Adjusts XYZ to Mol and XYZ File to Mol modules to assume angstrom and convert to bohr #9
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jwaldrop107
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Oct 6, 2025
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This is on the right track, but I think we'll want to go about it differently. Instead of changing the default behavior, I would add an input to the module called "units" that defaults to "bohr". Then have the module check the value of that input to determine if the coordinate values need to be converted (and throw on non-permissible values).
ryanmrichard
reviewed
Oct 6, 2025
…ent of the xyz to molecule
jwaldrop107
approved these changes
Oct 8, 2025
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I added in the unit scaling factor, I also "stress tested" the XYZ File to Molecule module with both a converted protein pdb from RCSB (4EMU, 2977 atoms) as well as an OpenMM generated solvent box, converted to an xyz (98880 atoms). The 4EMU took 290 ms, and the solvated box took 56952 ms. |
ryanmrichard
approved these changes
Oct 8, 2025
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🚀 [bumpr] Bumped! |
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Description
Converts angstrom-based XYZ files to bohr coordinates for Chemist conventions.
TODOs
None, r2g.