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PR2025 for covalent protein-ligand binding #39

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PR2025 for covalent protein-ligand binding #39

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15 changes: 10 additions & 5 deletions fragit/fragmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
except ImportError:
raise OBNotFoundException("OpenBabel not found. Please install OpenBabel to use FragIt.")

from fragit.util import remove_duplicates, flatten, difference, uniqifyListOfLists, is_tuple_values_in_either_list, LABEL2Z
from fragit.util import remove_duplicates, flatten, difference, uniqifyListOfLists, is_tuple_values_in_either_list, LABEL2Z, Z2LABEL
from fragit.config import FragItConfig, FragItDataBase


Expand Down Expand Up @@ -97,7 +97,8 @@ def _remove_metal_atoms(self):
break
for i in range(1, self.mol.NumAtoms()+1):
atom = self.mol.GetAtom(i)
if atom.GetAtomicNum() in [1, 6, 7, 8, 9, 12, 15, 16]:
# PX: not make Cl to Cl-
if atom.GetAtomicNum() in [1, 6, 7, 8, 9, 12, 15, 16, 17]:
if atom not in self._atoms:
self._atoms.append(atom)
added += 1
Expand All @@ -108,8 +109,8 @@ def _remove_metal_atoms(self):
atomic_charge = 0 # default
if atom.GetAtomicNum() in [11, 19]: # Na+ and K+:
atomic_charge = 1
elif atom.GetAtomicNum() in [9, 17]: # F- and Cl-
atomic_charge = -1
#elif atom.GetAtomicNum() in [9, 17]: # F- and Cl-
# atomic_charge = -1

new_atom = openbabel.OBAtom()
new_atom.Duplicate(atom)
Expand Down Expand Up @@ -191,6 +192,10 @@ def do_fragment_merging(self):
fragments = self.get_fragments()
fragments_to_merge.reverse()
for fragment_id in fragments_to_merge:
#PX : for edge case,
# when the first fragment is glycine,do not merge.
if fragment_id == 0:
continue
previous_fragment = fragment_id-1
ifrag = fragments.pop(fragment_id)
jfrag = fragments[previous_fragment].extend(ifrag)
Expand Down Expand Up @@ -580,7 +585,7 @@ def name_fragment(self, atoms: List[int]) -> str:
if len(atoms) == 1:
atom = self.mol.GetAtom(atoms[0])
charge_lbl = charge_lbls[atom.GetFormalCharge()]
element = LABEL2Z[atom.GetAtomicNum()]
element = Z2LABEL[atom.GetAtomicNum()]
return "{0:s}{1:s}".format(element, charge_lbl)
else:
for residue in openbabel.OBResidueIter(self.mol):
Expand Down
1 change: 1 addition & 0 deletions fragit/gamessfmo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@
GAMESS_BASIS_GROUP['cc-pVTZ'] = "GBASIS=CCT"
GAMESS_BASIS_GROUP['aug-cc-pVDZ'] = "GBASIS=ACCD"
GAMESS_BASIS_GROUP['aug-cc-pVTZ'] = "GBASIS=ACCT"
GAMESS_BASIS_GROUP['DFTB-C'] = "GBASIS=DFTB"

# basis set data for atoms in $DATA group
GAMESS_DATA_BASIS: Dict[str, Dict[str, str]] = dict()
Expand Down
5 changes: 5 additions & 0 deletions share/hmo/DFTB-C
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
DFTB-C 4 4
1 0 0.558756 0.000000 0.000000 0.829332
0 1 0.558757 0.781901 0.000000 -0.276445
0 1 0.558756 -0.390951 0.677146 -0.276445
0 1 0.558756 -0.390951 -0.677146 -0.276445