Merge pull request #41 from UC-Davis-molecular-computing/dev

Dev

MANIFEST

@@ -2,5 +2,6 @@
 setup.cfg
 setup.py
 scadnano\__init__.py
+scadnano\modifications.py
 scadnano\origami_rectangle.py
 scadnano\scadnano.py

examples/16_helix_origami_barrel_from_algoSST_paper.py

@@ -14,7 +14,7 @@ def main():
 
     set_helix_major_tickets(design)
     move_top_and_bottom_staples_within_column_boundaries(design)
-    add_substrands_for_barrel_seam(design)
+    add_domains_for_barrel_seam(design)
     add_toeholds_for_seam_displacement(design)
     add_adapters(design)
     add_twist_correct_deletions(design)
@@ -51,53 +51,53 @@ def move_top_and_bottom_staples_within_column_boundaries(design: sc.DNADesign):
     bot_staples.remove(design.scaffold)
 
     for top_staple in top_staples:
-        current_end = top_staple.substrands[0].end
-        design.set_end(top_staple.substrands[0], current_end - 8)
+        current_end = top_staple.domains[0].end
+        design.set_end(top_staple.domains[0], current_end - 8)
 
     for bot_staple in bot_staples:
-        current_start = bot_staple.substrands[0].start
-        design.set_start(bot_staple.substrands[0], current_start + 8)
+        current_start = bot_staple.domains[0].start
+        design.set_start(bot_staple.domains[0], current_start + 8)
 
 
-def add_substrands_for_barrel_seam(design):
+def add_domains_for_barrel_seam(design):
     top_staples_5p = design.strands_starting_on_helix(2)
     top_staples_3p = design.strands_ending_on_helix(2)
     bot_staples_5p = design.strands_starting_on_helix(17)
     bot_staples_3p = design.strands_ending_on_helix(17)
 
     # remove scaffold
-    top_staples_5p = [st for st in top_staples_5p if len(st.substrands) <= 3]
-    top_staples_3p = [st for st in top_staples_3p if len(st.substrands) <= 3]
-    bot_staples_5p = [st for st in bot_staples_5p if len(st.substrands) <= 3]
-    bot_staples_3p = [st for st in bot_staples_3p if len(st.substrands) <= 3]
+    top_staples_5p = [st for st in top_staples_5p if len(st.domains) <= 3]
+    top_staples_3p = [st for st in top_staples_3p if len(st.domains) <= 3]
+    bot_staples_5p = [st for st in bot_staples_5p if len(st.domains) <= 3]
+    bot_staples_3p = [st for st in bot_staples_3p if len(st.domains) <= 3]
 
     top_staples_5p.sort(key=lambda stap: stap.offset_5p())
     top_staples_3p.sort(key=lambda stap: stap.offset_3p())
     bot_staples_5p.sort(key=lambda stap: stap.offset_5p())
     bot_staples_3p.sort(key=lambda stap: stap.offset_3p())
 
     for top_5p, top_3p, bot_5p, bot_3p in zip(top_staples_5p, top_staples_3p, bot_staples_5p, bot_staples_3p):
-        ss_top = sc.Substrand(helix=2, forward=False,
-                              start=top_5p.first_substrand().end, end=top_3p.last_substrand().start)
-        ss_bot = sc.Substrand(helix=17, forward=True,
-                              start=bot_3p.last_substrand().end, end=bot_5p.first_substrand().start)
-        design.insert_substrand(bot_5p, 0, ss_top)
-        design.insert_substrand(top_5p, 0, ss_bot)
+        ss_top = sc.Domain(helix=2, forward=False,
+                           start=top_5p.first_domain().end, end=top_3p.last_domain().start)
+        ss_bot = sc.Domain(helix=17, forward=True,
+                           start=bot_3p.last_domain().end, end=bot_5p.first_domain().start)
+        design.insert_domain(bot_5p, 0, ss_top)
+        design.insert_domain(top_5p, 0, ss_bot)
 
 
 def add_toeholds_for_seam_displacement(design: sc.DNADesign):
     for helix in [2, 17]:
         staples_5p = design.strands_starting_on_helix(helix)
 
         # remove scaffold
-        staples_5p = [st for st in staples_5p if len(st.substrands) <= 3]
+        staples_5p = [st for st in staples_5p if len(st.domains) <= 3]
 
         staples_5p.sort(key=lambda stap: stap.offset_5p())
 
         for stap_5p in staples_5p:
-            toe_ss = sc.Substrand(helix=1 if helix == 2 else 18, forward=helix == 2,
-                                  start=stap_5p.first_substrand().start, end=stap_5p.first_substrand().end)
-            design.insert_substrand(stap_5p, 0, toe_ss)
+            toe_ss = sc.Domain(helix=1 if helix == 2 else 18, forward=helix == 2,
+                               start=stap_5p.first_domain().start, end=stap_5p.first_domain().end)
+            design.insert_domain(stap_5p, 0, toe_ss)
 
 
 def add_adapters(design):
@@ -106,27 +106,27 @@ def add_adapters(design):
     left_outside_seed = left_inside_seed - 26
     for bot_helix in range(2, 18, 2):
         top_helix = bot_helix - 1 if bot_helix != 2 else 17
-        ss_top = sc.Substrand(helix=top_helix, forward=True,
-                              start=left_outside_seed, end=left_inside_seed)
-        ss_bot = sc.Substrand(helix=bot_helix, forward=False,
-                              start=left_outside_seed, end=left_inside_seed)
+        ss_top = sc.Domain(helix=top_helix, forward=True,
+                           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(name=f'adap-left-{top_helix}-{bot_helix}',
                            scale='25nm', purification='STD')
-        adapter = sc.Strand(substrands=[ss_bot, ss_top], idt=idt)
+        adapter = sc.Strand(domains=[ss_bot, ss_top], idt=idt)
         design.add_strand(adapter)
 
     # right adapters
     right_inside_seed = 464
     right_outside_seed = right_inside_seed + 26
     for bot_helix in range(2, 18, 2):
         top_helix = bot_helix - 1 if bot_helix != 2 else 17
-        ss_top = sc.Substrand(helix=top_helix, forward=True,
-                              start=right_inside_seed, end=right_outside_seed)
-        ss_bot = sc.Substrand(helix=bot_helix, forward=False,
-                              start=right_inside_seed, end=right_outside_seed)
+        ss_top = sc.Domain(helix=top_helix, forward=True,
+                           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(name=f'adap-right-{top_helix}-{bot_helix}',
                            scale='25nm', purification='STD')
-        adapter = sc.Strand(substrands=[ss_top, ss_bot], idt=idt)
+        adapter = sc.Strand(domains=[ss_top, ss_bot], idt=idt)
         design.add_strand(adapter)
 
 
@@ -159,11 +159,11 @@ def add_tiles_and_assign_dna(design):
     left_right = 32
     for top_helix, seq in zip(range(2, 18, 2), tile_dna_seqs):
         bot_helix = top_helix + 1
-        ss_top = sc.Substrand(helix=top_helix, forward=True,
-                              start=left_left, end=left_right)
-        ss_bot = sc.Substrand(helix=bot_helix, forward=False,
-                              start=left_left, end=left_right)
-        tile = sc.Strand(substrands=[ss_bot, ss_top], color=sc.Color(0, 0, 0))
+        ss_top = sc.Domain(helix=top_helix, forward=True,
+                           start=left_left, end=left_right)
+        ss_bot = sc.Domain(helix=bot_helix, forward=False,
+                           start=left_left, end=left_right)
+        tile = sc.Strand(domains=[ss_bot, ss_top], color=sc.Color(0, 0, 0))
         design.add_strand(tile)
         design.assign_dna(tile, seq)
 
@@ -172,11 +172,11 @@ def add_tiles_and_assign_dna(design):
     right_right = 501
     for top_helix, seq in zip(range(2, 18, 2), tile_dna_seqs):
         bot_helix = top_helix + 1
-        ss_top = sc.Substrand(helix=top_helix, forward=True,
-                              start=right_left, end=right_right)
-        ss_bot = sc.Substrand(helix=bot_helix, forward=False,
-                              start=right_left, end=right_right)
-        tile = sc.Strand(substrands=[ss_bot, ss_top], color=sc.Color(0, 0, 0))
+        ss_top = sc.Domain(helix=top_helix, forward=True,
+                           start=right_left, end=right_right)
+        ss_bot = sc.Domain(helix=bot_helix, forward=False,
+                           start=right_left, end=right_right)
+        tile = sc.Strand(domains=[ss_bot, ss_top], color=sc.Color(0, 0, 0))
         design.add_strand(tile)
         design.assign_dna(tile, seq)
 
@@ -233,11 +233,11 @@ def assign_dna_to_unzipper_toeholds(design):
     uz_toes = [sc.wc(seq) for seq in uz_toes_wc]
 
     strands_h1 = design.strands_starting_on_helix(1)
-    strands_h1.sort(key=lambda _strand: _strand.first_substrand().offset_5p())
+    strands_h1.sort(key=lambda _strand: _strand.first_domain().offset_5p())
     strands_h1.reverse()
 
     strands_h18 = design.strands_starting_on_helix(18)
-    strands_h18.sort(key=lambda _strand: _strand.first_substrand().offset_5p())
+    strands_h18.sort(key=lambda _strand: _strand.first_domain().offset_5p())
 
     for strand, toe in zip(strands_h1 + strands_h18, uz_toes):
         seq = toe + sc.DNA_base_wildcard * (strand.dna_length() - 8)

examples/16_helix_origami_rectangle_seed_tiles_grow_from_top.py

@@ -55,12 +55,12 @@ def move_top_and_bottom_staples_within_column_boundaries(design: sc.DNADesign):
     bot_staples.remove(design.scaffold)
 
     for top_staple in top_staples:
-        current_end = top_staple.substrands[0].end
-        design.set_end(top_staple.substrands[0], current_end - 8)
+        current_end = top_staple.domains[0].end
+        design.set_end(top_staple.domains[0], current_end - 8)
 
     for bot_staple in bot_staples:
-        current_start = bot_staple.substrands[0].start
-        design.set_start(bot_staple.substrands[0], current_start + 8)
+        current_start = bot_staple.domains[0].start
+        design.set_start(bot_staple.domains[0], current_start + 8)
 
 
 def add_adapters(design):
@@ -69,27 +69,27 @@ def add_adapters(design):
     left_outside_seed = left_inside_seed - 26
     for bot_helix in range(2, 18, 2):
         top_helix = bot_helix - 1 if bot_helix != 2 else 17
-        ss_top = sc.Substrand(helix=top_helix, forward=True,
-                              start=left_outside_seed, end=left_inside_seed)
-        ss_bot = sc.Substrand(helix=bot_helix, forward=False,
-                              start=left_outside_seed, end=left_inside_seed)
+        ss_top = sc.Domain(helix=top_helix, forward=True,
+                           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(name=f'adap-left-{top_helix}-{bot_helix}',
                            scale='25nm', purification='STD')
-        adapter = sc.Strand(substrands=[ss_bot, ss_top], idt=idt)
+        adapter = sc.Strand(domains=[ss_bot, ss_top], idt=idt)
         design.add_strand(adapter)
 
     # right adapters
     right_inside_seed = 464
     right_outside_seed = right_inside_seed + 26
     for bot_helix in range(2, 18, 2):
         top_helix = bot_helix - 1 if bot_helix != 2 else 17
-        ss_top = sc.Substrand(helix=top_helix, forward=True,
-                              start=right_inside_seed, end=right_outside_seed)
-        ss_bot = sc.Substrand(helix=bot_helix, forward=False,
-                              start=right_inside_seed, end=right_outside_seed)
+        ss_top = sc.Domain(helix=top_helix, forward=True,
+                           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(name=f'adap-right-{top_helix}-{bot_helix}',
                            scale='25nm', purification='STD')
-        adapter = sc.Strand(substrands=[ss_top, ss_bot], idt=idt)
+        adapter = sc.Strand(domains=[ss_top, ss_bot], idt=idt)
         design.add_strand(adapter)
 
 
@@ -122,11 +122,11 @@ def add_tiles_and_assign_dna(design):
     left_right = 32
     for col, seq in zip(range(2, 18, 2), tile_dna_seqs):
         bot_helix = top_helix + 1
-        ss_top = sc.Substrand(helix=top_helix, forward=True,
-                              start=left_left, end=left_right)
-        ss_bot = sc.Substrand(helix=bot_helix, forward=False,
-                              start=left_left, end=left_right)
-        tile = sc.Strand(substrands=[ss_bot, ss_top], color=sc.Color(0, 0, 0))
+        ss_top = sc.Domain(helix=top_helix, forward=True,
+                           start=left_left, end=left_right)
+        ss_bot = sc.Domain(helix=bot_helix, forward=False,
+                           start=left_left, end=left_right)
+        tile = sc.Strand(domains=[ss_bot, ss_top], color=sc.Color(0, 0, 0))
         design.add_strand(tile)
         design.assign_dna(tile, seq)
 
@@ -135,11 +135,11 @@ def add_tiles_and_assign_dna(design):
     right_right = 501
     for top_helix, seq in zip(range(2, 18, 2), tile_dna_seqs):
         bot_helix = top_helix + 1
-        ss_top = sc.Substrand(helix=top_helix, forward=True,
-                              start=right_left, end=right_right)
-        ss_bot = sc.Substrand(helix=bot_helix, forward=False,
-                              start=right_left, end=right_right)
-        tile = sc.Strand(substrands=[ss_bot, ss_top], color=sc.Color(0, 0, 0))
+        ss_top = sc.Domain(helix=top_helix, forward=True,
+                           start=right_left, end=right_right)
+        ss_bot = sc.Domain(helix=bot_helix, forward=False,
+                           start=right_left, end=right_right)
+        tile = sc.Strand(domains=[ss_bot, ss_top], color=sc.Color(0, 0, 0))
         design.add_strand(tile)
         design.assign_dna(tile, seq)
 

examples/1_staple_1_helix_origami.py

@@ -3,8 +3,8 @@
 def main():
     length = 9
     helices = [sc.Helix(max_offset=length, major_ticks=[2,5])]
-    stap_ss = sc.Substrand(0, sc.forward, 0, length)
-    scaf_ss = sc.Substrand(0, sc.reverse, 0, length)
+    stap_ss = sc.Domain(0, sc.forward, 0, length)
+    scaf_ss = sc.Domain(0, sc.reverse, 0, length)
     stap = sc.Strand([stap_ss])
     scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
     strands = [stap, scaf]

examples/1_staple_1_helix_origami_idt_duplicate_names.py

@@ -1,10 +1,10 @@
 import scadnano as sc
 
 def main():
-    ss1_r = sc.Substrand(0, sc.forward, 0, 4)
-    ss2_r = sc.Substrand(0, sc.forward, 4, 8)
-    ss3_r = sc.Substrand(0, sc.forward, 8, 12)
-    ss_l = sc.Substrand(0, sc.reverse, 0, 12)
+    ss1_r = sc.Domain(0, sc.forward, 0, 4)
+    ss2_r = sc.Domain(0, sc.forward, 4, 8)
+    ss3_r = sc.Domain(0, sc.forward, 8, 12)
+    ss_l = sc.Domain(0, sc.reverse, 0, 12)
 
     s1_r = sc.Strand([ss1_r], idt=sc.IDTFields('s1_r'))
     s2_r = sc.Strand([ss2_r], idt=sc.IDTFields('s1_r'))

examples/1_staple_1_helix_origami_mismatches.py

@@ -3,8 +3,8 @@
 
 def main():
     length = 10
-    stap_ss = sc.Substrand(0, sc.forward, 0, length)
-    scaf_ss = sc.Substrand(0, sc.reverse, 0, length)
+    stap_ss = sc.Domain(0, sc.forward, 0, length)
+    scaf_ss = sc.Domain(0, sc.reverse, 0, length)
     stap = sc.Strand([stap_ss])
     scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
     strands = [stap, scaf]

examples/1_staple_1_helix_origami_rotation.py

@@ -5,8 +5,8 @@
 def main():
     length = 9
     helices = [sc.Helix(max_offset=length, rotation=math.pi/2, rotation_anchor=2)]
-    stap_ss = sc.Substrand(0, sc.forward, 0, length)
-    scaf_ss = sc.Substrand(0, sc.reverse, 0, length)
+    stap_ss = sc.Domain(0, sc.forward, 0, length)
+    scaf_ss = sc.Domain(0, sc.reverse, 0, length)
     stap = sc.Strand([stap_ss])
     scaf = sc.Strand([scaf_ss], color=sc.default_scaffold_color)
     strands = [stap, scaf]

examples/24_helix_origami_rectangle_twist_corrected.py

@@ -46,15 +46,15 @@ def add_staple_nicks(design: sc.DNADesign):
 
 
 def add_precursor_staples(design: sc.DNADesign):
-    staples = [sc.Strand([sc.Substrand(helix=helix, forward=helix % 2 == 1, start=8, end=296)])
+    staples = [sc.Strand([sc.Domain(helix=helix, forward=helix % 2 == 1, start=8, end=296)])
                for helix in range(24)]
     for staple in staples:
         design.add_strand(staple)
 
 
 def precursor_scaffolds() -> sc.DNADesign:
     helices = [sc.Helix(max_offset=304) for _ in range(24)]
-    scaffolds = [sc.Strand([sc.Substrand(helix=helix, forward=helix % 2 == 0, start=8, end=296)])
+    scaffolds = [sc.Strand([sc.Domain(helix=helix, forward=helix % 2 == 0, start=8, end=296)])
                  for helix in range(24)]
     return sc.DNADesign(helices=helices, strands=scaffolds, grid=sc.square)
 

examples/2_helix_2_strands_multiple_substrands_no_seq.py

@@ -4,15 +4,15 @@
 # If running in scadnano, define a function called main() that returns design.
 # It will be displayed in the browser by scadnano.
 def main():
-    # multiple-substrand
-    ss0_1 = sc.Substrand(helix=0, forward=False, start=0, end=4)
-    ss1 = sc.Substrand(helix=1, forward=True, start=0, end=8)
-    ss0_2 = sc.Substrand(helix=0, forward=False, start=4, end=8)
-    strand_multi = sc.Strand(substrands=[ss0_1, ss1, ss0_2])
+    # multiple-domain
+    ss0_1 = sc.Domain(helix=0, forward=False, start=0, end=4)
+    ss1 = sc.Domain(helix=1, forward=True, start=0, end=8)
+    ss0_2 = sc.Domain(helix=0, forward=False, start=4, end=8)
+    strand_multi = sc.Strand(domains=[ss0_1, ss1, ss0_2])
 
-    # single substrand
-    ss0_single = sc.Substrand(helix=0, forward=True, start=0, end=8)
-    strand_single = sc.Strand(substrands=[ss0_single])
+    # single domain
+    ss0_single = sc.Domain(helix=0, forward=True, start=0, end=8)
+    strand_single = sc.Strand(domains=[ss0_single])
 
     # whole design
     design = sc.DNADesign(strands=[strand_multi, strand_single], grid=sc.square)

examples/2_staple_2_helix_modifications.py

@@ -3,13 +3,13 @@
 import dataclasses
 
 def main():
-    stap_left_ss1 = sc.Substrand(1, sc.forward, 0, 16)
-    stap_left_ss0 = sc.Substrand(0, sc.reverse, 0, 16)
-    stap_right_ss0 = sc.Substrand(0, sc.reverse, 16, 32)
-    stap_right_ss1 = sc.Substrand(1, sc.forward, 16, 32)
-    scaf_ss1_left = sc.Substrand(1, sc.reverse, 0, 16)
-    scaf_ss0 = sc.Substrand(0, sc.forward, 0, 32)
-    scaf_ss1_right = sc.Substrand(1, sc.reverse, 16, 32)
+    stap_left_ss1 = sc.Domain(1, sc.forward, 0, 16)
+    stap_left_ss0 = sc.Domain(0, sc.reverse, 0, 16)
+    stap_right_ss0 = sc.Domain(0, sc.reverse, 16, 32)
+    stap_right_ss1 = sc.Domain(1, sc.forward, 16, 32)
+    scaf_ss1_left = sc.Domain(1, sc.reverse, 0, 16)
+    scaf_ss0 = sc.Domain(0, sc.forward, 0, 32)
+    scaf_ss1_right = sc.Domain(1, sc.reverse, 16, 32)
     stap_left = sc.Strand([stap_left_ss1, stap_left_ss0])
     stap_right = sc.Strand([stap_right_ss0, stap_right_ss1])
     scaf = sc.Strand([scaf_ss1_left, scaf_ss0, scaf_ss1_right], color=sc.default_scaffold_color)

examples/2_staple_2_helix_origami_6bases_wide.py

@@ -3,13 +3,13 @@
 def main():
     width = 6
     width_h = width // 2
-    stap_left_ss1 = sc.Substrand(1, sc.forward, 0, width_h)
-    stap_left_ss0 = sc.Substrand(0, sc.reverse, 0, width_h)
-    stap_right_ss0 = sc.Substrand(0, sc.reverse, width_h, width)
-    stap_right_ss1 = sc.Substrand(1, sc.forward, width_h, width)
-    scaf_ss1_left = sc.Substrand(1, sc.reverse, 0, width_h)
-    scaf_ss0 = sc.Substrand(0, sc.forward, 0, width)
-    scaf_ss1_right = sc.Substrand(1, sc.reverse, width_h, width)
+    stap_left_ss1 = sc.Domain(1, sc.forward, 0, width_h)
+    stap_left_ss0 = sc.Domain(0, sc.reverse, 0, width_h)
+    stap_right_ss0 = sc.Domain(0, sc.reverse, width_h, width)
+    stap_right_ss1 = sc.Domain(1, sc.forward, width_h, width)
+    scaf_ss1_left = sc.Domain(1, sc.reverse, 0, width_h)
+    scaf_ss0 = sc.Domain(0, sc.forward, 0, width)
+    scaf_ss1_right = sc.Domain(1, sc.reverse, width_h, width)
     stap_left = sc.Strand([stap_left_ss1, stap_left_ss0])
     stap_right = sc.Strand([stap_right_ss0, stap_right_ss1])
     scaf = sc.Strand([scaf_ss1_left, scaf_ss0, scaf_ss1_right], color=sc.default_scaffold_color)