fix fragment charges bug

selimsami · Dec 9, 2023 · bbcd2fe · bbcd2fe
1 parent 1de59bb
commit bbcd2fe
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Showing 4 changed files with 19 additions and 19 deletions.
diff --git a/qforce/molecule/non_bonded.py b/qforce/molecule/non_bonded.py
@@ -87,7 +87,7 @@ def subset(cls, non_bonded, frag_charges, mapping):
         rev_map = {v: k for k, v in mapping.items()}
         h_cap = non_bonded.h_cap
 
-        if frag_charges != []:
+        if list(frag_charges) != []:
             q = frag_charges
         else:
             q = np.array([non_bonded.q[rev_map[i]] for i in range(n_atoms)])

diff --git a/qforce/qm/orca.py b/qforce/qm/orca.py
@@ -461,26 +461,25 @@ def _read_orca_bond_order(out_file, n_atoms):
         item_match = re.compile('^\(\s*(\d+)-\w{1,2}\s*,\s*(\d+)-\w{1,2}\s*\)\s*:\s*(-?\w.+)$')
         b_orders = [[0, ] * n_atoms for _ in range(n_atoms)]
 
-        file = open(out_file, 'r')
-        line = file.readline()
-        # Skip to the step after geometry optimisation
-        while 'Mayer bond orders larger than' not in line:
+        with open(out_file, 'r') as file:
             line = file.readline()
-
-        line = file.readline()
-        while "-------" not in line:
-            items = line.split('B')
-            for item in items:
-                if item.strip():
-                    _m = re.match(item_match, item)
-                    i = int(_m.group(1))
-                    j = int(_m.group(2))
-                    bond_order = float(_m.group(3))
-                    b_orders[i][j] = bond_order
-                    b_orders[j][i] = bond_order
+            # Skip to the step after geometry optimisation
+            while 'Mayer bond orders larger than' not in line:
+                line = file.readline()
+
             line = file.readline()
+            while "-------" not in line:
+                items = line.split('B')
+                for item in items:
+                    if item.strip():
+                        _m = re.match(item_match, item)
+                        i = int(_m.group(1))
+                        j = int(_m.group(2))
+                        bond_order = float(_m.group(3))
+                        b_orders[i][j] = bond_order
+                        b_orders[j][i] = bond_order
+                line = file.readline()
 
-        file.close()
         return b_orders
 
     @staticmethod

diff --git a/qforce/qm/qchem.py b/qforce/qm/qchem.py
@@ -83,6 +83,7 @@ def scan(self, config, file_name):
                 if not found_n_atoms and " NAtoms, " in line:
                     line = file.readline()
                     n_atoms = int(line.split()[0])
+                    found_n_atoms = True
 
                 elif "OPTIMIZATION CONVERGED" in line:
                     coord = []

diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = qforce
-version = 0.6.12
+version = 0.6.13
 description = Q-Force: Quantum mechanically augmented molecular force fields 
 long_description = file: README.md
 long_description_content_type = text/markdown