bis_protein_structure.MMEVAL.get_contact

bis_protein_structure.MMEVAL.get_contact(pdb_path, residue_dict=None, coord_masks=None, interface='all', show=True)[source]

Calculates the contact map between residues in a PDB file.

Parameters:

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

  • residue_dict (dict, optional) – Predefined residue dictionary (default is None).

  • coord_masks (numpy.ndarray, optional) – Mask of residue coordinates (default is None).

  • interface (str, optional) – Specifies the chains for which the contact map should be calculated. If ‘all’, contacts across all chains are calculated (default is ‘all’).

  • show (bool, optional) – Whether to display the contact map (default is True).

Returns:

  • contact_map (numpy.ndarray) – The contact map where values represent the number of contacting atoms.

  • residue_dict (dict) – Residue dictionary mapping chain IDs to residue names.

  • coord_masks (numpy.ndarray) – Residue coordinate masks.