binana.load_ligand_receptor package

This module contains functions for loading ligands and receptors. Note that while BINANA can process PDB files, the PDB format lacks some information required for a full BINANA analysis. PDBQT recommended.

binana.load_ligand_receptor.from_files(ligand_filename, receptor_filename, max_cutoff=None)[source]

Loads a ligand and receptor from PDBQT or PDB files. PDBQT recommended.

Parameters

  • ligand_pdbqt_filename (str) – The ligand filename to load. Preferably PDBQT formatted, though BINANA and perform most analyses on PDB files as well.

  • receptor_pdbqt_filename (str) – The receptor filename to load. Preferably PDBQT formatted, though BINANA and perform most analyses on PDB files as well.

  • max_cutoff (float, optional) – If specified, will only load receptor atoms that fall within a cube extending this many angstroms beyond the ligand in the x, y, and z directions. Can dramatically speed calculations on large proteins, if an appropriate max_cutoff is known beforehand. On the other hand, may prevent proper assignment of secondary structure. Defaults to None, meaning load all receptor atoms.

Returns

A list of binana._structure.mol.Mol objects, for the ligand and receptor, respectively.

Return type

list

binana.load_ligand_receptor.from_texts(ligand_text, receptor_text, max_cutoff=None)[source]

Loads a ligand and receptor from a PDBQT- or PDB-formatted string (text). PDBQT recommended.

Parameters

  • ligand_text (str) – The ligand text to load. Preferably PDBQT formatted, though BINANA and perform most analyses on PDB files as well.

  • receptor_text (str) – The receptor text to load. Preferably PDBQT formatted, though BINANA and perform most analyses on PDB files as well.

  • max_cutoff (float, optional) – If specified, will only load receptor atoms that fall within a cube extending this many angstroms beyond the ligand in the x, y, and z directions. Can dramatically speed calculations on large proteins, if an appropriate max_cutoff is known beforehand. On the other hand, may prevent proper assignment of secondary structure. Defaults to None, meaning load all receptor atoms.

Returns

A list of binana._structure.mol.Mol objects, for the ligand and receptor, respectively.

Return type

list