v0.19.4

Release notes

Changed type of Design.to_oxview_format from dict to str to keep convention with similar other methods such as Design.to_oxdna_format.

This is a breaking change, although the minor version number did not change. The method Design.to_oxview_json has the same functionality that Design.to_oxview_format, namely that it returns a JSON-serializable dict. Calling json.dumps on this dict produces the same output as Design.to_oxview_format.

v0.19.3

Release notes

Mostly fixes this bug with oxView export: #297.

We jumped straight from v0.19.0 to v0.19.3 due to some testing that happened in the dev branch.

Commits

• a78b395: bumped version (David Doty) #299
• 5cf25e3: changed parameter type of Strand.set_domains to allow Extension's (David Doty) #299
• 1128beb: added the required build section (RayBipse) #292
• dcede52: Removed python.version (RayBipse) #293
• 3d20590: Removed python.version and added back tools.python (RayBipse) #294
• 4380042: Changed to use mamba and added python version requirement to environment.yml (RayBipse) #295
• 21aa34a: Added pip packages used to environment.yml (RayBipse) #296
• e5572ad: fixes #297: fix oxView export exception on Loopouts (David Doty) #298
• a220c32: Update scadnano.py (David Doty) #299

v0.19.0

Release notes

BREAKING CHANGE: Renamed IDT-specific fields

Some names related to the DNA synthesis company IDT have been renamed to be more general. You will have to rename these in your own code for it to run:

• class IDTFields --> VendorFields
• field Modification.idt_text --> Modification.vendor_code
• field Strand.idt --> Strand.vendor_fields

Additionally, some keys in the JSON format for .sc files have changed as well. Scadnano (both the web interface and the Python package) should be able to read files with the old keys and convert them to the new keys upon saving. However, if you are manually editing the .sc file then use the new keys.

Some IDT-specific methods remain, such as Design.write_idt_plate_excel_file. These use the values in Strand.vendor_fields and Modification.vendor_code, but since the file format actually is specific to IDT, the method name is unchanged.

Although currently there are no methods for exporting to file formats recognized by other synthesis companies, in the meantime it should be straightforward to use the values in VendorFields to write custom code for such exports.

Field Modification.id removed

Previously, scadnano used Modification.id as a unique identifier for modifications.

The field id has been removed. Now, the field vendor_code is used as a unique identifier for the modification, where id was previously used.

Previously, if no id was specified, but vendor_code/idt_text was, then id was set to the latter. Such code should continue to work unmodified. But code referencing id should now refer to vendor_code instead. Additionally, if a script used the same vendor_code for different Modifications, then this will break. Each Modification should now have a unique vendor_code field.

Note that some vendors such as Eurofins use the same code for 5'/3' modifications (see issue #283). For this reason, the modifications internally are stored in a way that encodes their location (5', 3', internal). But for any two modifications of the same "location" (both 5' modifications, both 3' modifications, or both internal modifications) the vendor_code must be unique to the type of modification.

Commits

• 99e16d2: bumped version (David Doty) #285
• bd12d4d: Update scadnano.py (David Doty) #285
• dbc1058: Update scadnano.py (David Doty) #285
• ddc8eee: Update README.md (David Doty) #285
• 34211de: Update scadnano.py (David Doty) #285
• 3ed8158: Update scadnano.py (David Doty) #285
• 0bd7995: Update scadnano.py (David Doty) #285
• d012f17: Update scadnano.py (David Doty) #285
• 1c39fbc: closes #279: rename IDTFields to VendorFields (David Doty) #280
• 5fefd41: re-ran examples to alter changed name of IDT fields (David Doty) #280
• f679027: fixed docstrings (David Doty) #280
• 65630f4: fixed docstrings (David Doty) #280
• 3bb1373: Update scadnano.py (David Doty) #285
• 6356689: closes #281: remove field Modification.id (David Doty) #282
• 4c52f52: Update scadnano.py (David Doty) #285
• 032ebde: Update scadnano.py (David Doty) #285
• 4795224: Update scadnano.py (David Doty) #285
• b72a5c7: Update scadnano.py (David Doty) #285
• db9ec53: Update scadnano.py (David Doty) #285
• 41d93e3: removed Position3D.clone(), which is unnecessary since Position3D is frozen (David Doty) #285
• 6465434: Update scadnano.py (David Doty) #285
• fc30862: Update scadnano.py (David Doty) #285
• 37fa350: fixes #283: deal with non-unique Modification vendor codes (David Doty) #284
• 09ad91b: Update scadnano.py (David Doty) #285
• 82661bb: Update scadnano.py (David Doty) #285

v0.18.3

Release notes

Custom delimiter between DNA sequences of domains

A custom delimiter string to go in between DNA sequences of different domains on a strand can be specified, e.g., a space (which is ignored by IDT), so that the exported IDT sequences might look like this for a 3-domain strand:

ST0[8]0[15];/5Biosg/ ACGTCGT ACGTC ACGTAC;25nm;STD

See

https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Strand.vendor_dna_sequence
https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Design.to_idt_bulk_input_format
https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Design.write_idt_bulk_input_file

Commits

• 301edc4: bumped version (David Doty) #278
• 315c0f3: fixes #276: customize delimiter between domains in exported DNA sequences (David Doty) #277
• 5d8b61d: updated unit test to test for non-default delimiter (David Doty) #277
• 96b5e0d: removed delimiters between internal modifications and rest of sequence (David Doty) #277
• 93431b4: Update scadnano.py (David Doty) #277
• 19975dd: added unit test for internal modification that goes between bases (David Doty) #278

v0.18.2

Bug fixes related to relaxing helix rolls.

Commits

• 8165951: bumped version (David Doty) #275
• 3f5bb6e: fixed one unit test (David Doty) #275
• a37b35a: Update scadnano.py (David Doty) #275
• 0837366: Update scadnano.py (David Doty) #275
• caf20e1: fixed bug in calculating minimum strain angle for helices with no crossovers (David Doty) #275
• e832e53: Update scadnano_tests.py (David Doty) #275
• 25fa92f: fixes #268: ignore loopouts when relaxing Helix rolls (David Doty) #269
• 9ea350b: fixed bug with relaxing roll starting from non-0 roll (David Doty) #275
• 7d938b5: cleaned up unit test (David Doty) #275
• 15c1514: Update scadnano.py (David Doty) #275
• 770366a: fixes #270: ignore "same helix" crossovers when relaxing helix rolls; also ensures domains on helix are stored in increasing order of start offsets (David Doty) #272
• 888565c: added new example (David Doty) #272
• 832c503: Update scadnano_tests.py (David Doty) #275
• d84419f: added unit test for relaxing helix rolls with intrahelix crossovers and fixed bug in relax code that didn't account for that case (David Doty) #275
• d3a6d7d: change parameter name (David Doty) #275
• a2d4e52: fixes #273: deal with inter-group crossovers when relaxing helix rolls (David Doty) #274
• 27568e4: Update scadnano_tests.py (David Doty) #275
• 1dedd8b: fixed relax helix rolls to ignore intergroup crossovers (David Doty) #275
• 51fbc9c: Update tutorial.md (David Doty) #275
• 5189e8d: Update scadnano.py (David Doty) #275

v0.18.1

Release notes

automatically set Helix rolls based on crossover locations ("relax" the rolls)

In this design, the crossovers are well placed relative to each other, but the helix rolls need to be rotated. As the slice bar shows, with the default roll of 0, the crossovers do not point at the helices they connect to:

By calling Design.relax_helix_rolls, the helix rolls are set to minimize "strain" in the crossovers:

Formally, the strain is defined as the square of the angular distance between the "ideal" angle for the crossover (i.e., the relative angle of the other helix to which it is connecting) and the crossover's current angle. The roll is set so as to minimize this total strain across all crossovers in each helix.

The reason to minimize the sum of the squared angular distances is that, if we model each crossover as an angular spring exerting a rotational force on the helix proportional to its displacement from the "ideal" angle (pointing directly at the other helix), this minimizes the total energy stored in the springs.

Commits

• 2b11342: bumped version (David Doty) #267
• 49867e3: Merge branch 'dev' into 257-automatically-set-helix-rolls-based-on-crossover-locations-relax-the-rolls (David Doty) #264
• 123e001: closes #257: automatically set Helix rolls based on crossover locations (relax the rolls) (David Doty) #264
• 5208be3: fixed some unit tests (David Doty) #264
• c370a1f: Update scadnano.py (David Doty) #264
• c26dbe6: fixed dependencies (David Doty) #266
• 62c5dd5: changed unit test versions for openpyxl and tabulate to versions matching what is in Anaconda package repository (David Doty) #266
• 7b963c5: added instructions for installing openpyxl and tabulate to README (David Doty) #266
• f45d3f0: fixes #234: export new Excel format (David Doty) #266
• 3da4763: added openpyxl to tests_require (David Doty) #266
• c177ef0: added openpyxl installation to docs-check GitHub action (David Doty) #266
• 50899e3: Merge branch 'dev' into 257-automatically-set-helix-rolls-based-on-crossover-locations-relax-the-rolls (David Doty) #264

v0.18.0

Release notes

BREAKING CHANGE: label type is now str

Strands, domains, loopouts, and extensions have a field label. Previously the declared type was arbitrary, though at runtime it was required to be JSON-serializable.

Now we have changed the type of label field in Strand, Domain, Loopout, and Extension to str instead of an arbitrary object.

This is a breaking change because existing code using non-string labels will have to be altered to change the data to a string before storing and change it back to structured data when reading.

If you would like to store "structured data" (e.g., lists or dicts) in the label, you can serialize to a string and deserialize back to structured data manually using the json package.

Before, this was possible:

from typing import List

# previously was possible, now is not supported
nums = [1, 2, 3]
strand.label = nums   # stores strand.label as the list [1, 2, 3]; would be a mypy type error now

# and to get the structured data back out:
nums: List[int] = strand.label  # would be a mypy type error now

Now this is necessary to store a list of int's in the label:

import json
from typing import List

nums = [1, 2, 3]
strand.label = json.dumps(nums)  # stores strand.label as the string '[1, 2, 3]'

# and to get the structured data back out:
nums: List[int] = json.loads(strand.label)  # nums is now the list [1, 2, 3]

added p8634 variant of M13

There is a variant of M13 mentioned in a few papers (e.g., https://doi.org/10.1038/s41565-022-01283-1) called "p8634". It can be obtained from Tilibit (though not listed on their website). This sequence is now available as a predefined sequence. See https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.M13Variant.p8634

Commits

• d955eda: bumped version (David Doty) #258
• 2f58b2b: updated docstrings (David Doty) #258
• 0a482a7: Update scadnano.py (David Doty) #258
• c55411e: Update scadnano.py (David Doty) #258
• fca673a: added test generated by GitHub Copilot (David Doty) #258
• 3e84a38: changed docstring for Design.base_pairs (David Doty) #258
• fc2176b: added examples (David Doty) #258
• 7b0603b: changed to LR newlines (David Doty) #258
• 01c43e3: added p8634 variant of M13 (David Doty) #258
• 0678d55: formatting (David Doty) #258
• e8211db: fixed PyCharm warnings (David Doty) #258
• 602575d: closes #261: change label type to str (David Doty) #262
• a292757: removed all string type hints and replaced with forward references (not supported in Python 3.6) (David Doty) #262

v0.17.7

Release notes

new method Design.base_pairs()

This method returns a dict mapping helix idx's where base pairs exist to a list of offsets where those base pairs are.

Domain/Extension/Loopout colors

Individual Domain's, Extension's, and Loopout's now have a color field. If specified, then this overrides the field Strand.color when displayed in the web interface. There is also a new method StrandBuilder.with_domain_color():

helices = [sc.Helix(max_offset=100) for _ in range(4)]
design = sc.Design(helices=helices, grid=sc.square)

red = sc.Color(255, 0, 0)
dark_red = sc.Color(150, 0, 0)
green = sc.Color(0, 255, 0)
dark_green = sc.Color(0, 150, 0)
blue = sc.Color(0, 0, 255)
dark_blue = sc.Color(0, 0, 150)
black = sc.Color(0, 0, 0)

design.draw_strand(0, 0) \
    .extension_5p(num_bases=5).with_domain_color(red) \
    .move(8).with_domain_color(green) \
    .loopout(1, 5).with_domain_color(dark_blue) \
    .move(-8).with_domain_color(dark_red) \
    .cross(2) \
    .move(8).with_domain_color(dark_green) \
    .cross(3) \
    .move(-8) \
    .extension_3p(num_bases=5).with_domain_color(black) \
    .with_color(blue)

Commits

• 5586c9f: bumped version (David Doty) #256
• 6463865: closes #252: add method Design.base_pairs() (David Doty) #254
• fec6f43: changed return type of Design.base_pairs() to dict and added allow_mismatches parameter (David Doty) #254
• e795627: fixed unit tests after updating with_sequence and with_domain_sequence to default to not assigning complement (David Doty) #254
• 6b6001a: removed unused _popleft() function (David Doty) #254
• e55609d: Update scadnano.py (David Doty) #256
• afc44b8: don't put Helix idx in base_pairs dict if Helix has no base pairs (David Doty) #256
• 1049cdc: fixed base pair calculation to allow for deletions/insertions/wildcards/None if DNA sequence is not assigned (David Doty) #256
• e6c0737: added unit test for no base pairs (David Doty) #256
• f81b8ff: Update scadnano_tests.py (David Doty) #256
• 7b83a43: fixed bug in Design.base_pairs() when no reverse domains on helix (David Doty) #256
• 5312a59: Update scadnano_tests.py (David Doty) #256
• 1b7e605: closes #238: Domain colors (David Doty) #255
• fea3b32: added example with domain colors (David Doty) #256

v0.17.6

Release notes

Two big updates:

1. support Extensions in oxDNA export (#240); note it can have problems with large extensions between two close domains, see #253
2. preliminary oxView export (#173)

Commits

• 5cfa122: fixed docstrings for Extension (David Doty) #250
• 9b0d3e3: Update scadnano.py (David Doty) #250
• f84594e: Update scadnano.py (David Doty) #250
• 04a4e9d: Update scadnano.py (David Doty) #250
• 4ae1d93: formatting (David Doty) #250
• 357a59a: updated extensions example (David Doty) #241
• b477328: closes #240: support Extensions in oxDNA export (David Doty) #241
• 895469e: fix bug in assigning DNA sequence to strand bound to another strand with an extension (David Doty) #250
• 897f66d: fixed bug in oxDNA export when extension has no DNA sequence (David Doty) #250
• d1c38b9: Add add_extension to file creation (Constantine Evans) #247
• 1400ade: add test (Constantine Evans) #247
• d9160d6: Initial oxview export implementation (Constantine Evans) #246
• 176811f: Add documentation. (Constantine Evans) #246
• a823fee: Add tests. (Constantine Evans) #246
• 7086a55: probably-working, probably-bad bp implementation (Constantine Evans) #246
• 39b29c0: Tests for bp (Constantine Evans) #246
• 6f95338: add mismatch exclusion (Constantine Evans) #246
• ed71923: added method Design.add_helix (David Doty) #250
• d32537b: swapped order of directory and filename in Design.write_scadnano_file (David Doty) #250
• b0fee20: changed default display angle to 35 to match Web interface default (David Doty) #250
• 400cc3e: bumped version (David Doty) #250
• b9912ee: drop Python 3.6 on unit tests, add 3.10 and 3.11 (David Doty) #250
• 2c3b85f: adding quotes to python versions to try to fix pip install error on github actions (David Doty) #250
• e133772: fixed unit test to ensure helix max offset is sufficiently large (David Doty) #250
• 03d54ae: fixed unit test to ensure helix max offset is sufficiently large (David Doty) #250
• 931f22d: delete temp file manually in unit test for oxDNA export to avoid error where it cannot be read while open for writing (David Doty) #250
• 8e78237: added example of oxDNA export of extension and loopouts (David Doty) #250

v0.17.5

Several small bug fixes, plus one big new feature:

Introducing DNA Extension API

This feature is supported on the web interface dev branch (https://scadnano.org/dev) at the time of this writing, and in the next release will be on the stable server (https://scadnano.org). See UC-Davis-molecular-computing/scadnano#34 (comment)

DNA Extensions can now be represented. This gives a nice way to specify toeholds and other single-stranded extensions common in DNA strand displacement designs, which are single-stranded (unlike most Domains on a Helix) but are at the end of a strand (unlike a Loopout that is flanked by two Domains on a Strand).

They can be created using the Extension class. See full API here: https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Extension

import scadnano as sc

domain = sc.Domain(helix=0, forward=True, start=0, end=10)
left_toehold = sc.Extension(num_bases=6)
right_toehold = sc.Extension(num_bases=5)
strand = sc.Strand([left_toehold, domain, right_toehold])

They can also be created with chained method calls (see https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.StrandBuilder.extension_3p and https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.StrandBuilder.extension_5p)

import scadnano as sc

design = sc.Design(helices=[sc.Helix(max_offset=10)])
design.draw_strand(0,0).extension_5p(6).move(10).extension_3p(5)

See also documentation for this feature in the web interface: https://github.com/UC-Davis-molecular-computing/scadnano/releases/tag/v0.17.6

Commits

• c8a8970: Update scadnano.py (David Doty) #237
• d482066: fixed docstring with string literal '\n\n' (David Doty) #237
• 03f1142: closes #228: option to export cadnano with no whitespace (David Doty) #229
• f25a28f: added with_deletions and with_insertions methods to StrandBuilder and used them in unit tests (David Doty) #237
• 00451a8: added check for deletion/insertion in range in StrandBuilder.with_deletions and StrandBuilder.with_insertions (David Doty) #237
• 4e60f9b: Add UT for chained methods for DNA extensions (Benjamin Lee) #230
• 78c716d: Add TestExportCadnanoV2.test_extension (Benjamin Lee) #230
• f16b629: Use self.design_6helix for extension chain method tests (Benjamin Lee) #230
• 2cdf023: Add move extension move test (Benjamin Lee) #230
• 28b0ded: Add extension ligate test (Benjamin Lee) #230
• a0170e9: Add crossover test (Benjamin Lee) #230
• e8725cc: test_add_full_crossover_on_extension_error (Benjamin Lee) #230
• 738979b: test_add_half_crossover_on_extension_ok (Benjamin Lee) #230
• 3615afb: test_add_half_crossover_on_extension_error (Benjamin Lee) #230
• 2feed8a: test_nick_on_extension (Benjamin Lee) #230
• 1433022: test_from_json_extension_design (Benjamin Lee) #230
• de44f47: test_to_json_extension_design (Benjamin Lee) #230
• e06ac96: Add "relative_offset" field (Benjamin Lee) #230
• d2f1afb: test_strand__with_relative_offset (Benjamin Lee) #230
• faa0a33: test_strand__with_relative_offset_on_domain_error and test_strand__with_relative_offset_on_empty_error (Benjamin Lee) #230
• a1601b7: test_strand__3p_extension_forward_default_relative_offset (Benjamin Lee) #230
• daad677: test_strand__5p_extension_forward_default_relative_offset (Benjamin Lee) #230
• 4c459ea: test_strand__3p_extension_reverse_default_relative_offset (Benjamin Lee) #230
• 0941030: test_strand__5p_extension_reverse_default_relative_offset (Benjamin Lee) #230
• 8f48617: Implement 3' extension (Benjamin Lee) #230
• 5574331: Implement 5p extension (Benjamin Lee) #230
• 8b6c060: Raise StrandError in as_circular if strand contains Extension (Benjamin Lee) #230
• 04b25df: Add 5p_extension test case for circular strand (Benjamin Lee) #230
• 6a2c101: Start docstring for extension (Benjamin Lee) #230
• fdbdf1c: Begin replacing extension -> extension_3p and add extension_5p_length argument to draw_strand (Benjamin Lee) #230
• 3048af8: Redo test_strand__3p_extension (Benjamin Lee) #230
• 0e4c694: Redo test_strand__5p_extension (Benjamin Lee) #230
• b8077c6: delete default relative_offset tests (Benjamin Lee) #230
• 122445c: In to, check for 3' extension; fixed some tests (Benjamin Lee) #230
• c45b916: Check for extension in cross (Benjamin Lee) #230
• cd8edaf: Fix test_strand__cross_after_3p_extension_should_raise_error (Benjamin Lee) #230
• 68466c8: Pass test_strand__extension_3p_after_loopout_should_raise_error (Benjamin Lee) #230
• de3175c: Pass test_strand__extension_3p_after_extension_should_raise_error (Benjamin Lee) #230
• 173fc34: Pass test_strand__update_to_after_3p_extension_should_raise_error (Benjamin Lee) #230
• 5610cf8: Pass test_strand__extension_3p_on_circular_strand_should_raise_error (Benjamin Lee) #230
• 185d097: Extension name, label, and sequence (Benjamin Lee) #230
• 43e06bf: Remove relative_offset and ExtensionBuilder (Benjamin Lee) #230
• 9b9e401: Fix some json and cadnano tests (Benjamin Lee) #230
• 819d0d8: Implement Extension from_json, and fix bug with default color from json (Benjamin Lee) #230
• 860be06: Implement Extension.to_json_serializable (Benjamin Lee) #230
• 06fe222: Fix nick,ligate,and crossover tests (Benjamin Lee) #230
• 2b485be: Add ligate and half crossover error cases (Benjamin Lee) #230
• 63fbd53: Fix middle domain bug in ligate (Benjamin Lee) #230
• 4a2023a: Handle ligate and crossover error case (Benjamin Lee) #230
• a27bcc7: Merge branch 'dev' into 2-support-loopouts-on-the-end-of-a-strand (Benjamin Lee) #230
• 75e4740: fixed errors in plate map documentation (David Doty) #237
• 996e59b: U...