check bad charges

forlilab · Jul 28, 2023 · 6ee171c · 6ee171c
1 parent 6e839ce
commit 6ee171c
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Showing 2 changed files with 11 additions and 3 deletions.
diff --git a/meeko/writer.py b/meeko/writer.py
@@ -6,6 +6,7 @@
 
 import sys
 import json
+import math
 
 import numpy as np
 from rdkit import Chem
@@ -102,7 +103,7 @@ def _walk_graph_recursive(cls, setup, node, data, edge_start=0, first=False):
         return data
 
     @classmethod
-    def write_string(cls, setup, add_index_map=False, remove_smiles=False):
+    def write_string(cls, setup, add_index_map=False, remove_smiles=False, bad_charge_ok=False):
         """Output a PDBQT file as a string.
 
         Args:
@@ -122,9 +123,15 @@ def write_string(cls, setup, add_index_map=False, remove_smiles=False):
             success = False
 
         for idx, atom_type in setup.atom_type.items():
+            if setup.atom_ignore[idx]:
+                continue
             if atom_type is None:
                 error_msg += 'atom number %d has None type, mol name: %s\n' % (idx, setup.get_mol_name())
                 success = False
+            c = setup.charge[idx]
+            if not bad_charge_ok and (type(c) != float and type(c) != int or math.isnan(c) or math.isinf(c)):
+                error_msg += 'atom number %d has non finite charge, mol name: %s, charge: %s\n' % (idx, setup.get_mol_name(), str(c))
+                success = False
 
         if not success:
             pdbqt_string = ""

diff --git a/scripts/mk_prepare_ligand.py b/scripts/mk_prepare_ligand.py
@@ -96,6 +96,7 @@ def cmd_lineparser():
     config_group.add_argument("-aa", "--add_atom_types", dest="add_atom_types_json",
                         action="append", help="Additional atom types to assign (JSON formated)", metavar="[{'smarts': '<smarts pattern>', 'atype': ',atomtype name>'}, {'smarts': '<smarts pattern>', 'atype': ',atomtype name>'}]")
     config_group.add_argument("--double_bond_penalty", help="penalty > 100 prevents breaking double bonds", type=int)
+    config_group.add_argument("--bad_charge_ok", help="NaN and Inf charges allowed in PDBQT", action="store_true")
     config_group.add_argument("--add_index_map", dest="add_index_map",
                         action="store_true", help="write map of atom indices from input to pdbqt")
     config_group.add_argument("--remove_smiles", dest="remove_smiles",
@@ -337,7 +338,7 @@ def get_suffixes(molsetups):
                 res, chain, num = cov_lig.res_id
                 suffixes = output.get_suffixes(molsetups)
                 for molsetup, suffix in zip(molsetups, suffixes):
-                    pdbqt_string, success, error_msg = PDBQTWriterLegacy.write_string(molsetup)
+                    pdbqt_string, success, error_msg = PDBQTWriterLegacy.write_string(molsetup, bad_charge_ok=args.bad_charge_ok)
                     if success:
                         pdbqt_string = PDBQTWriterLegacy.adapt_pdbqt_for_autodock4_flexres(pdbqt_string, res, chain, num)
                         name = molsetup.name
@@ -351,7 +352,7 @@ def get_suffixes(molsetups):
             molsetups = preparator.prepare(mol)
             suffixes = output.get_suffixes(molsetups) 
             for molsetup, suffix in zip(molsetups, suffixes):
-                pdbqt_string, success, error_msg = PDBQTWriterLegacy.write_string(molsetup)
+                pdbqt_string, success, error_msg = PDBQTWriterLegacy.write_string(molsetup, bad_charge_ok=args.bad_charge_ok)
                 if success:
                     name = molsetup.name
                     output(pdbqt_string, name, (suffix,))