u

.pre-commit-config.yaml

@@ -22,13 +22,13 @@ repos:
     - id: black
       args: [--line-length=80]
 - repo: https://github.com/pycqa/isort
-  rev: 5.11.1
+  rev: 5.11.4
   hooks:
     - id: isort
       name: isort (python)
       args: [--profile=black, --line-length=80]
 - repo: https://github.com/pycqa/pydocstyle
-  rev: '6.1.1'
+  rev: '6.2.3'
   hooks:
     - id: pydocstyle
       exclude: ^(mbuild/tests/|docs/|devtools/|setup.py|setup.cfg|mbuild/formats/charmm_writer.py|mbuild/formats/gomc_conf_writer.py|mbuild/utils/specific_ff_to_residue.py)

mbuild/compound.py

@@ -2384,7 +2384,7 @@ def _energy_minimize_openbabel(
             # if a user passes single constraint as a 1-D array,
             # i.e., [(p1,p2), 2.0]  rather than [[(p1,p2), 2.0]],
             # just add it to a list so we can use the same looping code
-            if len(np.array(distance_constraints).shape) == 1:
+            if len(np.array(distance_constraints, dtype=object).shape) == 1:
                 distance_constraints = [distance_constraints]
 
             for con_temp in distance_constraints:
@@ -2415,7 +2415,7 @@ def _energy_minimize_openbabel(
 
             # if fixed_compounds is a 1-d array and it is of length 2, we need to determine whether it is
             # a list of two Compounds or if fixed_compounds[1] should correspond to the directions to constrain
-            if len(np.array(fixed_compounds).shape) == 1:
+            if len(np.array(fixed_compounds, dtype=object).shape) == 1:
                 if len(fixed_compounds) == 2:
                     if not isinstance(fixed_compounds[1], Compound):
                         # if it is not a list of two Compounds, make a 2d array so we can use the same looping code
@@ -2493,7 +2493,7 @@ def _energy_minimize_openbabel(
                                 ob_constraints.AddAtomZConstraint(pid)
 
         if ignore_compounds is not None:
-            temp1 = np.array(ignore_compounds)
+            temp1 = np.array(ignore_compounds, dtype=object)
             if len(temp1.shape) == 2:
                 ignore_compounds = list(temp1.reshape(-1))
 

mbuild/formats/hoomd_snapshot.py

@@ -77,6 +77,7 @@ def from_snapshot(snapshot, scale=1.0):
         comp.add(atom, label=str(i))
 
     # Add bonds
+    particle_dict = {idx: p for idx, p in enumerate(comp.particles())}
     for i in range(bond_array.shape[0]):
         atom1 = int(bond_array[i][0])
         atom2 = int(bond_array[i][1])