diff options
Diffstat (limited to 'fix_matchedatoms.patch')
| -rw-r--r-- | fix_matchedatoms.patch | 34 |
1 files changed, 34 insertions, 0 deletions
diff --git a/fix_matchedatoms.patch b/fix_matchedatoms.patch new file mode 100644 index 000000000000..ce1b64135cf0 --- /dev/null +++ b/fix_matchedatoms.patch @@ -0,0 +1,34 @@ +--- 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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