License: MIT License
PDBInf allows you to read PDB files using RDKit and assign bond orders from .cif (PDBx) template files.
# provide a PDBx defining the TPO nonstandard residue
nonstandard_residues = gemmi.cif.read('./tpo.cif')
# load a PDB file using the built-in standard amino acid doc and providing information on the nonstandard residues
pdbinf.load_pdb_file('./tpo.pdb', templates=[pdbinf.STANDARD_AA_DOC, nonstandard_residues])
Hello,
Please can you provide a link or guidance on how to generate CIF files for nonstandard residues.
Thanks,
Dave
we currently do grouping of atoms into residue blocks by edge detection. often H atoms are appended onto PDB blocks, so these would get missed
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