Have molecule cookbook only use Topology.from_pdb

openforcefield / openff-toolkit

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

http://openforcefield.org

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Have molecule cookbook only use Topology.from_pdb #1709

Closed j-wags closed 10 months ago

j-wags commented 10 months ago

In the long run I'd like to deprecate Molecule.from_pdb_and_smiles and Molecule.from_polymer_pdb in favor of the maximally-capable Topology.from_pdb. This PR begins the process in our molecule cookbook.

closes #1657

cc #1708

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codecov[bot] commented 10 months ago

Codecov Report

Merging #1709 (75e2925) into main (7fd1a21) will decrease coverage by 0.03%. The diff coverage is n/a.

Additional details and impacted files

mattwthompson commented 10 months ago

Is there any way we could avoid duplicating the 5tbm files? I got confused looking around for the different versions of this PDB file in the repo since this one isn't in the released package, and it seems like the new one with appended underscore mostly duplicates the existing one with an extra 1.2 MB file in the repo