Polymer from PQR

[rwxayheee]

This is for #264. PQR is a file format similar to PDB and contains Q (charge) and R (radius). The major programs that uses PQR are PDB2PQR and APBS. Being able to parse PQR would allow us to directly get the computed charges for Polymers with available models in PDB2PQR (PARSE, AMBER, etc.).

This PR is adapted from the PQR parser in PDB2PQR and the existing (RDKit-based) method in Meeko to create Polymer from PDB. Specifically, the partial charge will be first parsed into atoms in a monomer's raw_rdkit_mol. Next, to transfer it to the monomer's padded_mol and molsetup, a get_atomprop_from_raw option is added to function monomer.parameterize. This needs to be a dict, with keys of atom property name and values of corresponding default values. This additional function may be re-used to pass on other properties. Radius from PQR is also parsed, but currently not transferred to raw_rdkit_mol, padded_mol or molsetup.

If more people find it useful, we can add option --read_pqr, and expose option --charge_model to mk_prepare_receptor.py. Might need #277 to merge first before further edits on the command line scripts.

[rwxayheee]

Python Usage at 29b1464

Input:
1FAS_dry.pqr.txt

from meeko import Polymer
from meeko import ResidueChemTemplates
from meeko import MoleculePreparation
from meeko import PDBQTWriterLegacy

pqr_fn = "1FAS_dry.pqr"
templates = ResidueChemTemplates.create_from_defaults()
with open(pqr_fn, "r") as f:
    pqr_string = f.read()

mk_prep = MoleculePreparation(charge_model="read", charge_atom_prop="PQRCharge")
pol1 = Polymer.from_pqr_string(pqr_string, templates, mk_prep)

pdbqt_name1 = "1FAS_charge_from_pqr.pdbqt"
pdbqt_rigid = PDBQTWriterLegacy.write_from_polymer(pol1)[0]
with open(pdbqt_name1, "w") as f:
    f.write(pdbqt_rigid)

mk_prep = MoleculePreparation()
pol2 = Polymer.from_pqr_string(pqr_string, templates, mk_prep)

pdbqt_name2 = "1FAS_charge_default.pdbqt"
pdbqt_rigid = PDBQTWriterLegacy.write_from_polymer(pol2)[0]
with open(pdbqt_name2, "w") as f:
    f.write(pdbqt_rigid)

Output:
1FAS_charge_from_pqr.pdbqt.txt
1FAS_charge_default.pdbqt.txt