ProtoCaller.Wrappers.charmmguiwrapper module

This module accesses CHARMM-GUI (http://charmm-gui.org) using an external headless driver which simulates a web browser and automatically performs clicks on the webserver. This means that the user needs a common web browser (firefox or chrome) and in some cases (depending on the operating system) an extra chromedriver which can be installed from your favourite package manager.

This wrapper can upload a PDB file to the server and add missing residues using CHARMM-GUI’s defaults. Any PDB information lost by the CHARMM-GUI wrapper is automatically restored by ProtoCaller. If this procedure doesn’t work, the user should either go through the procedure manually, or resort to using other modelling codes. In this case, the user should make sure that no PDB file information is lost.

There are also wrappers for CHARMM-GUI’s PDB Reader and Ligand Reader which are gateways for parametrising proteins and ligands using the CHARMM force field. However, ProtoCaller can not yet handle this force field and as such these routines are not yet very useful.

ProtoCaller.Wrappers.charmmguiwrapper.PDBReader(file, timeout=600)

Accesses http://charmm-gui.org and uses the PDB Reader.

Parameters

  • file (str) – Path to the input PDB file.

  • timeout (int) – Timeout in seconds.

Returns

filename_output – The absolute path to the output TGZ archive.

Return type

str

ProtoCaller.Wrappers.charmmguiwrapper.charmmguiTransform(filename, **kwargs)

Adds missing residues to a PDB file.

Parameters

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

  • kwargs – Keyword arguments to be passed to PDBReader.

Returns

filename_output – Absolute path to the modified file.

Return type

str

ProtoCaller.Wrappers.charmmguiwrapper.ligandReader(file, timeout=60, find_similar_residues=False)

Accesses http://charmm-gui.org and uses the Ligand Reader.

Parameters

  • file (str) – Path to the input ligand file.

  • timeout (int) – Timeout in seconds.

  • find_similar_residues (bool) – Whether to tick the “Find similar residues” checkbox before searching.

Returns

filename_output – The absolute path to the output TGZ archive.

Return type

str