INNER CODE UNIT · Python

setup_molecule

Electrostatics/pdb2pqr · pdb2pqr/main.py:421

def setup_molecule(pdblist, definition, ligand_path):
    """Set up the molecular system.

    :param pdblist:  list of PDB records
    :type pdblist:  list
    :param definition:  topology definition
    :type definition:  Definition
    :param ligand_path:  path to ligand (may be None)
    :type ligand_path:  str
    :return: (biomolecule object, definition object--revised if ligand was
        parsed, ligand object--may be None)
    :rtype: (Biomolecule, Definition, Ligand)
    """
    if ligand_path is not None:
        ligand = Mol2Molecule()
        with open(ligand_path, encoding="utf-8") as ligand_file:
            ligand.read(ligand_file)
    else:

View source record →