deepfold.relax.cleanup.fix_pdb

deepfold.relax.cleanup.fix_pdb(pdbfile, alterations_info)[source]

Apply pdbfixer to the contents of a PDB file; return a PDB string result.

  1. Replaces nonstandard residues.

  2. Removes heterogens (non protein residues) including water.

  3. Adds missing residues and missing atoms within existing residues.

  4. Adds hydrogens assuming pH=7.0.

  5. KeepIds is currently true, so the fixer must keep the existing chain and residue identifiers. This will fail for some files in wider PDB that have invalid IDs.

Parameters:

  • pdbfile – Input PDB file handle.

  • alterations_info – A dict that will store details of changes made.

Returns:

A PDB string representing the fixed structure.