From 3da8acc5a6513bf8c7a83c6f8a140b4bde7e5312 Mon Sep 17 00:00:00 2001
From: Peng Xu <xupengpeng02@gmail.com>
Date: Thu, 22 May 2025 12:30:05 -0700
Subject: [PATCH] adding DFTB-C HMO file; handle Cl; handle edge case when
 glycine-merge enable; bug fix

---
 fragit/fragmentation.py | 15 ++++++++++-----
 fragit/gamessfmo.py     |  1 +
 share/hmo/DFTB-C        |  5 +++++
 3 files changed, 16 insertions(+), 5 deletions(-)
 create mode 100644 share/hmo/DFTB-C

diff --git a/fragit/fragmentation.py b/fragit/fragmentation.py
index b654f72..d36253f 100644
--- a/fragit/fragmentation.py
+++ b/fragit/fragmentation.py
@@ -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
 
 
@@ -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
@@ -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)
@@ -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)
@@ -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):
diff --git a/fragit/gamessfmo.py b/fragit/gamessfmo.py
index 6b9eec7..6d070de 100644
--- a/fragit/gamessfmo.py
+++ b/fragit/gamessfmo.py
@@ -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()
diff --git a/share/hmo/DFTB-C b/share/hmo/DFTB-C
new file mode 100644
index 0000000..417413d
--- /dev/null
+++ b/share/hmo/DFTB-C
@@ -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