From 9b54b1e5fc8d18960aef068fae487862a5d8eac9 Mon Sep 17 00:00:00 2001 From: Cosmo Date: Tue, 8 Sep 2020 17:01:00 +0100 Subject: [PATCH 1/6] Export code supports helix groups and associated unittest. test_6_helix_bundle_honeycomb restored. --- doc/compile.py | 7 +++++ doc/index.rst.in | 52 ++++++++++++++++++++++++++++++++++++ scadnano/scadnano.py | 31 +++++++++++++++------- tests/scadnano_tests.py | 59 ++++++++++++++++++++++++++++++++++++++++- 4 files changed, 139 insertions(+), 10 deletions(-) create mode 100644 doc/compile.py create mode 100644 doc/index.rst.in diff --git a/doc/compile.py b/doc/compile.py new file mode 100644 index 00000000..e22882f7 --- /dev/null +++ b/doc/compile.py @@ -0,0 +1,7 @@ +""" Take index.rst.in as input and populate with classes of scadnano.py +""" + +import scadnano as sc + +for elem in dir(sc): + if \ No newline at end of file diff --git a/doc/index.rst.in b/doc/index.rst.in new file mode 100644 index 00000000..c7394eab --- /dev/null +++ b/doc/index.rst.in @@ -0,0 +1,52 @@ +.. scadnano documentation master file, created by + sphinx-quickstart on Tue Jul 16 10:14:04 2019. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +scadnano documentation +==================================== + +.. toctree:: + :maxdepth: 3 + :caption: Contents: + +.. scadnano + +origami_rectangle +===================== +.. automodule:: origami_rectangle + :members: + +Interoperability - cadnano v2 +============================= + +Scadnano provides function to convert design to and from cadnano v2: + +* :py:meth:`DNADesign.from_cadnano_v2` will create a scadnano DNADesign from a ``cadnanov2`` json file. +* :py:meth:`DNADesign.export_cadnano_v2` will produce a ``cadnanov2`` json file from a scadnano design. + +**Important** + +All ``cadnanov2`` designs can be imported to scadnano. However **not all scadnano designs can be imported +to cadnanov2**, to be importable to ``cadnanov2`` a scadnano design need to comply with the following points: + +* The design cannot feature any :py:class:`Loopout` as it is not a concept that exists in ``cadnanov2``. +* Following ``cadnanov2`` conventions, helices with **even** number must have their scaffold going **forward** and helices with **odd** number **backward**. + +Also note that maximum helices offsets can be altered in a ``scadnano`` to ``cadnanov2`` conversion as ``cadnanov2`` needs max offsets to be a multiple of 21 in the hex grid and 32 in the rectangular grid. +The conversion algorithm will choose the lowest multiple of 21 or 32 which fits the entire design. + +The ``cadnanov2`` json format does not embed sequences hence they will be lost after conversion. + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + + +.. |br| raw:: html + +
+ diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index d859c87c..63041280 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -4022,7 +4022,7 @@ def _cadnano_v2_place_strand(self, strand: Strand, dct: dict, self._cadnano_v2_place_crossover(which_helix, next_helix, domain, next_domain, strand_type) - def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int) -> dict: + def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int, design_grid: Grid) -> dict: """Creates blank cadnanov2 helices in and initialized all their fields. """ helices_ids_reverse = {} @@ -4030,11 +4030,11 @@ def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int) -> dict: helix_dct = OrderedDict() helix_dct['num'] = helix.idx - if self.grid == Grid.square: + if design_grid == Grid.square: helix_dct['row'] = helix.grid_position[1] helix_dct['col'] = helix.grid_position[0] - if self.grid == Grid.honeycomb: + if design_grid == Grid.honeycomb: helix_dct['row'], helix_dct['col'] = helix.grid_position[1], helix.grid_position[0] helix_dct['scaf'] = [] @@ -4063,9 +4063,22 @@ def to_cadnano_v2(self): dct = OrderedDict() dct['vstrands'] = [] - if self.__class__ != Design: - raise ValueError( - 'Please export DNAOrigamiDesign only as we need to know which strand is the scaffold.') + '''Check if helix group are used or if only one grid is used''' + design_grid = None + if self._has_default_groups(): + design_grid = self.grid + else: + gridUsed = {} + grid_type = None + for group_name in self.groups: + gridUsed[self.groups[group_name].grid] = True + grid_type = self.groups[group_name].grid + if len(gridUsed) > 1: + raise ValueError('Designs using helix groups can be exported to cadnano v2 \ + only if all groups share the same grid type.') + else: + design_grid = grid_type + '''Figuring out the type of grid. In cadnano v2, all helices have the same max offset @@ -4077,9 +4090,9 @@ def to_cadnano_v2(self): for helix in self.helices.values(): num_bases = max(num_bases, helix.max_offset) - if self.grid == Grid.square: + if design_grid == Grid.square: num_bases = self._get_multiple_of_x_sup_closest_to_y(32, num_bases) - elif self.grid == Grid.honeycomb: + elif design_grid == Grid.honeycomb: num_bases = self._get_multiple_of_x_sup_closest_to_y(21, num_bases) else: raise NotImplementedError('We can export to cadnano v2 `square` and `honeycomb` grids only.') @@ -4102,7 +4115,7 @@ def to_cadnano_v2(self): '''Filling the helices with blank. ''' - helices_ids_reverse = self._cadnano_v2_fill_blank(dct, num_bases) + helices_ids_reverse = self._cadnano_v2_fill_blank(dct, num_bases, design_grid) '''Putting the scaffold in place. ''' diff --git a/tests/scadnano_tests.py b/tests/scadnano_tests.py index 8bcacdcd..7d10c48f 100644 --- a/tests/scadnano_tests.py +++ b/tests/scadnano_tests.py @@ -607,6 +607,64 @@ class TestExportCadnanoV2(unittest.TestCase): output_path = os.path.join('tests_outputs', folder) ext = sc.default_scadnano_file_extension + def test_export_design_with_helix_group(self): + e = 'east' + s = 'south' + helices = [ + sc.Helix(max_offset=24, group=s), + sc.Helix(max_offset=25, group=s), + ] + helices.extend([ + sc.Helix(max_offset=22, group=e), + sc.Helix(max_offset=23, group=e), + ]) + + group_south = sc.HelixGroup(position=sc.Position3D(x=0, y=10, z=0), + grid=sc.square) + group_east = sc.HelixGroup(position=sc.Position3D(x=10, y=0, z=0), grid=sc.square) + + groups = { + e: group_east, + s: group_south + } + + design = sc.Design(helices=helices, groups=groups, strands=[]) + design.write_scadnano_file(directory=self.input_path, + filename=f'test_export_design_with_helix_group.{self.ext}') + design.export_cadnano_v2(directory=self.output_path, + filename='test_export_design_with_helix_group.json') + + def test_export_design_with_helix_group_not_same_grid(self): + e = 'east' + s = 'south' + helices = [ + sc.Helix(max_offset=24, group=s), + sc.Helix(max_offset=25, group=s), + ] + helices.extend([ + sc.Helix(max_offset=22, group=e), + sc.Helix(max_offset=23, group=e), + ]) + + group_south = sc.HelixGroup(position=sc.Position3D(x=0, y=10, z=0), + grid=sc.square) + group_east = sc.HelixGroup(position=sc.Position3D(x=10, y=0, z=0), grid=sc.honeycomb) + + groups = { + e: group_east, + s: group_south + } + + design = sc.Design(helices=helices, groups=groups, strands=[]) + design.write_scadnano_file(directory=self.input_path, + filename=f'test_export_design_with_helix_group_not_same_grid.{self.ext}') + + with self.assertRaises(ValueError) as context: + design.export_cadnano_v2(directory=self.output_path, + filename='test_export_design_with_helix_group_not_same_grid.json') + self.assertTrue('helix groups' in context.exception.args[0]) + + def test_2_staple_2_helix_origami_extremely_simple(self): helices = [sc.Helix(max_offset=32), sc.Helix(max_offset=32)] scaf_part = sc.Domain(helix=0, forward=True, start=0, end=32) @@ -676,7 +734,6 @@ def test_6_helix_origami_rectangle(self): design.export_cadnano_v2(directory=self.output_path, filename='test_6_helix_origami_rectangle.json') - @unittest.skip('DD: I cannot find where this file is. Is it supposed to be generated by some code?') def test_6_helix_bundle_honeycomb(self): design = sc.Design.from_scadnano_file( os.path.join(self.input_path, f'test_6_helix_bundle_honeycomb.{self.ext}')) From 4d622123c3bbc11bbb99c2c826a9d3504fd9ac49 Mon Sep 17 00:00:00 2001 From: Cosmo Date: Tue, 8 Sep 2020 17:01:39 +0100 Subject: [PATCH 2/6] Export code supports helix groups and associated unittest. test_6_helix_bundle_honeycomb restored. --- doc/compile.py | 7 ------- doc/index.rst.in | 52 ------------------------------------------------ 2 files changed, 59 deletions(-) delete mode 100644 doc/compile.py delete mode 100644 doc/index.rst.in diff --git a/doc/compile.py b/doc/compile.py deleted file mode 100644 index e22882f7..00000000 --- a/doc/compile.py +++ /dev/null @@ -1,7 +0,0 @@ -""" Take index.rst.in as input and populate with classes of scadnano.py -""" - -import scadnano as sc - -for elem in dir(sc): - if \ No newline at end of file diff --git a/doc/index.rst.in b/doc/index.rst.in deleted file mode 100644 index c7394eab..00000000 --- a/doc/index.rst.in +++ /dev/null @@ -1,52 +0,0 @@ -.. scadnano documentation master file, created by - sphinx-quickstart on Tue Jul 16 10:14:04 2019. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -scadnano documentation -==================================== - -.. toctree:: - :maxdepth: 3 - :caption: Contents: - -.. scadnano - -origami_rectangle -===================== -.. automodule:: origami_rectangle - :members: - -Interoperability - cadnano v2 -============================= - -Scadnano provides function to convert design to and from cadnano v2: - -* :py:meth:`DNADesign.from_cadnano_v2` will create a scadnano DNADesign from a ``cadnanov2`` json file. -* :py:meth:`DNADesign.export_cadnano_v2` will produce a ``cadnanov2`` json file from a scadnano design. - -**Important** - -All ``cadnanov2`` designs can be imported to scadnano. However **not all scadnano designs can be imported -to cadnanov2**, to be importable to ``cadnanov2`` a scadnano design need to comply with the following points: - -* The design cannot feature any :py:class:`Loopout` as it is not a concept that exists in ``cadnanov2``. -* Following ``cadnanov2`` conventions, helices with **even** number must have their scaffold going **forward** and helices with **odd** number **backward**. - -Also note that maximum helices offsets can be altered in a ``scadnano`` to ``cadnanov2`` conversion as ``cadnanov2`` needs max offsets to be a multiple of 21 in the hex grid and 32 in the rectangular grid. -The conversion algorithm will choose the lowest multiple of 21 or 32 which fits the entire design. - -The ``cadnanov2`` json format does not embed sequences hence they will be lost after conversion. - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` - - -.. |br| raw:: html - -
- From 62330752fbe511c95c6a1d1e8688f03467c99639 Mon Sep 17 00:00:00 2001 From: Cosmo Date: Tue, 8 Sep 2020 17:05:02 +0100 Subject: [PATCH 3/6] Export code supports helix groups and associated unittest. test_6_helix_bundle_honeycomb restored. --- scadnano/scadnano.py | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 24e5bc17..24632248 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -4133,11 +4133,7 @@ def _cadnano_v2_place_strand(self, strand: Strand, dct: dict, self._cadnano_v2_place_crossover(which_helix, next_helix, domain, next_domain, strand_type) -<<<<<<< HEAD - def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int) -> Dict[int, int]: -======= def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int, design_grid: Grid) -> dict: ->>>>>>> master """Creates blank cadnanov2 helices in and initialized all their fields. """ helices_ids_reverse = {} @@ -4145,23 +4141,11 @@ def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int, design_grid: Grid) - helix_dct: Dict[str, Any] = OrderedDict() helix_dct['num'] = helix.idx -<<<<<<< HEAD - if self.grid == Grid.square: - if helix.grid_position is None: - raise ValueError('cannot have grid_position == None if grid is square') - helix_dct['row'] = helix.grid_position[1] - helix_dct['col'] = helix.grid_position[0] - - elif self.grid == Grid.honeycomb: - if helix.grid_position is None: - raise ValueError('cannot have grid_position == None if grid is honeycomb') -======= if design_grid == Grid.square: helix_dct['row'] = helix.grid_position[1] helix_dct['col'] = helix.grid_position[0] if design_grid == Grid.honeycomb: ->>>>>>> master helix_dct['row'], helix_dct['col'] = helix.grid_position[1], helix.grid_position[0] helix_dct['scaf'] = [] @@ -4244,11 +4228,7 @@ def to_cadnano_v2(self) -> Dict[str, Any]: '''Filling the helices with blank. ''' -<<<<<<< HEAD - helices_ids_reverse: Dict[int, int] = self._cadnano_v2_fill_blank(dct, num_bases) -======= helices_ids_reverse = self._cadnano_v2_fill_blank(dct, num_bases, design_grid) ->>>>>>> master '''Putting the scaffold in place. ''' From a274a98999c94f7c5bf11b9c64a1b4af1ef50b0c Mon Sep 17 00:00:00 2001 From: Cosmo Date: Tue, 8 Sep 2020 17:29:18 +0100 Subject: [PATCH 4/6] Forcing the add of test_6_helix_bundle_honeycomb.sc which was ignored --- .../test_6_helix_bundle_honeycomb.sc | 1870 +++++++++++++++++ 1 file changed, 1870 insertions(+) create mode 100644 tests_inputs/cadnano_v2_export/test_6_helix_bundle_honeycomb.sc diff --git a/tests_inputs/cadnano_v2_export/test_6_helix_bundle_honeycomb.sc b/tests_inputs/cadnano_v2_export/test_6_helix_bundle_honeycomb.sc new file mode 100644 index 00000000..482e378f --- /dev/null +++ b/tests_inputs/cadnano_v2_export/test_6_helix_bundle_honeycomb.sc @@ -0,0 +1,1870 @@ +{ + "version": "0.12.0", + "grid": "honeycomb", + "helices": [ + {"grid_position": [1, 1], "max_offset": 1295}, + {"grid_position": [0, 1], "max_offset": 1295}, + {"grid_position": [0, 2], "max_offset": 1295}, + {"grid_position": [1, 2], "max_offset": 1295}, + {"grid_position": [2, 2], "max_offset": 1295}, 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"CATTAAAAGAAGTGCCACCACCCTCAGACAGCATTGACAGCA", + "domains": [ + {"helix": 0, "forward": false, "start": 763, "end": 770}, + {"helix": 5, "forward": true, "start": 763, "end": 770}, + {"helix": 4, "forward": false, "start": 756, "end": 770}, + {"helix": 3, "forward": true, "start": 756, "end": 770} + ] + }, + { + "color": "#03b6a2", + "sequence": "AAAGAGTCATCTTTTCATAGCCCCCTTAACCGTCAGACTGTA", + "domains": [ + {"helix": 5, "forward": true, "start": 798, "end": 805}, + {"helix": 0, "forward": false, "start": 798, "end": 805}, + {"helix": 1, "forward": true, "start": 798, "end": 812}, + {"helix": 2, "forward": false, "start": 798, "end": 812} + ] + }, + { + "color": "#007200", + "sequence": "CGTTTGCCTGTCCAATGAAACCATCGATGTTTGCCTTTAGCA", + "domains": [ + {"helix": 0, "forward": false, "start": 805, "end": 812}, + {"helix": 5, "forward": true, "start": 805, "end": 812}, + {"helix": 4, "forward": false, "start": 798, "end": 812}, + {"helix": 3, "forward": true, "start": 798, "end": 812} + ] + }, + { + "color": "#aaaa00", + "sequence": "TTCTTTGATCACCGGGAAATTATTCATTCGATTCAACCGATT", + "domains": [ + {"helix": 5, "forward": true, "start": 840, "end": 847}, + {"helix": 0, "forward": false, "start": 840, "end": 847}, + {"helix": 1, "forward": true, "start": 840, "end": 854}, + {"helix": 2, "forward": false, "start": 840, "end": 854} + ] + }, + { + "color": "#f7931e", + "sequence": "GTGAATTATTAGTATTGTCACAATCAATCAAAAGGGCGACCA", + "domains": [ + {"helix": 0, "forward": false, "start": 847, "end": 854}, + {"helix": 5, "forward": true, "start": 847, "end": 854}, + {"helix": 4, "forward": false, "start": 840, "end": 854}, + {"helix": 3, "forward": true, "start": 840, "end": 854} + ] + }, + { + "color": "#007200", + "sequence": "TCAAACTATTACGCAGAACTGGCATGATCAAAACCGAGGAAA", + "domains": [ + {"helix": 5, "forward": true, "start": 882, "end": 889}, + {"helix": 0, "forward": false, "start": 882, "end": 889}, + {"helix": 1, "forward": true, "start": 882, "end": 896}, + {"helix": 2, "forward": false, "start": 882, "end": 896} + ] + }, + { + "color": "#57bb00", + "sequence": "ACTCCTTATCGGCCCTTACCGAAGCCCTGTTACCAGAAGGAG", + "domains": [ + {"helix": 0, "forward": false, "start": 889, "end": 896}, + {"helix": 5, "forward": true, "start": 889, "end": 896}, + {"helix": 4, "forward": false, "start": 882, "end": 896}, + {"helix": 3, "forward": true, "start": 882, "end": 896} + ] + }, + { + "color": "#f7931e", + "sequence": "CGCCAGCGTAATTGTGAACACCCTGAACCATAAAAACAGGGA", + "domains": [ + {"helix": 5, "forward": true, "start": 924, "end": 931}, + {"helix": 0, "forward": false, "start": 924, "end": 931}, + {"helix": 1, "forward": true, "start": 924, "end": 938}, + {"helix": 2, "forward": false, "start": 924, "end": 938} + ] + }, + { + "color": "#32b86c", + "sequence": "TCAGAGGCATTGCAAACGATTTTTTGTTGAGAGAATAACATA", + "domains": [ + {"helix": 0, "forward": false, "start": 931, "end": 938}, + {"helix": 5, "forward": true, "start": 931, "end": 938}, + {"helix": 4, "forward": false, "start": 924, "end": 938}, + {"helix": 3, "forward": true, "start": 924, "end": 938} + ] + }, + { + "color": "#57bb00", + "sequence": "CATTTTGAATCTTATGCACCCAGCTACACCGGTTTTGAAGCC", + "domains": [ + {"helix": 5, "forward": true, "start": 966, "end": 973}, + {"helix": 0, "forward": false, "start": 966, "end": 973}, + {"helix": 1, "forward": true, "start": 966, "end": 980}, + {"helix": 2, "forward": false, "start": 966, "end": 980} + ] + }, + { + "color": "#320096", + "sequence": "TATCCTGACGCTCAGGCTTATCCGGTATCGACTTGCGGGACA", + "domains": [ + {"helix": 0, "forward": false, "start": 973, "end": 980}, + {"helix": 5, "forward": true, "start": 973, "end": 980}, + {"helix": 4, "forward": false, "start": 966, "end": 980}, + {"helix": 3, "forward": true, "start": 966, "end": 980} + ] + }, + { + "color": "#32b86c", + "sequence": "CAGATTCAGTACCGCATTCCAAGAACGGTTGTAGAAACCAAT", + "domains": [ + {"helix": 5, "forward": true, "start": 1008, "end": 1015}, + {"helix": 0, "forward": false, "start": 1008, "end": 1015}, + {"helix": 1, "forward": true, "start": 1008, "end": 1022}, + {"helix": 2, "forward": false, "start": 1008, "end": 1022} + ] + }, + { + "color": "#7300de", + "sequence": "TAAACCAACCAGTCTCAACAATAGATAAATTTACGAGCATCA", + "domains": [ + {"helix": 0, "forward": false, "start": 1015, "end": 1022}, + {"helix": 5, "forward": true, "start": 1015, "end": 1022}, + {"helix": 4, "forward": false, "start": 1008, "end": 1022}, + {"helix": 3, "forward": true, "start": 1008, "end": 1022} + ] + }, + { + "color": "#320096", + "sequence": "GGCCAACAGAATATGAGGCATTTTCGAGAGCGCCATATTTAA", + "domains": [ + {"helix": 5, "forward": true, "start": 1050, "end": 1057}, + {"helix": 0, "forward": false, "start": 1050, "end": 1057}, + {"helix": 1, "forward": true, "start": 1050, "end": 1064}, + {"helix": 2, "forward": false, "start": 1050, "end": 1064} + ] + }, + { + "color": "#b8056c", + "sequence": "TAATAAGAGAGATATTATACAAATTCTTTTAATTGAGAATAA", + "domains": [ + {"helix": 0, "forward": false, "start": 1057, "end": 1064}, + {"helix": 5, "forward": true, "start": 1057, "end": 1064}, + {"helix": 4, "forward": false, "start": 1050, "end": 1064}, + {"helix": 3, "forward": true, "start": 1050, "end": 1064} + ] + }, + { + "color": "#7300de", + "sequence": "TACGTGGGAAATACTCTTCTGACCTAAAGAGAGAAAACTTTT", + "domains": [ + {"helix": 5, "forward": true, "start": 1092, "end": 1099}, + {"helix": 0, "forward": false, "start": 1092, "end": 1099}, + {"helix": 1, "forward": true, "start": 1092, "end": 1106}, + {"helix": 2, "forward": false, "start": 1092, "end": 1106} + ] + }, + { + "color": "#cc0000", + "sequence": "ATGGTTTCACAGACTGGGTTATATAACTGACAAAGAACGCCT", + "domains": [ + {"helix": 0, "forward": false, "start": 1099, "end": 1106}, + {"helix": 5, "forward": true, "start": 1099, "end": 1106}, + {"helix": 4, "forward": false, "start": 1092, "end": 1106}, + {"helix": 3, "forward": true, "start": 1092, "end": 1106} + ] + }, + { + "color": "#b8056c", + "sequence": "ATGCGCGATAGCTTCCTTAGAATCCTTGACCTTGCTTCTGTA", + "domains": [ + {"helix": 5, "forward": true, "start": 1134, "end": 1141}, + {"helix": 0, "forward": false, "start": 1134, "end": 1141}, + {"helix": 1, "forward": true, "start": 1134, "end": 1148}, + {"helix": 2, "forward": false, "start": 1134, "end": 1148} + ] + }, + { + "color": "#f74308", + "sequence": "CATAGCGAACTGATTTTGAATTACCTTTTGAGTGAATAACAA", + "domains": [ + {"helix": 0, "forward": false, "start": 1141, "end": 1148}, + {"helix": 5, "forward": true, "start": 1141, "end": 1148}, + {"helix": 4, "forward": false, "start": 1134, "end": 1148}, + {"helix": 3, "forward": true, "start": 1134, "end": 1148} + ] + }, + { + "color": "#cc0000", + "sequence": "CGAACGAAGAGGCGTGAATACCAAGTTATTATCGGGAGAAAC", + "domains": [ + {"helix": 5, "forward": true, "start": 1176, "end": 1183}, + {"helix": 0, "forward": false, "start": 1176, "end": 1183}, + {"helix": 1, "forward": true, "start": 1176, "end": 1190}, + {"helix": 2, "forward": false, "start": 1176, "end": 1190} + ] + }, + { + "color": "#888888", + "sequence": "ATCGCGCACCACCAAATTGCGTAGATTTAGTACCTTTTACAT", + "domains": [ + {"helix": 0, "forward": false, "start": 1183, "end": 1190}, + {"helix": 5, "forward": true, "start": 1183, "end": 1190}, + {"helix": 4, "forward": false, "start": 1176, "end": 1190}, + {"helix": 3, "forward": true, "start": 1176, "end": 1190} + ] + }, + { + "color": "#f74308", + "sequence": "CAGTATTTAATCCTATCAGATGATGGCATCACCAGAAGGAGC", + "domains": [ + {"helix": 5, "forward": true, "start": 1218, "end": 1225}, + {"helix": 0, "forward": false, "start": 1218, "end": 1225}, + {"helix": 1, "forward": true, "start": 1218, "end": 1232}, + {"helix": 2, "forward": false, "start": 1218, "end": 1232} + ] + }, + { + "color": "#333333", + "sequence": "ATCAATAAACACCGGAACGTTATTAATTAACAAAGAAACCGA", + "domains": [ + {"helix": 0, "forward": false, "start": 1225, "end": 1232}, + {"helix": 5, "forward": true, "start": 1225, "end": 1232}, + {"helix": 4, "forward": false, "start": 1218, "end": 1232}, + {"helix": 3, "forward": true, "start": 1218, "end": 1232} + ] + }, + { + "color": "#cc0000", + "sequence": "ACTGCCCGAAATTGTCATGGTCATAGCTAAACGGAGGATCCC", + "domains": [ + {"helix": 5, "forward": true, "start": 42, "end": 49}, + {"helix": 0, "forward": false, "start": 42, "end": 49}, + {"helix": 1, "forward": true, "start": 42, "end": 56}, + {"helix": 2, "forward": false, "start": 42, "end": 56} + ] + }, + { + "color": "#f74308", + "sequence": "CCTGTGTGCTTTCCGGTTGGTGTAATGAACCTCGATAAAGAT", + "domains": [ + {"helix": 0, "forward": false, "start": 49, "end": 56}, + {"helix": 5, "forward": true, "start": 49, "end": 56}, + {"helix": 4, "forward": false, "start": 42, "end": 56}, + {"helix": 3, "forward": true, "start": 42, "end": 56} + ] + }, + { + "color": "#007200", + "sequence": "CTAATCCTTTGCCCCCTGCAACAGTGCCAATACATTTGAGTC", + "domains": [ + {"helix": 4, "forward": false, "start": 1232, "end": 1246}, + {"helix": 5, "forward": true, "start": 1232, "end": 1246}, + {"helix": 0, "forward": false, "start": 1232, "end": 1246} + ] + }, + { + "color": "#320096", + "sequence": "CAACTCGTATTACAACTTTACAAACAATATGATTTAGAAGTA", + "domains": [ + {"helix": 3, "forward": true, "start": 1232, "end": 1246}, + {"helix": 2, "forward": false, "start": 1232, "end": 1246}, + {"helix": 1, "forward": true, "start": 1232, "end": 1246} + ] + }, + { + "color": "#0066cc", + "sequence": 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ATTTGGATTGGGATAAATAATATGGCTGTTTATTTTGTAACTGGCAAATTAGGCTCTGGAAAGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAAATTGTAGCTGGGTGCAAAATAGCAACTAATCTTGATTTAAGGCTTCAAAACCTCCCGCAAGTCGGGAGGTTCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTGCTTGCTATTGGGCGCGGTAATGATTCCTACGATGAAAATAAAAACGGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAGCCGATTATTGATTGGTTTCTACATGCTCGTAAATTAGGATGGGATATTATTTTTCTTGTTCAGGACTTATCTATTGTTGATAAACAGGCGCGTTCTGCATTAGCTGAACATGTTGTTTATTGTCGTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCTGCCTAAATTACATGTTGGCGTTGTTAAATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACGCATATGATACTAAACAGGCTTTTTCTAGTAATTATGATTCCGGTGTTTATTCTTATTTAACGCCTTATTTATCACACGGTCGGTATTTCAAACCATTAAATTTAGGTCAGAAGATGAAATTAACTAAAATATATTTGAAAAAGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGTTATATAACCCAACCTAAGCCGGAGGTTAAAAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAGCTATCGCTATGTTTTCAAGGATTCTAAGGGAAAATTAATTAATAGCGACGATTTACAGAAGCAAGGTTATTCACTCACATATATTGATTTATGTACTGTTTCCATTAAAAAAGGTAATTCAAATGAAATTGTTAAATGTAATTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGAAATGAATAATTCGCCTCTGCGCGATTTTGTAACTTGGTATTCAAAGCAATCAGGCGAATCCGTTATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACGCAATTTCTTTATTTCTGTTTTACGTGCAAATAATTTTGATATGGTAGGTTCTAACCCTTCCATTATTCAGAAGTATAATCCAAACAATCAGGATTATATTGATGAATTGCCATCATCTGATAATCAGGAATATGATGATAATTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTTTTAAAATTAATAACGTTCGGGCAAAGGATTTAATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGGCTCTAATCTATTAGTTGTTAGTGCTCCTAAAGATATTTTAGATAACCTTCCTCAATTCCTTTCAACTGTTGATTTGCCAACTGACCAGATATTGATTGAGGGTTTGATATTTGAGGTTCAGCAAGGTGATGCTTTAGATTTTTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACCGCCTCACCTCTGTTTTATCTTCTGCTGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAGCCATTCAAAAATATTGTCTGTGCCACGTATTCTTACGCTTTCAGGTCAGAAGGGTTCTATCTCTGTTGGCCAGAATGTCCCTTTTATTACTGGTCGTGTGACTGGTGAATCTGCCAATGTAAATAATCCATTTCAGACGATTGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCGGTAATATTGTTCTGGATATTACCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTGCTACAACGGTTAATTTGCGTGATGGACAGACTCTTTTACTCGGTGGCCTCACTGATTATAAAAACACTTCTCAGGATTCTGGCGTACCGTTCCTGTCTAAAATCCCTTTAATCGGCCTCCTGTTTAGCTCCCGCTCTGATTCTAACGAGGAAAGCACGTTATACGTGCTCGTCAAAGCAACCATAGTACGCGCCCTGTAGCGGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCGCAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCTTTCGCTTTCTTCCCTTCCTTTCTCGCCACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTCGACCCCAAAAAACTTGATTTGGGTGATGGTTCACGTAGTGGGCCATCGCCC", 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1146}, + {"helix": 4, "forward": true, "start": 1118, "end": 1160}, + {"helix": 3, "forward": false, "start": 1146, "end": 1160}, + {"helix": 2, "forward": true, "start": 1146, "end": 1164}, + {"helix": 1, "forward": false, "start": 1150, "end": 1164}, + {"helix": 0, "forward": true, "start": 1150, "end": 1192}, + {"helix": 1, "forward": false, "start": 1164, "end": 1192}, + {"helix": 2, "forward": true, "start": 1164, "end": 1188}, + {"helix": 3, "forward": false, "start": 1160, "end": 1188}, + {"helix": 4, "forward": true, "start": 1160, "end": 1202}, + {"helix": 3, "forward": false, "start": 1188, "end": 1202}, + {"helix": 2, "forward": true, "start": 1188, "end": 1206}, + {"helix": 1, "forward": false, "start": 1192, "end": 1206}, + {"helix": 0, "forward": true, "start": 1192, "end": 1234}, + {"helix": 1, "forward": false, "start": 1206, "end": 1234}, + {"helix": 2, "forward": true, "start": 1206, "end": 1230}, + {"helix": 3, "forward": false, "start": 1202, "end": 1230}, + {"helix": 4, "forward": true, "start": 1202, "end": 1244}, + {"helix": 3, "forward": false, "start": 1230, "end": 1244}, + {"helix": 2, "forward": true, "start": 1230, "end": 1248}, + {"helix": 1, "forward": false, "start": 1234, "end": 1248}, + {"helix": 0, "forward": true, "start": 1234, "end": 1276}, + {"helix": 1, "forward": false, "start": 1248, "end": 1276}, + {"helix": 2, "forward": true, "start": 1248, "end": 1272}, + {"helix": 3, "forward": false, "start": 1244, "end": 1272}, + {"helix": 4, "forward": true, "start": 1244, "end": 1279}, + {"helix": 5, "forward": false, "start": 399, "end": 1279} + ] + } + ] +} \ No newline at end of file From 3753e36022364d91fc9f4d6b55e739ee00f4234c Mon Sep 17 00:00:00 2001 From: Cosmo Date: Thu, 10 Sep 2020 13:53:19 +0100 Subject: [PATCH 5/6] Correct type annotation --- scadnano/scadnano.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 24632248..0e80c9fc 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -4133,7 +4133,7 @@ def _cadnano_v2_place_strand(self, strand: Strand, dct: dict, self._cadnano_v2_place_crossover(which_helix, next_helix, domain, next_domain, strand_type) - def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int, design_grid: Grid) -> dict: + def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int, design_grid: Grid) -> Dict[int, int]:: """Creates blank cadnanov2 helices in and initialized all their fields. """ helices_ids_reverse = {} From 627d45b993c9ebbbecd9aeaa493dafbadf2102ca Mon Sep 17 00:00:00 2001 From: Cosmo Date: Thu, 10 Sep 2020 16:18:35 +0100 Subject: [PATCH 6/6] Correcting syntax error --- scadnano/scadnano.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scadnano/scadnano.py b/scadnano/scadnano.py index 0e80c9fc..9f5bfd1a 100644 --- a/scadnano/scadnano.py +++ b/scadnano/scadnano.py @@ -4133,7 +4133,7 @@ def _cadnano_v2_place_strand(self, strand: Strand, dct: dict, self._cadnano_v2_place_crossover(which_helix, next_helix, domain, next_domain, strand_type) - def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int, design_grid: Grid) -> Dict[int, int]:: + def _cadnano_v2_fill_blank(self, dct: dict, num_bases: int, design_grid: Grid) -> Dict[int, int]: """Creates blank cadnanov2 helices in and initialized all their fields. """ helices_ids_reverse = {}