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--- pdb2pqr/main.py 2020-08-25 20:53:35.000000000 +0300
+++ pdb2pqr/main.py 2020-08-25 21:15:39.017396736 +0300
@@ -470,17 +470,16 @@
hydrogen_routines.optimize_hydrogens()
hydrogen_routines.cleanup()
_LOGGER.info("Applying force field to biomolecule states.")
protein.set_states()
- hitlist, misslist = protein.apply_force_field(forcefield_)
+ matched_atoms, missing_atoms = protein.apply_force_field(forcefield_)
if args.ligand is not None:
_LOGGER.info("Processing ligand.")
_LOGGER.warning("Using ZAP9 forcefield for ligand radii.")
ligand.assign_parameters()
- missing_atoms = []
lig_atoms = []
for residue in protein.residues:
tot_charge = 0
for pdb_atom in residue.atoms:
# Only check residues with HETATM
@@ -497,11 +496,11 @@
"Can't find HETATM {r.name} {r.res_seq} {a.name} "
"in MOL2 file").format(r=residue, a=pdb_atom)
_LOGGER.warning(err)
missing_atoms.append(pdb_atom)
- matched_atoms = hitlist + lig_atoms
+ matched_atoms += lig_atoms
for residue in protein.residues:
if not isclose(
residue.charge, int(residue.charge), abs_tol=CHARGE_ERROR):
err = (
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