ProtoCaller.Wrappers.pdbfixerwrapper module

This is a light wrapper around pdbfixer. Here the user can add missing residues and/or atoms to their structure and ProtoCaller keeps track of any PDB information lost in the process. It is also possible to replace nonstandard residues with their standard counterparts. This is highly recommended, since in most cases there are no reliable parameters for modified amino acid residues. If the user runs an external modelling code, they need to make sure that no missing atom/disulfide bond information is lost from the PDB file before passing it to ProtoCaller.

ProtoCaller.Wrappers.pdbfixerwrapper.pdbfixerTransform(filename, replace_nonstandard_residues, add_missing_residues, add_missing_atoms)

Adds missing residues and/or missing atoms to a PDB file.

Parameters

  • filename (str) – Name of the input PDB file.

  • replace_nonstandard_residues (bool) – Whether to replace nonstandard residues with their standard equivalents.

  • add_missing_residues (bool) – Whether to add missing residues.

  • add_missing_atoms (bool) – Whether to add missing atoms.

Returns

filename_output – Absolute path to the modified file.

Return type

str