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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 mmCIF files #206

Open stephaniewankowicz opened 2 years ago

stephaniewankowicz commented 2 years ago

Currently, qFit cannot read in mmCIF files.

This enhancement would allow qFit (in qfit_protein, qfit_residue, qfit_ligand) to read in mmCIF files, store appropriate header information (link data, nucleotide data, crystal record, scale data, and resolution), and convert it to a qfit structure object.

This will also include functionality for qFit to determine if it is a mmCIF or PDB file and output it in the same format.

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 The only remaining use case for mmCIF - and the only part still relying on the pymmlib parser - is reading ligand connectivity information. Unfortunately I have not been able to find an example of a CIF that works with the current code. Do you have a good test case for this anywhere? I think the code can actually be modified to be more compatible but without a working test I am nervous about breaking existing functionality.