Merge pull request #136 from UC-Davis-molecular-computing/dev

Dev

README.md

@@ -13,7 +13,7 @@ If you find scadnano useful in a scientific project, please cite its associated
 > scadnano: A browser-based, scriptable tool for designing DNA nanostructures.  
   David Doty, Benjamin L Lee, and Tristan Stérin.  
   DNA 2020: *Proceedings of the 26th International Conference on DNA Computing and Molecular Programming*  
-  [ [paper](https://arxiv.org/abs/2005.11841) | [BibTeX](https://web.cs.ucdavis.edu/~doty/papers/scadnano.bib) ]
+  [ [paper](https://doi.org/10.4230/LIPIcs.DNA.2020.9) | [BibTeX](https://web.cs.ucdavis.edu/~doty/papers/scadnano.bib) ]
 
 
 ## Overview

examples/names_domains_strands.py

@@ -0,0 +1,45 @@
+import scadnano as sc
+
+
+def create_design() -> sc.Design:
+    num_domains = 9
+    helices = [sc.Helix(max_offset=(num_domains) * 8)]
+    design: sc.Design = sc.Design(helices=helices, strands=[], grid=sc.square)
+    design.strand(0, (num_domains - 1) * 8) \
+        .move(-8).with_domain_name('domain 8*') \
+        .move(-8).with_domain_name('domain 7*') \
+        .move(-8).with_domain_name('domain 6*') \
+        .move(-8).with_domain_name('domain 5*') \
+        .move(-8).with_domain_name('domain 4*') \
+        .move(-8).with_domain_name('domain 3*') \
+        .move(-8).with_domain_name('domain 2*') \
+        .move(-8).with_domain_name('domain 1*') \
+        .with_name('bottom strand')
+
+    # domain names match
+    design.strand(0, 0).move(8).with_domain_name('domain 1').with_name('top strand 1')
+
+    # domains are aligns but names mismatch
+    design.strand(0, 8).move(8).with_domain_name('domain 50').with_name('top strand 2')
+
+    # domain names match
+    design.strand(0, 16).move(8).with_domain_name('domain 3').with_name('top strand 3')
+
+    # domain names are the same, not complementary
+    design.strand(0, 24).move(8).with_domain_name('domain 4*').with_name('top strand 4')
+
+    # domain names match but domains are mis-aligned
+    design.strand(0, 32).move(9).with_domain_name('domain 5').with_name('top strand 5')
+
+    # domain names match but domains are mis-aligned
+    design.strand(0, 48).move(7).with_domain_name('domain 7').with_name('top strand 7')
+
+    # no overlap so no mismatch
+    design.strand(0, 64).move(8).with_domain_name('domain 9').with_name('top strand 9')
+
+    return design
+
+
+if __name__ == '__main__':
+    design = create_design()
+    design.write_scadnano_file(directory='output_designs')

examples/output_designs/names_domains_strands.sc

@@ -0,0 +1,72 @@
+{
+  "version": "0.12.0",
+  "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}
+      ]
+    }
+  ]
+}

scadnano/origami_rectangle.py

@@ -2,14 +2,13 @@
 The :mod:`origami_rectangle` module defines the function :py:func:`origami_rectangle.create` for creating a DNA origami rectangle
 using the :mod:`scadnano` module.
 """
-
-from dataclasses import dataclass, field
-
+from typing import List, Union, cast
 # from . import scadnano as sc
 import scadnano as sc
 from enum import Enum, auto
 
-#TODO: write version of origami_rectangle.create that uses add_nick and add_crossover.
+
+# TODO: write version of origami_rectangle.create that uses add_nick and add_crossover.
 
 class NickPattern(Enum):
     """Represents options for where to place nicks between staples."""
@@ -62,12 +61,11 @@ class NickPattern(Enum):
 CURRENTLY UNSUPPORTED."""
 
 
-
-def create(*, num_helices: int, num_cols: int, assign_seq: bool = True, seam_left_column=-1,
+def create(*, num_helices: int, num_cols: int, assign_seq: bool = True, seam_left_column: int = -1,
            nick_pattern: NickPattern = NickPattern.staggered,
            twist_correction_deletion_spacing: int = 0, twist_correction_start_col: int = 1,
-           twist_correction_deletion_offset=-1,
-           num_flanking_columns: int = 1, num_flanking_helices=0,
+           twist_correction_deletion_offset: int = -1,
+           num_flanking_columns: int = 1, num_flanking_helices: int = 0,
            custom_scaffold: str = None, edge_staples: bool = True,
            scaffold_nick_offset: int = -1, use_idt_defaults: bool = False) -> sc.Design:
     """
@@ -234,7 +232,7 @@ def create(*, num_helices: int, num_cols: int, assign_seq: bool = True, seam_lef
     scaffold = _create_scaffold(offset_start, offset_end, offset_mid, num_helices, num_flanking_helices,
                                 scaffold_nick_offset)
     staples = _create_staples(offset_start, offset_end, offset_mid, num_helices, num_flanking_helices,
-                              num_cols, nick_pattern, edge_staples, use_idt_defaults)
+                              num_cols, nick_pattern, edge_staples)
 
     design = sc.Design(helices=helices, strands=[scaffold] + staples, grid=sc.square)
 
@@ -262,15 +260,15 @@ def create(*, num_helices: int, num_cols: int, assign_seq: bool = True, seam_lef
 BASES_PER_COLUMN = 16
 
 
-def _create_helices(num_helices: int, num_bases_per_helix: int):
+def _create_helices(num_helices: int, num_bases_per_helix: int) -> List[sc.Helix]:
     return [sc.Helix(max_offset=num_bases_per_helix) for _ in range(num_helices)]
 
 
 def _create_scaffold(offset_start: int, offset_end: int, offset_mid: int, num_helices: int,
-                     num_flanking_helices: int, scaffold_nick_offset: int):
+                     num_flanking_helices: int, scaffold_nick_offset: int) -> sc.Strand:
     # top domain is continguous
     top_domain = sc.Domain(helix=0 + num_flanking_helices, forward=True,
-                              start=offset_start, end=offset_end)
+                           start=offset_start, end=offset_end)
     domains_left = []
     domains_right = []
     if scaffold_nick_offset < 0:
@@ -281,32 +279,33 @@ def _create_scaffold(offset_start: int, offset_end: int, offset_mid: int, num_he
         center_offset = offset_mid if helix < num_helices + num_flanking_helices - 1 else scaffold_nick_offset
         forward = (helix % 2 == num_flanking_helices % 2)
         left_domain = sc.Domain(helix=helix, forward=forward,
-                                   start=offset_start, end=center_offset)
+                                start=offset_start, end=center_offset)
         right_domain = sc.Domain(helix=helix, forward=forward,
-                                    start=center_offset, end=offset_end)
+                                 start=center_offset, end=offset_end)
         domains_left.append(left_domain)
         domains_right.append(right_domain)
     domains_left.reverse()
-    domains = domains_left + [top_domain] + domains_right
+    domains = cast(List[Union[sc.Domain, sc.Loopout]],  # noqa
+                   domains_left + [top_domain] + domains_right)  # type: ignore
     return sc.Strand(domains=domains, color=sc.default_scaffold_color, is_scaffold=True)
 
 
 def _create_staples(offset_start: int, offset_end: int, offset_mid: int, num_helices: int,
                     num_flanking_helices: int, num_cols: int,
-                    nick_pattern: NickPattern, edge_staples, idt: bool):
+                    nick_pattern: NickPattern, edge_staples: bool) -> List[sc.Strand]:
     if edge_staples:
-        left_edge_staples = _create_left_edge_staples(offset_start, num_helices, num_flanking_helices, idt)
-        right_edge_staples = _create_right_edge_staples(offset_end, num_helices, num_flanking_helices, idt)
+        left_edge_staples = _create_left_edge_staples(offset_start, num_helices, num_flanking_helices)
+        right_edge_staples = _create_right_edge_staples(offset_end, num_helices, num_flanking_helices)
     else:
         left_edge_staples = []
         right_edge_staples = []
-    seam_staples = _create_seam_staples(offset_mid, num_helices, num_flanking_helices, idt)
+    seam_staples = _create_seam_staples(offset_mid, num_helices, num_flanking_helices)
     inner_staples = _create_inner_staples(offset_start, offset_end, offset_mid, num_helices,
-                                          num_flanking_helices, num_cols, nick_pattern, idt)
+                                          num_flanking_helices, num_cols, nick_pattern)
     return left_edge_staples + right_edge_staples + seam_staples + inner_staples
 
 
-def _create_seam_staples(offset_mid: int, num_helices: int, num_flanking_helices: int, idt: bool):
+def _create_seam_staples(offset_mid: int, num_helices: int, num_flanking_helices: int) -> List[sc.Strand]:
     staples = []
     crossover_left = offset_mid - BASES_PER_COLUMN
     crossover_right = offset_mid + BASES_PER_COLUMN
@@ -339,7 +338,8 @@ def _create_seam_staples(offset_mid: int, num_helices: int, num_flanking_helices
     return [first_staple] + staples + [last_staple]
 
 
-def _create_left_edge_staples(offset_start: int, num_helices: int, num_flanking_helices: int, idt: bool):
+def _create_left_edge_staples(offset_start: int, num_helices: int,
+                              num_flanking_helices: int) -> List[sc.Strand]:
     staples = []
     crossover_right = offset_start + BASES_PER_COLUMN
     for helix in range(0 + num_flanking_helices, num_helices + num_flanking_helices, 2):
@@ -353,7 +353,8 @@ def _create_left_edge_staples(offset_start: int, num_helices: int, num_flanking_
     return staples
 
 
-def _create_right_edge_staples(offset_end: int, num_helices: int, num_flanking_helices: int, idt: bool):
+def _create_right_edge_staples(offset_end: int, num_helices: int,
+                               num_flanking_helices: int) -> List[sc.Strand]:
     staples = []
     crossover_left = offset_end - BASES_PER_COLUMN
     for helix in range(0 + num_flanking_helices, num_helices + num_flanking_helices, 2):
@@ -369,7 +370,7 @@ def _create_right_edge_staples(offset_end: int, num_helices: int, num_flanking_h
 
 def _create_inner_staples(offset_start: int, offset_end: int, offset_mid: int, num_helices: int,
                           num_flanking_helices: int, num_cols: int,
-                          nick_pattern: NickPattern, idt: bool):
+                          nick_pattern: NickPattern) -> List[sc.Strand]:
     if nick_pattern is not NickPattern.staggered:
         raise NotImplementedError("Currently can only handle staggered nick pattern")
     # if ((num_cols - 4) // 2) % 2 != 0:
@@ -434,11 +435,11 @@ def _create_inner_staples(offset_start: int, offset_end: int, offset_mid: int, n
     return staples
 
 
-def add_deletion_in_range(design: sc.Design, helix: int, start: int, end: int, deletion_offset: int):
-    #Inserts deletion somewhere in given range.
+def add_deletion_in_range(design: sc.Design, helix: int, start: int, end: int, deletion_offset: int) -> None:
+    # Inserts deletion somewhere in given range.
 
-    #`offset` is the relative offset within a column at which to put the deletions.
-    #If negative, chooses first available offset.
+    # `offset` is the relative offset within a column at which to put the deletions.
+    # If negative, chooses first available offset.
     candidate_offsets = []
     for candidate_deletion_offset in range(start, end):
         if valid_deletion_offset(design, helix, candidate_deletion_offset):
@@ -455,7 +456,7 @@ def add_deletion_in_range(design: sc.Design, helix: int, start: int, end: int, d
     design.add_deletion(helix, deletion_absolute_offset)
 
 
-def valid_deletion_offset(design: sc.Design, helix: int, offset: int):
+def valid_deletion_offset(design: sc.Design, helix: int, offset: int) -> bool:
     domains_at_offset = design.domains_at(helix, offset)
     if len(domains_at_offset) > 2:
         raise ValueError(f'Invalid Design; more than two Substrands found at '
@@ -482,7 +483,7 @@ def add_twist_correction_deletions(design: sc.Design,
                                    deletion_offset: int,
                                    num_helices: int,
                                    num_cols: int,
-                                   num_flanking_helices: int):
+                                   num_flanking_helices: int) -> None:
     for col in range(deletion_start_col, num_cols):
         col_start = offset_start + col * BASES_PER_COLUMN
         col_end = offset_start + (col + 1) * BASES_PER_COLUMN