Several 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.
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:
Release notes
Several 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: