[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

docs/sphinxext/notebook_sphinxext.py

@@ -61,7 +61,6 @@ class NotebookDirective(Directive):
     final_argument_whitespace = True
 
     def run(self):
-
         # check if raw html is supported
         if not self.state.document.settings.raw_enabled:
             raise self.warning('"%s" directive disabled.' % self.name)

mbuild/compound.py

@@ -2427,7 +2427,6 @@ def _energy_minimize_openbabel(
                 # if an individual entry is a list, validate the input
                 if isinstance(fixed_temp, list):
                     if len(fixed_temp) == 2:
-
                         msg1 = (
                             "Expected tuple or list of length 3 to set"
                             "which dimensions to fix motion."

mbuild/formats/cassandramcf.py

@@ -165,7 +165,6 @@ def write_mcf(
 
     # Now we write the MCF file
     with open(filename, "w") as mcf_file:
-
         header = (
             "!***************************************"
             "****************************************\n"

mbuild/formats/lammpsdata.py

@@ -360,7 +360,6 @@ def write_lammpsdata(
 
     # Write lammps data file https://docs.lammps.org/2001/data_format.html
     with open(filename, "w") as data:
-
         data.write(f"{filename} - created by mBuild; units = {unit_style}\n")
         if unit_style == "lj":
             data.write("#Normalization factors: ")
@@ -938,7 +937,6 @@ def _get_dihedral_types(
             for dihedral in structure.rb_torsions
         ]
     elif use_dihedrals:
-
         dihedral_types = [
             unique_dihedral_types[dihedral_info]
             for dihedral_info in charmm_dihedrals

mbuild/lattice.py

@@ -523,7 +523,6 @@ def _from_lattice_vectors(self):
         return np.asarray([alpha, beta, gamma], dtype=np.float64)
 
     def _sanitize_populate_args(self, x, y, z):
-
         error_dict = {0: "X", 1: "Y", 2: "Z"}
 
         # Make sure neither x, y, z input is None

mbuild/lib/recipes/monolayer.py

@@ -71,7 +71,6 @@ def __init__(
             # Attach chains of each type to binding sites based on
             # respective fractions.
             for chain, fraction in zip(chains[:-1], fractions[:-1]):
-
                 # Create sub-pattern for this chain type
                 subpattern = deepcopy(pattern)
                 n_points = int(round(fraction * n_chains))

mbuild/lib/recipes/tiled_compound.py

@@ -86,7 +86,6 @@ def __init__(self, tile, n_tiles, name=None, **kwargs):
         # Bonds that were periodic in the original tile.
         periodic_bonds = set()
         for particle1, particle2 in tile.bonds():
-
             if np.linalg.norm(particle1.pos - particle2.pos) > dist_thresh:
                 periodic_bonds.add((particle1.index, particle2.index))
 
@@ -98,7 +97,10 @@ def __init__(self, tile, n_tiles, name=None, **kwargs):
         bonds_to_remove = set()
         bonds_to_add = set()
         for particle1, particle2 in self.bonds():
-            if (particle1.index, particle2.index,) not in periodic_bonds and (
+            if (
+                particle1.index,
+                particle2.index,
+            ) not in periodic_bonds and (
                 particle2.index,
                 particle1.index,
             ) not in periodic_bonds:

mbuild/packing.py

@@ -720,9 +720,7 @@ def solvate(
             overlap, solvated_xyz.name, seed, sidemax * 10
         ) + PACKMOL_SOLUTE.format(solute_xyz.name, *center_solute.tolist())
 
-        for (solv, m_solvent, rotate) in zip(
-            solvent, n_solvent, fix_orientation
-        ):
+        for solv, m_solvent, rotate in zip(solvent, n_solvent, fix_orientation):
             m_solvent = int(m_solvent)
             solvent_xyz = _new_xyz_file()
             solvent_xyz_list.append(solvent_xyz)

mbuild/pattern.py

@@ -241,7 +241,6 @@ class Grid2DPattern(Pattern):
     """
 
     def __init__(self, n, m, **kwargs):
-
         points = np.zeros(shape=(n * m, 3), dtype=float)
         for i, j in product(range(n), range(m)):
             points[i * m + j, 0] = i / n

mbuild/tests/test_compound.py

@@ -1579,7 +1579,6 @@ def test_energy_minimize_fix_compounds(self, octane):
             octane.energy_minimize(fixed_compounds=[methyl_end0, (True)])
 
         with pytest.raises(Exception):
-
             octane.energy_minimize(
                 fixed_compounds=[methyl_end0, ("True", True, True)]
             )

setup.py

@@ -60,7 +60,6 @@ def compile_proto(protoc):
 
 
 if __name__ == "__main__":
-
     proto_procedure()
 
     setup(