closes #219: change Design.strand to Design.draw_strand

README.md

@@ -232,14 +232,14 @@ def create_design():
 
     # for absolute offsets, call method "to"
     # left staple
-    design.strand(1, 8).to(24).cross(0).to(8)
+    design.draw_strand(1, 8).to(24).cross(0).to(8)
 
     # for relative offsets, call method "move"
     # right staple
-    design.strand(0, 40).move(-16).cross(1).move(16).with_modification_5p(mod.biotin_5p)
+    design.draw_strand(0, 40).move(-16).cross(1).move(16).with_modification_5p(mod.biotin_5p)
 
     # scaffold
-    design.strand(1, 24).move(-16).cross(0).move(32).loopout(1, 3).move(-16).as_scaffold()
+    design.draw_strand(1, 24).move(-16).cross(0).move(32).loopout(1, 3).move(-16).as_scaffold()
 
     # deletions and insertions added to design are added to both strands on a helix
     design.add_deletion(helix=1, offset=20)
@@ -257,7 +257,7 @@ if __name__ == '__main__':
     design.write_scadnano_file(directory='output_designs')
 ```
 
-Documentation is available in the [API docs](https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Design.strand).
+Documentation is available in the [API docs](https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Design.draw_strand).
 
 
 

examples/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.py

@@ -9,9 +9,9 @@ def create_design() -> sc.Design:
     # whole design
     design = sc.Design(helices=helices, strands=[], grid=sc.square)
 
-    design.strand(1, 8).to(24).cross(0).to(8) # left staple
-    design.strand(0, 40).to(24).cross(1).to(40).with_modification_5p(mod.biotin_5p) # right staple
-    design.strand(1, 24).to(8).cross(0).to(40).loopout(1, 3).to(24).as_scaffold()
+    design.draw_strand(1, 8).to(24).cross(0).to(8) # left staple
+    design.draw_strand(0, 40).to(24).cross(1).to(40).with_modification_5p(mod.biotin_5p) # right staple
+    design.draw_strand(1, 24).to(8).cross(0).to(40).loopout(1, 3).to(24).as_scaffold()
 
     # deletions and insertions added to design are added to both strands on a helix
     design.add_deletion(helix=1, offset=20)

examples/circular.py

@@ -5,9 +5,9 @@ def create_design() -> sc.Design:
     helices = [sc.Helix(max_offset=24) for _ in range(2)]
     design = sc.Design(helices=helices, grid=sc.square)
 
-    design.strand(0,0).move(8).cross(1).move(-8).as_circular()
-    design.strand(0,8).move(8).loopout(1, 5).move(-8).as_circular()
-    design.strand(0,16).move(8).cross(1).move(-8)
+    design.draw_strand(0, 0).move(8).cross(1).move(-8).as_circular()
+    design.draw_strand(0, 8).move(8).loopout(1, 5).move(-8).as_circular()
+    design.draw_strand(0, 16).move(8).cross(1).move(-8)
 
     return design
 

examples/helix_groups.py

@@ -48,25 +48,25 @@ def create_design() -> sc.Design:
 
     design = sc.Design(helices=helices, groups=groups, strands=[])
 
-    design.strand(0, 0).to(8) \
+    design.draw_strand(0, 0).to(8) \
         .cross(1).to(0) \
         .cross(2).to(8) \
         .cross(3).to(0) \
         .cross(4).to(8) \
         .cross(5).to(0)
 
-    design.strand(4, 10).to(13)
+    design.draw_strand(4, 10).to(13)
 
-    design.strand(6, 0).to(8).cross(7).to(0)
-    design.strand(8, 0).to(8).cross(9).to(0)
-    design.strand(13, 0).to(8).cross(15).to(0)
+    design.draw_strand(6, 0).to(8).cross(7).to(0)
+    design.draw_strand(8, 0).to(8).cross(9).to(0)
+    design.draw_strand(13, 0).to(8).cross(15).to(0)
 
-    design.strand(8, 8).to(11)
-    design.strand(13, 8).to(11)
+    design.draw_strand(8, 8).to(11)
+    design.draw_strand(13, 8).to(11)
 
 
     if include_rot:
-        design.strand(10, 0).to(8).cross(11).to(0)
+        design.draw_strand(10, 0).to(8).cross(11).to(0)
 
     return design
 

examples/names_domains_strands.py

@@ -5,7 +5,7 @@ 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) \
+    design.draw_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*') \
@@ -17,25 +17,25 @@ def create_design() -> sc.Design:
         .with_name('bottom strand')
 
     # domain names match
-    design.strand(0, 0).move(8).with_domain_name('domain 1').with_name('top strand 1')
+    design.draw_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')
+    design.draw_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')
+    design.draw_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')
+    design.draw_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')
+    design.draw_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')
+    design.draw_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')
+    design.draw_strand(0, 64).move(8).with_domain_name('domain 9').with_name('top strand 9')
 
     return design
 

examples/tutorial-examples/24_helix_rectangle.py

@@ -26,11 +26,11 @@ def create_design() -> sc.Design:
 
 def add_scaffold_precursors(design: sc.Design) -> None:
     for helix in range(0, 23, 2):  # scaffold goes forward on even helices
-        design.strand(helix, 0).move(288).as_scaffold()
+        design.draw_strand(helix, 0).move(288).as_scaffold()
     for helix in range(1, 23, 2):  # scaffold goes reverse on odd helices
-        design.strand(helix, 288).move(-288).as_scaffold()
-    design.strand(23, 288).move(-144).as_scaffold()  # bottom part of scaffold has a "nick"
-    design.strand(23, 144).move(-144).as_scaffold()  #
+        design.draw_strand(helix, 288).move(-288).as_scaffold()
+    design.draw_strand(23, 288).move(-144).as_scaffold()  # bottom part of scaffold has a "nick"
+    design.draw_strand(23, 144).move(-144).as_scaffold()  #
 
 
 def add_scaffold_crossovers(design: sc.Design) -> None:

scadnano/scadnano.py

@@ -4859,14 +4859,14 @@ def _ensure_mods_unique_names(all_mods: Set[Modification]) -> None:
                 raise IllegalDesignError(f'two different modifications share the id {mod.id}; '
                                          f'one is\n  {mod}\nand the other is\n  {other_mod}')
 
-    def strand(self, helix: int, offset: int) -> StrandBuilder:
+    def draw_strand(self, helix: int, offset: int) -> StrandBuilder:
         """Used for chained method building by calling
         :py:meth:`Design.strand` to build the :any:`Strand` domain by domain, in order from 5' to 3'.
         For example
 
         .. code-block:: Python
 
-            design.strand(0, 7).to(10).cross(1).to(5).cross(2).to(15)
+            design.draw_strand(0, 7).to(10).cross(1).to(5).cross(2).to(15)
 
         This creates a :any:`Strand` in this :any:`Design` equivalent to
 
@@ -4882,7 +4882,7 @@ def strand(self, helix: int, offset: int) -> StrandBuilder:
 
         .. code-block:: Python
 
-            design.strand(0, 7).to(10).cross(1).to(5).loopout(2, 3).to(15)
+            design.draw_strand(0, 7).to(10).cross(1).to(5).loopout(2, 3).to(15)
 
         This creates a :any:`Strand` in this :any:`Design` equivalent to
 
@@ -4918,6 +4918,17 @@ def strand(self, helix: int, offset: int) -> StrandBuilder:
         """
         return StrandBuilder(self, helix, offset)
 
+    # def strand(self, helix: int, offset: int) -> StrandBuilder:
+    #     """
+    #     Same as :meth:`Design.draw_strand`.
+    #
+    #     .. deprecated:: 0.18.0
+    #        Use :meth:`Design.draw_strand` instead. This method will be removed.
+    #     """
+    #     print('WARNING: The method Design.strand is deprecated. Use Design.draw_strand instead, '
+    #           'which has the same functionality.')
+    #     return self.draw_strand(helix, offset)
+
     def assign_m13_to_scaffold(self, rotation: int = 5587, variant: M13Variant = M13Variant.p7249) -> None:
         """Assigns the scaffold to be the sequence of M13: :py:func:`m13` with the given `rotation`
         and :any:`M13Variant`.