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ExcitedStates / qfit-3.0

qFit: Automated and unbiased multi-conformer models from X-ray and EM maps.
MIT License
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CCTBX Conversion: Read in PDB File #203

Open stephaniewankowicz opened 2 years ago

stephaniewankowicz commented 2 years ago

Change the reading of PDB files from qFit infrastructure to CCTBX.

The main function that will need to change is fromfile(). The majority of this functionality is in the structure folder. The fromfile function should also store information from the PDB header including link data, nucleotide data, crystal record, scale data, and resolution. These pieces of data are not currently used in qFit but should be store for writing PDB file at the end.

The output of this conversion should still be a structure object as this is used in the rest of qFit.

These changes will need to be applied to the following qFit input functions: -qFit_protein.py -qFit_residue.py -qFit_ligand.py

natechols commented 2 years ago

@stephaniewankowicz This is a bit of a tangent, but the file elements.py appears to be lifted entirely from a library available on PyPI: https://pypi.org/project/molmass/. Any objection to adding the dependency and removing the local copy?