTCATTGTTTCTTGCTCTTATTATTGGGCTTAACTCAATTCTTGTGGGTTATCTCTCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTTTATGTTATTCTCTCTGTAAAGGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGTCGTGTGACTGGTGAATCTGCCAATGTAAATAATCCATTTCAGACGATTGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCGGTAATATTGTTCTGGATATTACCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTGCTACAACGGTTAATTTGCGTGATGGACAGACTCTTTTACTCGGTGGCCTCACTGATTATAAAAACACTTCTCAGGATTCTGGCGTACCGTTCCTGTCTAAAATCCCTTTAATCGGCCTCCTGTTTAGCTCCCGCTCTGATTCTAACGAGGAAAGCACGTTATACGTGCTCGTCAAAGCAACCATAGTACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCGCAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTTTC??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????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"????????????????????????????????", + "domains": [ + {"helix": 38, "forward": false, "start": 624, "end": 632}, + {"helix": 37, "forward": true, "start": 624, "end": 640}, + {"helix": 36, "forward": false, "start": 632, "end": 640} + ] + } + ] } \ No newline at end of file diff --git a/examples/oxdna_export_with_pitch.py b/examples/oxdna_export_with_pitch.py index a0ecf38..37f2511 100644 --- a/examples/oxdna_export_with_pitch.py +++ b/examples/oxdna_export_with_pitch.py @@ -1,7 +1,7 @@ import scadnano as sc -def create_design(pitch: float) -> sc.Design: +def create_design(pitch: float = 0) -> sc.Design: helices = [sc.Helix(max_offset=100) for _ in range(2)] design = sc.Design(helices=helices, grid=sc.square) From f679027e3745eebaa0d57ab47eb7f10e8013e181 Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 29 Aug 2023 17:40:48 -0700 Subject: [PATCH 11/25] fixed docstrings --- scadnano/scadnano.py | 16 ++++++++-------- tests/scadnano_tests.py | 8 ++++---- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index e303bfd..d02c5f8 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -2147,10 +2147,10 @@ def strand(self) -> Strand: raise ValueError('_parent_strand has not yet been set') return self._parent_strand - def idt_dna_sequence(self) -> Optional[str]: + def vendor_dna_sequence(self) -> Optional[str]: """ :return: - IDT DNA sequence of this :any:`Domain`, or ``None`` if no DNA sequence has been assigned. + vendor DNA sequence of this :any:`Domain`, or ``None`` if no DNA sequence has been assigned. The difference between this and the field :data:`Domain.dna_sequence` is that this will add internal modification codes. """ @@ -3918,7 +3918,7 @@ def vendor_export_name(self, unique_names: bool = False) -> str: If False (the default), uses cadnano's exact naming convention, which allows two strands to have the same default name, if they begin and end at the same (helix,offset) pair (but point in opposite directions at each). - Has no effect if :py:data:`Strand.idt` or :py:data:`Strand.name` are defined; + Has no effect if :data:`Strand.vendor_fields` or :py:data:`Strand.name` are defined; if those are used, they must be explicitly set to be unique. :return: If :py:data:`Strand.name` is not None, return :py:data:`Strand.name`, @@ -4333,7 +4333,7 @@ def vendor_dna_sequence(self, domain_delimiter: str = '') -> str: ret_list.append(self.modification_5p.vendor_code) for substrand in self.domains: - ret_list.append(substrand.idt_dna_sequence()) + ret_list.append(substrand.vendor_dna_sequence()) if self.modification_3p is not None and self.modification_3p.vendor_code is not None: ret_list.append(self.modification_3p.vendor_code) @@ -7459,7 +7459,7 @@ def write_idt_plate_excel_file(self, *, directory: str = '.', filename: Optional export_non_modified_strand_version: bool = False) -> None: """ Write ``.xls`` (Microsoft Excel) file encoding the strands of this :any:`Design` with the field - :py:data:`Strand.idt`, suitable for uploading to IDT + :data:`Strand.vendor_fields`, suitable for uploading to IDT (Integrated DNA Technologies, Coralville, IA, https://www.idtdna.com/) to describe a 96-well or 384-well plate (https://www.idtdna.com/site/order/plate/index/dna/), @@ -7490,7 +7490,7 @@ def write_idt_plate_excel_file(self, *, directory: str = '.', filename: Optional purifications. :param only_strands_with_idt: If False (the default), all non-scaffold sequences are output, with reasonable default values - chosen if the field :py:data:`Strand.idt` is missing. + chosen if the field :data:`Strand.vendor_fields` is missing. (though scaffold is included if `export_scaffold` is True). If True, then strands lacking the field :any:`Strand.idt` will not be exported. If False, then `use_default_plates` must be True. @@ -7501,11 +7501,11 @@ def write_idt_plate_excel_file(self, *, directory: str = '.', filename: Optional `only_strands_with_idt` is True). :param use_default_plates: Use default values for plate and well (ignoring those in idt fields, which may be None). - If False, each Strand to export must have the field :py:data:`Strand.idt`, so in particular + If False, each Strand to export must have the field :data:`Strand.vendor_fields`, so in particular the parameter `only_strands_with_idt` must be True. :param warn_using_default_plates: specifies whether, if `use_default_plates` is True, to print a warning for strands whose - :py:data:`Strand.idt` has the fields :data:`VendorFields.plate` and :data:`VendorFields.well`, + :data:`Strand.vendor_fields` has the fields :data:`VendorFields.plate` and :data:`VendorFields.well`, since `use_default_plates` directs these fields to be ignored. :param plate_type: a :any:`PlateType` specifying whether to use a 96-well plate or a 384-well plate diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index b063259..0f87ebe 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -670,25 +670,25 @@ def test_mod_illegal_exceptions_raised(self) -> None: # with self.assertRaises(sc.IllegalDesignError): # strand = sc.Strand(domains=[sc.Substrand(0, True, 0, 5)], dna_sequence='AATGC', # modifications=[biotin_i_small]) - # seq = strand.idt_dna_sequence() + # seq = strand.vendor_dna_sequence() # # biotin_i_large = mod.Biotin(location=sc.ModLocation.internal, offset=10) # with self.assertRaises(sc.IllegalDesignError): # strand = sc.Strand(domains=[sc.Substrand(0, True, 0, 5)], dna_sequence='AATGC', # modifications=[biotin_i_small]) - # seq = strand.idt_dna_sequence() + # seq = strand.vendor_dna_sequence() # # biotin_i_offset_not_T = mod.Biotin(location=sc.ModLocation.internal, offset=0) # with self.assertRaises(sc.IllegalDesignError): # strand = sc.Strand(domains=[sc.Substrand(0, True, 0, 5)], dna_sequence='AATGC', # modifications=[biotin_i_offset_not_T]) - # seq = strand.idt_dna_sequence() + # seq = strand.vendor_dna_sequence() # # cy3I_offset_off_end = mod.Cy3(location=sc.ModLocation.internal, offset=4) # with self.assertRaises(sc.IllegalDesignError): # strand = sc.Strand(domains=[sc.Substrand(0, True, 0, 5)], dna_sequence='AATGC', # modifications=[cy3I_offset_off_end]) - # seq = strand.idt_dna_sequence() + # seq = strand.vendor_dna_sequence() def test_Cy3(self) -> None: cy3_5 = mod.cy3_5p From 65630f49ea2de9f695714fd83dc4a3df4e54323a Mon Sep 17 00:00:00 2001 From: David Doty Date: Tue, 29 Aug 2023 21:11:39 -0700 Subject: [PATCH 12/25] fixed docstrings --- scadnano/scadnano.py | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index d02c5f8..3e2aabe 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -3950,7 +3950,7 @@ def default_export_name(self, unique_names: bool = False) -> str: default name to export (used, for example, by idt DNA export methods :py:meth:`Design.write_idt_plate_excel_file` and :py:meth:`Design.write_idt_bulk_input_file` - if :py:data:`Strand.name` and :py:data:`Strand.idt.name` are both not set) + if :py:data:`Strand.name` and :data:`Strand.vendor_fields.name` are both not set) """ start_helix = self.first_bound_domain().helix end_helix = self.last_bound_domain().helix @@ -4543,8 +4543,8 @@ def __init__(self, strand: Strand, the_cause: str) -> None: # def _plates(idt_strands) -> List[str]: # plates: Set[str] = set() # for strand in idt_strands: -# if strand.idt is not None and strand.idt.plate is not None: -# plates.add(strand.idt.plate) +# if strand.vendor_fields is not None and strand.vendor_fields.plate is not None: +# plates.add(strand.vendor_fields.plate) # return list(plates) @@ -5030,11 +5030,11 @@ def _plate_map(plate_name: str, strands_in_plate: List[Strand], plate_type: Plat """ Generates plate map from this :any:`Design` for plate with name `plate_name`. - All :any:`Strand`'s in the design that have a field :data:`Strand.idt` with :data:`Strand.idt.plate` - with value `plate_name` are exported. + All :any:`Strand`'s in the design that have a field :data:`Strand.vendor_fields` with + :data:`Strand.vendor_fields.plate` with value `plate_name` are exported. :return: - plate map for :any:`Strand`'s with :data:`Strand.idt.plate` equal to`plate_name` + plate map for :any:`Strand`'s with :data:`Strand.vendor_fields.plate` equal to`plate_name` """ well_to_strand = {} for strand in strands_in_plate: @@ -6236,10 +6236,10 @@ def plate_maps(self, See the documentation for :meth:`PlateMap.to_table` for more information on configuring the returned string format. - All :any:`Strand`'s in the design that have a field :data:`Strand.idt` with :data:`Strand.idt.plate` - specified are included in some returned :any:`PlateMap`. The number of :any:`PlateMap`'s in the - returned list is equal to the number of different plate names specified across all - :any:`Strand`'s in the design. + All :any:`Strand`'s in the design that have a field :data:`Strand.vendor_fields` with + :data:`Strand.vendor_fields.plate` specified are included in some returned :any:`PlateMap`. + The number of :any:`PlateMap`'s in the returned list is equal to the number of different plate names + specified across all :any:`Strand`'s in the design. If parameter `strands` is given, then a subset of strands is included. This is useful for specifying a mix of strands for a particular experiment, which come from a plate but does not @@ -7388,7 +7388,7 @@ def write_idt_bulk_input_file(self, *, directory: str = '.', filename: str = Non export_scaffold: bool = False, export_non_modified_strand_version: bool = False) -> None: """Write ``.idt`` text file encoding the strands of this :any:`Design` with the field - :any:`Strand.idt`, suitable for pasting into the "Bulk Input" field of IDT + :data:`Strand.vendor_fields`, suitable for pasting into the "Bulk Input" field of IDT (Integrated DNA Technologies, Coralville, IA, https://www.idtdna.com/), with the output file having the same name as the running script but with ``.py`` changed to ``.idt``, unless `filename` is explicitly specified. @@ -7425,13 +7425,13 @@ def write_idt_bulk_input_file(self, *, directory: str = '.', filename: str = Non purifications. :param only_strands_with_idt: If False (the default), all non-scaffold sequences are output, with reasonable default values - chosen if the field :data:`Strand.idt` is missing. + chosen if the field :data:`Strand.vendor_fields` is missing. (though scaffold is included if `export_scaffold` is True). - If True, then strands lacking the field :data:`Strand.idt` will not be exported. + If True, then strands lacking the field :data:`Strand.vendor_fields` will not be exported. :param export_scaffold: If False (the default), scaffold sequences are not exported. If True, scaffold sequences on strands output according to `only_strands_with_idt` - (i.e., scaffolds will be exported, unless they lack the field :any:`Strand.idt` and + (i.e., scaffolds will be exported, unless they lack the field :any:`Strand.vendor_fields` and `only_strands_with_idt` is True). :param export_non_modified_strand_version: For any :any:`Strand` with a :any:`Modification`, also export a version of the :any:`Strand` @@ -7492,12 +7492,12 @@ def write_idt_plate_excel_file(self, *, directory: str = '.', filename: Optional If False (the default), all non-scaffold sequences are output, with reasonable default values chosen if the field :data:`Strand.vendor_fields` is missing. (though scaffold is included if `export_scaffold` is True). - If True, then strands lacking the field :any:`Strand.idt` will not be exported. + If True, then strands lacking the field :data:`Strand.vendor_fields` will not be exported. If False, then `use_default_plates` must be True. :param export_scaffold: If False (the default), scaffold sequences are not exported. If True, scaffold sequences on strands output according to `only_strands_with_idt` - (i.e., scaffolds will be exported, unless they lack the field :any:`Strand.idt` and + (i.e., scaffolds will be exported, unless they lack the field :any:`Strand.vendor_fields` and `only_strands_with_idt` is True). :param use_default_plates: Use default values for plate and well (ignoring those in idt fields, which may be None). From 3bb13733e7a59005ebcf329c914d5223db51ec5c Mon Sep 17 00:00:00 2001 From: David Doty Date: Wed, 30 Aug 2023 11:50:21 -0700 Subject: [PATCH 13/25] Update scadnano.py --- scadnano/scadnano.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 3e2aabe..a2c0ed9 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -7458,15 +7458,15 @@ def write_idt_plate_excel_file(self, *, directory: str = '.', filename: Optional plate_type: PlateType = PlateType.wells96, export_non_modified_strand_version: bool = False) -> None: """ - Write ``.xls`` (Microsoft Excel) file encoding the strands of this :any:`Design` with the field + Write ``.xlsx`` (Microsoft Excel) file encoding the strands of this :any:`Design` with the field :data:`Strand.vendor_fields`, suitable for uploading to IDT (Integrated DNA Technologies, Coralville, IA, https://www.idtdna.com/) to describe a 96-well or 384-well plate (https://www.idtdna.com/site/order/plate/index/dna/), - with the output file having the same name as the running script but with ``.py`` changed to ``.xls``, - unless `filename` is explicitly specified. + with the output file having the same name as the running script but with ``.py`` changed to + ``.xlsx``, unless `filename` is explicitly specified. For instance, if the script is named ``my_origami.py``, - then the sequences will be written to ``my_origami.xls``. + then the sequences will be written to ``my_origami.xlsx``. If the last plate as fewer than 24 strands for a 96-well plate, or fewer than 96 strands for a 384-well plate, then the last two plates are rebalanced to ensure that each plate has at least From 63566899b9b7849709b54825647d926dcfe72266 Mon Sep 17 00:00:00 2001 From: David Doty Date: Wed, 30 Aug 2023 18:10:21 -0700 Subject: [PATCH 14/25] closes #281: remove field `Modification.id` --- scadnano/scadnano.py | 79 +++++++++++++++++++++++------------------ tests/scadnano_tests.py | 20 +++-------- 2 files changed, 48 insertions(+), 51 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index a2c0ed9..1d59003 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -77,6 +77,7 @@ # we import like this so that we can use openpyxl.Workbook in the type hints, but still allow # someone to use the library without having openpyxl installed try: + # noinspection PyUnresolvedReferences import openpyxl except ImportError as import_error: pass @@ -933,7 +934,6 @@ def m13(rotation: int = 5587, variant: M13Variant = M13Variant.p7249) -> str: mod_vendor_code_key = 'vendor_code' legacy_mod_vendor_code_keys = ['idt_text'] mod_font_size_key = 'font_size' -mod_display_connector_key = 'display_connector' mod_allowed_bases_key = 'allowed_bases' mod_connector_length_key = 'connector_length' @@ -956,7 +956,6 @@ def m13(rotation: int = 5587, variant: M13Variant = M13Variant.p7249) -> str: ########################################################################## # modification classes -_default_modification_id = "WARNING: no id assigned to modification" default_connector_length = 4 @@ -1002,36 +1001,36 @@ class was created to directly support this idea), """ display_text: str - """Short text to display in the web interface as an "icon" - visually representing the modification, e.g., ``'B'`` for biotin or ``'Cy3'`` for Cy3.""" - - id: str = _default_modification_id """ - Representation as a string; used to write in :any:`Strand` json representation, - while the full description of the modification is written under a global key in the :any:`Design`. - If not specified, but :data:`Modification.vendor_code` is specified, then it will be set equal to that. + Short text to display in the web interface as an "icon" + visually representing the modification, e.g., ``'B'`` for biotin or ``'Cy3'`` for Cy3. """ - vendor_code: Optional[str] = None - """Text string specifying this modification used by a vendor (a DNA synthesis company such as IDT). - For example, for IDT DNA (https://www.idtdna.com/), use '/5Biosg/' for 5' biotin.""" + vendor_code: str + """ + Text string specifying this modification used by a vendor (a DNA synthesis company such as IDT). + For example, for IDT DNA (https://www.idtdna.com/), use '/5Biosg/' for 5' biotin. + + This field must be unique to the :any:`Modification`; undefined behavior could result if two different + :any:`Modification` objects have the same :data:`Modification.vendor_code`. + """ connector_length: int = default_connector_length - """Length of "connector" displayed in web interface. + """ + Length of "connector" displayed in web interface. Drawn like a carbon chain to offset the display of the modification vertically from the DNA strand. This field is useful for putting two nearby modifications at different heights so that their - text does not overlap.""" - - def __post_init__(self) -> None: - if self.id == _default_modification_id and self.vendor_code is not None: - object.__setattr__(self, 'id', self.vendor_code) + text does not overlap. + + Set the length to 0 to not draw a connector. + """ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> Dict[str, Any]: - ret = {mod_display_text_key: self.display_text} - if self.vendor_code is not None: - ret[mod_vendor_code_key] = self.vendor_code - ret[mod_display_connector_key] = False # type: ignore + ret = { + mod_display_text_key: self.display_text, + mod_vendor_code_key: self.vendor_code, + } if self.connector_length != default_connector_length: ret[mod_connector_length_key] = self.connector_length return ret @@ -1147,7 +1146,6 @@ class ModificationInternal(Modification): """ def __post_init__(self) -> None: - super().__post_init__() if self.allowed_bases is not None and not isinstance(self.allowed_bases, frozenset): object.__setattr__(self, 'allowed_bases', frozenset(self.allowed_bases)) @@ -3718,13 +3716,13 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D dct[is_scaffold_key] = self.is_scaffold if self.modification_5p is not None: - dct[modification_5p_key] = self.modification_5p.id + dct[modification_5p_key] = self.modification_5p.vendor_code if self.modification_3p is not None: - dct[modification_3p_key] = self.modification_3p.id + dct[modification_3p_key] = self.modification_3p.vendor_code if len(self.modifications_int) > 0: mods_dict = {} for offset, mod in self.modifications_int.items(): - mods_dict[f"{offset}"] = mod.id + mods_dict[f"{offset}"] = mod.vendor_code dct[modifications_int_key] = NoIndent(mods_dict) if suppress_indent else mods_dict if self.label is not None: @@ -5769,7 +5767,11 @@ def from_scadnano_json_map( all_mods = {} for mod_key, mod_json in all_mods_json.items(): mod = Modification.from_json(mod_json) - mod = dataclasses.replace(mod, id=mod_key) + if mod_key != mod.vendor_code: + print(f'WARNING: key {mod_key} does not match vendor_code field {mod.vendor_code}' + f'for modification {mod}\n' + f'replacing with key = {mod.vendor_code}') + mod = dataclasses.replace(mod, vendor_code=mod_key) all_mods[mod_key] = mod Design.assign_modifications_to_strands(strands, strand_jsons, all_mods) @@ -5831,8 +5833,14 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D if len(mods) > 0: mods_dict = {} for mod in mods: - if mod.id not in mods_dict: - mods_dict[mod.id] = mod.to_json_serializable(suppress_indent) + if mod.vendor_code not in mods_dict: + mods_dict[mod.vendor_code] = mod.to_json_serializable(suppress_indent) + else: + if mod != mods_dict[mod.vendor_code]: + raise IllegalDesignError(f"Modifications must have unique vendor codes, but I found" + f"two different Modifications that share vendor code " + f"{mod.vendor_code}:\n{mod}\nand\n" + f"{mods_dict[mod.vendor_code]}") dct[design_modifications_key] = mods_dict dct[strands_key] = [strand.to_json_serializable(suppress_indent) for strand in self.strands] @@ -6319,19 +6327,20 @@ def modifications(self, mod_type: Optional[ModificationType] = None) -> Set[Modi else: raise AssertionError('should be unreachable') - self._ensure_mods_unique_names(all_mods) + self._ensure_mods_have_unique_vendor_codes(all_mods) return all_mods @staticmethod - def _ensure_mods_unique_names(all_mods: Set[Modification]) -> None: + def _ensure_mods_have_unique_vendor_codes(all_mods: Set[Modification]) -> None: mods_dict = {} for mod in all_mods: - if mod.id not in mods_dict: - mods_dict[mod.id] = mod + if mod.vendor_code not in mods_dict: + mods_dict[mod.vendor_code] = mod else: - other_mod = mods_dict[mod.id] - raise IllegalDesignError(f'two different modifications share the id {mod.id}; ' + other_mod = mods_dict[mod.vendor_code] + raise IllegalDesignError(f'two different modifications share the vendor code ' + f'{mod.vendor_code}; ' f'one is\n {mod}\nand the other is\n {other_mod}') def draw_strand(self, helix: int, offset: int) -> StrandBuilder: diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 0f87ebe..ddeb33a 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -632,9 +632,9 @@ def test_to_json__names_unique_for_modifications_raises_no_error(self) -> None: design: sc.Design = sc.Design(helices=helices, strands=[], grid=sc.square) name = 'mod_name' design.draw_strand(0, 0).move(5).with_modification_5p( - sc.Modification5Prime(display_text=name, id=name)) + sc.Modification5Prime(display_text=name, vendor_code=name)) design.draw_strand(0, 5).move(5).with_modification_3p( - sc.Modification3Prime(display_text=name, id=name + '3')) + sc.Modification3Prime(display_text=name, vendor_code=name + '3')) design.to_json(True) def test_to_json__names_not_unique_for_modifications_raises_error(self) -> None: @@ -642,9 +642,9 @@ def test_to_json__names_not_unique_for_modifications_raises_error(self) -> None: design: sc.Design = sc.Design(helices=helices, strands=[], grid=sc.square) name = 'mod_name' design.draw_strand(0, 0).move(5).with_modification_5p( - sc.Modification5Prime(display_text=name, id=name)) + sc.Modification5Prime(display_text=name, vendor_code=name)) design.draw_strand(0, 5).move(5).with_modification_3p( - sc.Modification3Prime(display_text=name, id=name)) + sc.Modification3Prime(display_text=name, vendor_code=name)) with self.assertRaises(sc.IllegalDesignError): design.to_json(True) @@ -693,21 +693,17 @@ def test_mod_illegal_exceptions_raised(self) -> None: def test_Cy3(self) -> None: cy3_5 = mod.cy3_5p self.assertEqual(r'/5Cy3/', cy3_5.vendor_code) - self.assertEqual(r'/5Cy3/', cy3_5.id) self.assertEqual('Cy3', cy3_5.display_text) cy3_3 = mod.cy3_3p self.assertEqual(r'/3Cy3Sp/', cy3_3.vendor_code) - self.assertEqual(r'/3Cy3Sp/', cy3_3.id) self.assertEqual('Cy3', cy3_3.display_text) # cy3_i1 = mod.Cy3(location=sc.ModLocation.internal, offset=1) cy3_i1 = mod.cy3_int self.assertEqual(r'/iCy3/', cy3_i1.vendor_code) - self.assertEqual(r'/iCy3/', cy3_i1.id) self.assertEqual('Cy3', cy3_i1.display_text) # cy3_i2 = mod.Cy3(location=sc.ModLocation.internal, offset=3) cy3_i2 = mod.cy3_int self.assertEqual(r'/iCy3/', cy3_i2.vendor_code) - self.assertEqual(r'/iCy3/', cy3_i2.id) self.assertEqual('Cy3', cy3_i2.display_text) strand5 = sc.Strand(domains=[sc.Domain(0, True, 0, 5)], dna_sequence='ATTGC', @@ -731,21 +727,17 @@ def test_Cy3(self) -> None: def test_biotin(self) -> None: biotin5 = mod.biotin_5p self.assertEqual(r'/5Biosg/', biotin5.vendor_code) - self.assertEqual(r'/5Biosg/', biotin5.id) self.assertEqual('B', biotin5.display_text) biotin3 = mod.biotin_3p self.assertEqual(r'/3Bio/', biotin3.vendor_code) - self.assertEqual(r'/3Bio/', biotin3.id) self.assertEqual('B', biotin3.display_text) # biotin_i_1 = mod.Biotin(location=sc.ModLocation.internal, offset=1) biotin_i_1 = mod.biotin_int self.assertEqual(r'/iBiodT/', biotin_i_1.vendor_code) - self.assertEqual(r'/iBiodT/', biotin_i_1.id) self.assertEqual('B', biotin_i_1.display_text) # biotin_i_2 = mod.Biotin(location=sc.ModLocation.internal, offset=2) biotin_i_2 = mod.biotin_int self.assertEqual(r'/iBiodT/', biotin_i_2.vendor_code) - self.assertEqual(r'/iBiodT/', biotin_i_2.id) self.assertEqual('B', biotin_i_2.display_text) strand5 = sc.Strand(domains=[sc.Domain(0, True, 0, 5)], dna_sequence='ATTGC', @@ -769,22 +761,18 @@ def test_to_json_serializable(self) -> None: biotin5 = mod.biotin_5p biotin5 = dataclasses.replace(biotin5, connector_length=6) self.assertEqual(r'/5Biosg/', biotin5.vendor_code) - self.assertEqual(r'/5Biosg/', biotin5.id) self.assertEqual('B', biotin5.display_text) self.assertEqual(6, biotin5.connector_length) biotin3 = mod.biotin_3p self.assertEqual(r'/3Bio/', biotin3.vendor_code) - self.assertEqual(r'/3Bio/', biotin3.id) self.assertEqual('B', biotin3.display_text) # biotin_i_1 = mod.Biotin(location=sc.ModLocation.internal, offset=1) biotin_i_1 = mod.biotin_int self.assertEqual(r'/iBiodT/', biotin_i_1.vendor_code) - self.assertEqual(r'/iBiodT/', biotin_i_1.id) self.assertEqual('B', biotin_i_1.display_text) # biotin_i_2 = mod.Biotin(location=sc.ModLocation.internal, offset=2) biotin_i_2 = mod.biotin_int self.assertEqual(r'/iBiodT/', biotin_i_2.vendor_code) - self.assertEqual(r'/iBiodT/', biotin_i_2.id) self.assertEqual('B', biotin_i_2.display_text) strand5 = sc.Strand(domains=[sc.Domain(0, True, 0, 5)], dna_sequence='ATTGC', From 4c52f524a867b227985a95faa243eaee7e3bff8f Mon Sep 17 00:00:00 2001 From: David Doty Date: Thu, 31 Aug 2023 12:40:14 -0700 Subject: [PATCH 15/25] Update scadnano.py --- scadnano/scadnano.py | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 1d59003..9cfe362 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -981,8 +981,14 @@ class Modification(_JSONSerializable, ABC): :any:`Modification3Prime`, :any:`Modification5Prime`, or :any:`ModificationInternal` to instantiate. - If :data:`Modification.id` is not specified, then :data:`Modification.vendor_code` is used as - the unique ID. Each :data:`Modification.id` must be unique. For example if you create a 5' modification + :data:`Modification.vendor_code` is used as a unique ID. + Each :data:`Modification.vendor_code` must be unique. + This can cause problems with some vendors such as Eurofins + (https://eurofinsgenomics.com/en/products/dnarna-synthesis/mods/) that reuse the same vendor code + such as [BIOTEG]. + See issue https://github.com/UC-Davis-molecular-computing/scadnano-python-package/issues/283. + + For example if you create a 5' modification to represent 6 T bases: ``t6_5p = Modification5Prime(display_text='6T', vendor_code='TTTTTT')`` (this was a useful hack for putting single-stranded extensions on strands before the :any:`Extension` class was created to directly support this idea), @@ -1004,6 +1010,8 @@ class was created to directly support this idea), """ Short text to display in the web interface as an "icon" visually representing the modification, e.g., ``'B'`` for biotin or ``'Cy3'`` for Cy3. + Note that this can be arbitrary Unicode, for example, to represent a fluorophore as a star, + one can use ``\u2728``, and to represent a quencher as a black circle, one can use ``\u2B24``. """ vendor_code: str From 032ebdeb69e921a329477f7f5e10abf52d67e42b Mon Sep 17 00:00:00 2001 From: David Doty Date: Thu, 31 Aug 2023 12:42:20 -0700 Subject: [PATCH 16/25] Update scadnano.py --- scadnano/scadnano.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 9cfe362..3c01a2b 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1010,7 +1010,7 @@ class was created to directly support this idea), """ Short text to display in the web interface as an "icon" visually representing the modification, e.g., ``'B'`` for biotin or ``'Cy3'`` for Cy3. - Note that this can be arbitrary Unicode, for example, to represent a fluorophore as a star, + Note that this can be arbitrary Unicode, for example, to represent a fluorophore as a glowing star, one can use ``\u2728``, and to represent a quencher as a black circle, one can use ``\u2B24``. """ From 4795224699240176620ff8958e84e355b32caa6d Mon Sep 17 00:00:00 2001 From: David Doty Date: Thu, 31 Aug 2023 15:04:26 -0700 Subject: [PATCH 17/25] Update scadnano.py --- scadnano/scadnano.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 3c01a2b..00dde35 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1010,8 +1010,9 @@ class was created to directly support this idea), """ Short text to display in the web interface as an "icon" visually representing the modification, e.g., ``'B'`` for biotin or ``'Cy3'`` for Cy3. - Note that this can be arbitrary Unicode, for example, to represent a fluorophore as a glowing star, - one can use ``\u2728``, and to represent a quencher as a black circle, one can use ``\u2B24``. + Note that this can be arbitrary Unicode, for example, to represent a fluorophore, + one can use the "glowing star" symbol \u2728, + or to represent a quencher, one can use the "large black circle" symbol \u2B24. """ vendor_code: str From b72a5c7846918a44a78feb9ceccbab659e0f81fc Mon Sep 17 00:00:00 2001 From: David Doty Date: Thu, 31 Aug 2023 15:06:49 -0700 Subject: [PATCH 18/25] Update scadnano.py --- scadnano/scadnano.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 00dde35..6ef534b 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1010,7 +1010,7 @@ class was created to directly support this idea), """ Short text to display in the web interface as an "icon" visually representing the modification, e.g., ``'B'`` for biotin or ``'Cy3'`` for Cy3. - Note that this can be arbitrary Unicode, for example, to represent a fluorophore, + This can be arbitrary Unicode; for example, to represent a fluorophore, one can use the "glowing star" symbol \u2728, or to represent a quencher, one can use the "large black circle" symbol \u2B24. """ From db9ec53379f889ffc42c480302989b9e1b02e19a Mon Sep 17 00:00:00 2001 From: David Doty Date: Thu, 31 Aug 2023 16:45:01 -0700 Subject: [PATCH 19/25] Update scadnano.py --- scadnano/scadnano.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 6ef534b..743d77c 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1011,7 +1011,7 @@ class was created to directly support this idea), Short text to display in the web interface as an "icon" visually representing the modification, e.g., ``'B'`` for biotin or ``'Cy3'`` for Cy3. This can be arbitrary Unicode; for example, to represent a fluorophore, - one can use the "glowing star" symbol \u2728, + one can use the "glowing star" symbol \U0001F31F, or to represent a quencher, one can use the "large black circle" symbol \u2B24. """ From 41d93e38c5016b14d330c1f2705dbd48f7211847 Mon Sep 17 00:00:00 2001 From: David Doty Date: Thu, 31 Aug 2023 16:48:16 -0700 Subject: [PATCH 20/25] removed `Position3D.clone()`, which is unnecessary since `Position3D` is frozen --- scadnano/scadnano.py | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 743d77c..b77caa0 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1236,13 +1236,6 @@ def __add__(self, other: Position3D) -> Position3D: """ return Position3D(self.x + other.x, self.y + other.y, self.z + other.z) - def clone(self) -> Position3D: - """ - :return: - copy of this :any:`Position3D` - """ - return Position3D(self.x, self.y, self.z) - origin: Position3D = Position3D(x=0, y=0, z=0) @@ -8883,7 +8876,7 @@ def _oxdna_get_helix_vectors(design: Design, helix: Helix) -> Tuple[_OxdnaVector position = Position3D() if grid == Grid.none: if helix.position is not None: - position = helix.position.clone() + position = helix.position else: if helix.grid_position is None: raise AssertionError('helix.grid_position should be assigned if grid is not Grid.none') From 64654346dfe36ab19ffae8d064c269db974d9a20 Mon Sep 17 00:00:00 2001 From: David Doty Date: Thu, 31 Aug 2023 16:48:58 -0700 Subject: [PATCH 21/25] Update scadnano.py --- scadnano/scadnano.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index b77caa0..b08f6fc 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -8873,7 +8873,7 @@ def _oxdna_get_helix_vectors(design: Design, helix: Helix) -> Tuple[_OxdnaVector forward = roll_axis normal = -yaw_axis - position = Position3D() + position = origin if grid == Grid.none: if helix.position is not None: position = helix.position From fc3086264e1e5857f7585b2e382d4330cee60822 Mon Sep 17 00:00:00 2001 From: David Doty Date: Thu, 31 Aug 2023 16:50:56 -0700 Subject: [PATCH 22/25] Update scadnano.py --- scadnano/scadnano.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index b08f6fc..8cec304 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -1381,7 +1381,7 @@ def helices_view_order_inverse(self, idx: int) -> int: @dataclass class Geometry(_JSONSerializable): - """Parameters controlling some geometric visualization/physical aspects of Design.""" + """Parameters controlling some geometric visualization/physical aspects of a :any:`Design`.""" rise_per_base_pair: float = 0.332 """Distance in nanometers between two adjacent base pairs along the length of a DNA double helix.""" From 37fa350a46d46daa3b0f4d948934215e83fda7eb Mon Sep 17 00:00:00 2001 From: David Doty Date: Sun, 3 Sep 2023 13:54:42 -0700 Subject: [PATCH 23/25] fixes #283: deal with non-unique Modification vendor codes --- scadnano/scadnano.py | 129 +++++++++++++++++++++++++++++----------- tests/scadnano_tests.py | 33 +++++----- 2 files changed, 113 insertions(+), 49 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 8cec304..fbd93bd 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -858,7 +858,10 @@ def m13(rotation: int = 5587, variant: M13Variant = M13Variant.p7249) -> str: scaffold_key = 'scaffold' helices_view_order_key = 'helices_view_order' is_origami_key = 'is_origami' -design_modifications_key = 'modifications_in_design' +design_modifications_key = 'modifications_in_design' # legacy key for when we stored all mods in one dict +design_modifications_5p_key = 'modifications_5p_in_design' +design_modifications_3p_key = 'modifications_3p_in_design' +design_modifications_int_key = 'modifications_int_in_design' geometry_key = 'geometry' groups_key = 'groups' @@ -966,12 +969,22 @@ class ModificationType(enum.Enum): five_prime = "5'" """5' modification type""" - three_prime = "5'" + three_prime = "3'" """3' modification type""" internal = "internal" """internal modification type""" + def key(self) -> str: + if self == ModificationType.five_prime: + return design_modifications_5p_key + elif self == ModificationType.three_prime: + return design_modifications_3p_key + elif self == ModificationType.internal: + return design_modifications_int_key + else: + raise AssertionError(f'unknown ModificationType {self}') + @dataclass(frozen=True, eq=True) class Modification(_JSONSerializable, ABC): @@ -3962,16 +3975,20 @@ def default_export_name(self, unique_names: bool = False) -> str: name = f'{start_helix}[{start_offset}]{forward_str}{end_helix}[{end_offset}]' return f'SCAF{name}' if self.is_scaffold else f'ST{name}' - def set_modification_5p(self, mod: Modification5Prime = None) -> None: - """Sets 5' modification to be `mod`. `mod` cannot be non-None if :any:`Strand.circular` is True.""" - if self.circular and mod is not None: + def set_modification_5p(self, mod: Modification5Prime) -> None: + """Sets 5' modification to be `mod`. :any:`Strand.circular` must be False.""" + if self.circular: raise StrandError(self, "cannot have a 5' modification on a circular strand") + if not isinstance(mod, Modification5Prime): + raise TypeError(f'mod must be a Modification5Prime but it is type {type(mod)}: {mod}') self.modification_5p = mod - def set_modification_3p(self, mod: Modification3Prime = None) -> None: - """Sets 3' modification to be `mod`. `mod` cannot be non-None if :any:`Strand.circular` is True.""" + def set_modification_3p(self, mod: Modification3Prime) -> None: + """Sets 3' modification to be `mod`. :any:`Strand.circular` must be False.""" if self.circular and mod is not None: raise StrandError(self, "cannot have a 3' modification on a circular strand") + if not isinstance(mod, Modification3Prime): + raise TypeError(f'mod must be a Modification3Prime but it is type {type(mod)}: {mod}') self.modification_3p = mod def remove_modification_5p(self) -> None: @@ -3999,6 +4016,8 @@ def set_modification_internal(self, idx: int, mod: ModificationInternal, elif warn_on_no_dna: print('WARNING: no DNA sequence has been assigned, so certain error checks on the internal ' 'modification were not done. To be safe, first assign DNA, then add the modifications.') + if not isinstance(mod, ModificationInternal): + raise TypeError(f'mod must be a ModificationInternal but it is type {type(mod)}: {mod}') self.modifications_int[idx] = mod def remove_modification_internal(self, idx: int) -> None: @@ -5763,10 +5782,27 @@ def from_scadnano_json_map( strand = Strand.from_json(strand_json) strands.append(strand) - # modifications in whole design + mods_5p: Dict[str, Modification5Prime] = {} + mods_3p: Dict[str, Modification3Prime] = {} + mods_int: Dict[str, ModificationInternal] = {} + for all_mods_key, mods in zip([design_modifications_5p_key, + design_modifications_3p_key, + design_modifications_int_key], [mods_5p, mods_3p, mods_int]): + if all_mods_key in json_map: + all_mods_json = json_map[all_mods_key] + for mod_key, mod_json in all_mods_json.items(): + mod = Modification.from_json(mod_json) + if mod_key != mod.vendor_code: + print(f'WARNING: key {mod_key} does not match vendor_code field {mod.vendor_code}' + f'for modification {mod}\n' + f'replacing with key = {mod.vendor_code}') + mod = dataclasses.replace(mod, vendor_code=mod_key) + mods[mod_key] = mod + + # legacy code; now we stored modifications in 3 separate dicts depending on 5', 3', internal + all_mods: Dict[str, Modification] = {} if design_modifications_key in json_map: all_mods_json = json_map[design_modifications_key] - all_mods = {} for mod_key, mod_json in all_mods_json.items(): mod = Modification.from_json(mod_json) if mod_key != mod.vendor_code: @@ -5775,7 +5811,8 @@ def from_scadnano_json_map( f'replacing with key = {mod.vendor_code}') mod = dataclasses.replace(mod, vendor_code=mod_key) all_mods[mod_key] = mod - Design.assign_modifications_to_strands(strands, strand_jsons, all_mods) + + Design.assign_modifications_to_strands(strands, strand_jsons, mods_5p, mods_3p, mods_int, all_mods) geometry = None if geometry_key in json_map: @@ -5831,19 +5868,25 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D self.helices_view_order) if suppress_indent else self.helices_view_order # modifications - mods = self.modifications() - if len(mods) > 0: - mods_dict = {} - for mod in mods: - if mod.vendor_code not in mods_dict: - mods_dict[mod.vendor_code] = mod.to_json_serializable(suppress_indent) - else: - if mod != mods_dict[mod.vendor_code]: - raise IllegalDesignError(f"Modifications must have unique vendor codes, but I found" - f"two different Modifications that share vendor code " - f"{mod.vendor_code}:\n{mod}\nand\n" - f"{mods_dict[mod.vendor_code]}") - dct[design_modifications_key] = mods_dict + for mod_type in [ModificationType.five_prime, + ModificationType.three_prime, + ModificationType.internal]: + mods = self.modifications(mod_type) + mod_key = mod_type.key() + if len(mods) > 0: + mods_dict = {} + for mod in mods: + if mod.vendor_code not in mods_dict: + mods_dict[mod.vendor_code] = mod.to_json_serializable(suppress_indent) + else: + if mod != mods_dict[mod.vendor_code]: + raise IllegalDesignError( + f"Modifications of type {mod_type} must have unique vendor codes, " + f"but I foundtwo different Modifications of that type " + f"that share vendor code " + f"{mod.vendor_code}:\n{mod}\nand\n" + f"{mods_dict[mod.vendor_code]}") + dct[mod_key] = mods_dict dct[strands_key] = [strand.to_json_serializable(suppress_indent) for strand in self.strands] @@ -5940,19 +5983,34 @@ def base_pairs(self, allow_mismatches: bool = False) -> Dict[int, List[int]]: @staticmethod def assign_modifications_to_strands(strands: List[Strand], strand_jsons: List[dict], + mods_5p: Dict[str, Modification5Prime], + mods_3p: Dict[str, Modification3Prime], + mods_int: Dict[str, ModificationInternal], all_mods: Dict[str, Modification]) -> None: + if len(all_mods) > 0: # legacy code for when modifications were stored in a single dict + assert len(mods_5p) == 0 and len(mods_3p) == 0 and len(mods_int) == 0 + legacy = True + elif len(mods_5p) > 0 or len(mods_3p) > 0 or len(mods_int) > 0: + assert len(all_mods) == 0 + legacy = False + else: # no modifications + return + for strand, strand_json in zip(strands, strand_jsons): if modification_5p_key in strand_json: - mod_name = strand_json[modification_5p_key] - strand.modification_5p = cast(Modification5Prime, all_mods[mod_name]) + mod_code = strand_json[modification_5p_key] + strand.modification_5p = cast(Modification5Prime, all_mods[mod_code]) \ + if legacy else mods_5p[mod_code] if modification_3p_key in strand_json: - mod_name = strand_json[modification_3p_key] - strand.modification_3p = cast(Modification3Prime, all_mods[mod_name]) + mod_code = strand_json[modification_3p_key] + strand.modification_3p = cast(Modification3Prime, all_mods[mod_code]) \ + if legacy else mods_3p[mod_code] if modifications_int_key in strand_json: mod_names_by_offset = strand_json[modifications_int_key] - for offset_str, mod_name in mod_names_by_offset.items(): + for offset_str, mod_code in mod_names_by_offset.items(): offset = int(offset_str) - strand.modifications_int[offset] = cast(ModificationInternal, all_mods[mod_name]) + strand.modifications_int[offset] = cast(ModificationInternal, all_mods[mod_code]) \ + if legacy else mods_int[mod_code] @staticmethod def _cadnano_v2_import_find_5_end(vstrands: VStrands, strand_type: str, helix_num: int, base_id: int, @@ -6079,7 +6137,7 @@ def _cadnano_v2_import_explore_domains(vstrands: VStrands, seen: Dict[Tuple[int, @staticmethod def _cadnano_v2_import_circular_strands_merge_first_last_domains(domains: List[Domain]) -> None: """ When we create domains for circular strands in the cadnano import routine, we may end up - with a fake crossover if first and last domain are on same helix, we have to merge them + with a fake crossover if first and last domain are on same helix, we have to merge them if it is the case. """ if domains[0].helix != domains[-1].helix: @@ -6210,9 +6268,9 @@ def from_cadnano_v2(directory: str = '', filename: Optional[str] = None, # TS: Dave, I have thorougly checked the code of Design constructor and the order of the helices # IS lost even if the helices were give as a list. # Indeed, you very early call `_normalize_helices_as_dict` in the constructor the order is lost. - # Later in the code, if no view order was given the code will choose the identity + # Later in the code, if no view order was given the code will choose the identity # in function `_check_helices_view_order_and_return`. - # Conclusion: do not assume that your constructor code deals with the ordering, even if + # Conclusion: do not assume that your constructor code deals with the ordering, even if # input helices is a list. I am un commenting the below: design.set_helices_view_order([num for num in helices]) @@ -7641,7 +7699,7 @@ def _write_plates_default(self, directory: str, filename: Optional[str], strands # IDT charges extra for a plate with < 24 strands for 96-well plate # or < 96 strands for 384-well plate. - # So if we would have fewer than that many on the last plate, + # So if we would have fewer than that many on the last plate, # shift some from the penultimate plate. if not on_final_plate and \ final_plate_less_than_min_required and \ @@ -7670,7 +7728,7 @@ def to_oxview_format(self, warn_duplicate_strand_names: bool = True, have duplicate names. (default: True) :param use_strand_colors: if True (default), sets the color of each nucleotide in a strand in oxView to the color - of the strand. + of the strand. """ import datetime self._check_legal_design(warn_duplicate_strand_names) @@ -8184,7 +8242,8 @@ def ligate(self, helix: int, offset: int, forward: bool) -> None: strand_3p.domains.append(dom_new) strand_3p.domains.extend(strand_5p.domains[1:]) strand_3p.is_scaffold = strand_left.is_scaffold or strand_right.is_scaffold - strand_3p.set_modification_3p(strand_5p.modification_3p) + if strand_5p.modification_3p is not None: + strand_3p.set_modification_3p(strand_5p.modification_3p) for idx, mod in strand_5p.modifications_int.items(): new_idx = idx + strand_3p.dna_length() strand_3p.set_modification_internal(new_idx, mod) diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index ddeb33a..62c0472 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -637,16 +637,17 @@ def test_to_json__names_unique_for_modifications_raises_no_error(self) -> None: sc.Modification3Prime(display_text=name, vendor_code=name + '3')) design.to_json(True) - def test_to_json__names_not_unique_for_modifications_raises_error(self) -> None: + def test_to_json__names_not_unique_for_modifications_5p_raises_error(self) -> None: helices = [sc.Helix(max_offset=100)] design: sc.Design = sc.Design(helices=helices, strands=[], grid=sc.square) - name = 'mod_name' + code1 = 'mod_code1' + code2 = 'mod_code2' design.draw_strand(0, 0).move(5).with_modification_5p( - sc.Modification5Prime(display_text=name, vendor_code=name)) - design.draw_strand(0, 5).move(5).with_modification_3p( - sc.Modification3Prime(display_text=name, vendor_code=name)) + sc.Modification5Prime(display_text=code1, vendor_code=code1)) + design.draw_strand(0, 5).move(5).with_modification_5p( + sc.Modification5Prime(display_text=code2, vendor_code=code1)) with self.assertRaises(sc.IllegalDesignError): - design.to_json(True) + design.to_json(False) def test_mod_illegal_exceptions_raised(self) -> None: strand = sc.Strand(domains=[sc.Domain(0, True, 0, 5)], dna_sequence='AATGC') @@ -793,18 +794,22 @@ def test_to_json_serializable(self) -> None: # print(design.to_json()) json_dict = design.to_json_serializable(suppress_indent=False) - self.assertTrue(sc.design_modifications_key in json_dict) - mods_dict = json_dict[sc.design_modifications_key] - self.assertTrue(r'/5Biosg/' in mods_dict) - self.assertTrue(r'/3Bio/' in mods_dict) - self.assertTrue(r'/iBiodT/' in mods_dict) - - biotin5_json = mods_dict[r'/5Biosg/'] + self.assertTrue(sc.design_modifications_5p_key in json_dict) + self.assertTrue(sc.design_modifications_3p_key in json_dict) + self.assertTrue(sc.design_modifications_int_key in json_dict) + mods_5p_dict = json_dict[sc.design_modifications_5p_key] + self.assertTrue(r'/5Biosg/' in mods_5p_dict) + mods_3p_dict = json_dict[sc.design_modifications_3p_key] + self.assertTrue(r'/3Bio/' in mods_3p_dict) + mods_int_dict = json_dict[sc.design_modifications_int_key] + self.assertTrue(r'/iBiodT/' in mods_int_dict) + + biotin5_json = mods_5p_dict[r'/5Biosg/'] self.assertEqual('/5Biosg/', biotin5_json[sc.mod_vendor_code_key]) self.assertEqual('B', biotin5_json[sc.mod_display_text_key]) self.assertEqual(6, biotin5_json[sc.mod_connector_length_key]) - biotin3_json = mods_dict[r'/3Bio/'] + biotin3_json = mods_3p_dict[r'/3Bio/'] self.assertEqual('/3Bio/', biotin3_json[sc.mod_vendor_code_key]) self.assertEqual('B', biotin3_json[sc.mod_display_text_key]) self.assertNotIn(sc.mod_connector_length_key, biotin3_json) From 09ad91bfa88bfc4c883fbd243567c659d7902642 Mon Sep 17 00:00:00 2001 From: David Doty Date: Sun, 3 Sep 2023 14:07:26 -0700 Subject: [PATCH 24/25] Update scadnano.py --- scadnano/scadnano.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index fbd93bd..2cc0ff4 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -5872,7 +5872,6 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D ModificationType.three_prime, ModificationType.internal]: mods = self.modifications(mod_type) - mod_key = mod_type.key() if len(mods) > 0: mods_dict = {} for mod in mods: @@ -5886,7 +5885,7 @@ def to_json_serializable(self, suppress_indent: bool = True, **kwargs: Any) -> D f"that share vendor code " f"{mod.vendor_code}:\n{mod}\nand\n" f"{mods_dict[mod.vendor_code]}") - dct[mod_key] = mods_dict + dct[mod_type.key()] = mods_dict dct[strands_key] = [strand.to_json_serializable(suppress_indent) for strand in self.strands] From 82661bb99e26d8e33e0a0ac8046d4544d6279695 Mon Sep 17 00:00:00 2001 From: David Doty Date: Sun, 3 Sep 2023 14:50:19 -0700 Subject: [PATCH 25/25] Update scadnano.py --- scadnano/scadnano.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 2cc0ff4..9b4e869 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -5746,8 +5746,7 @@ def _helices_and_groups_and_grid_from_json(json_map: Dict) \ return helices, groups, grid @staticmethod - def from_scadnano_json_map( - json_map: dict) -> Design: + def from_scadnano_json_map(json_map: dict) -> Design: """ Loads a :any:`Design` from the given JSON object (i.e., Python object obtained by calling json.loads(json_str) from a string representing contents of a JSON file. @@ -5809,7 +5808,7 @@ def from_scadnano_json_map( print(f'WARNING: key {mod_key} does not match vendor_code field {mod.vendor_code}' f'for modification {mod}\n' f'replacing with key = {mod.vendor_code}') - mod = dataclasses.replace(mod, vendor_code=mod_key) + mod_key = mod.vendor_code all_mods[mod_key] = mod Design.assign_modifications_to_strands(strands, strand_jsons, mods_5p, mods_3p, mods_int, all_mods)