Merge pull request #285 from UC-Davis-molecular-computing/dev

Dev
UC-Davis-molecular-computing · Sep 7, 2023 · f415a47 · f415a47
2 parents 976ee4d + 82661bb
commit f415a47
Show file tree

Hide file tree

Showing 70 changed files with 34,083 additions and 33,968 deletions.
diff --git 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)
 

diff --git 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
@@ -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
@@ -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/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/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):