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… constructor for ModificationInternal, instead of just frozenset
… delimiter symbols in between each Domain/Loopout
…me from output json
…dnano-export Refactor cadnano import/export
…it-tests-for-TestAssignDNA #186 add unit tests for test assign dna
…t_template Create pull_request_template.md
…xDNA-export-when-multiple-helix-groups-are-present closes #198: allow oxDNA export when multiple helix groups are present
Release notesSeveral bug fixes and one breaking change in how oxDNA export works. We have jumped from version 0.16.3 to 0.17.1 (skipping 0.17.0) because of a mistaken update to PyPI with version 0.17.0. That version has been "yanked" (https://pypi.org/project/scadnano/0.17.0/), but the PyPI site will not allow an update to that version, so we are skipping past it directly to version 0.17.1. Fix Pitch Angle on oxDNA Export(See also https://github.com/UC-Davis-molecular-computing/scadnano/releases/tag/v0.17.0) Note: This is a breaking change since it changes how oxDNA export is defined. If you were using oxDNA export before, you will have to change some helix angles (pitch and yaw) to create the same oxDNA output that was previously generated. Previously, scadnano interpreted the pitch angle as a clockwise rotation in the Y-Z plane, following SVG convention. For example, the following design has a helix group (containing helix 1) with pitch=45 (clockwise, away from the single strand on helix 0):
Previously, exporting to oxDNA rotates the helix in the opposite direction (counter-clockwise, towards the single strand on helix 0). Now, exporting to oxDNA rotates the helix in the same direction as in scadnano:
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UnHumbleBen
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There were a lot of changes in the scadnano.py and scadnano_tests.py file, but I figured that these changes have been reviewed already in earlier PRs so didn't examine too closely. Everything else looks good.
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