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

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gmso/formats/lammpsdata.py

@@ -705,15 +705,25 @@ def _write_header(out_file, top, atom_style):
     if top.n_dihedrals > 0 and atom_style in ["full", "molecular"]:
         unique_dtypes = top.dihedral_types(filter_by=pfilter)
         from itertools import chain
+
         nkeys = len(next(iter(unique_dtypes)).parameters.keys())
-        nparams = len(list(_flatten((map(lambda x: [val.tolist() for val in x.parameters.values()], unique_dtypes)))))
-        #nparams = len(list(chain([dt.parameters.values() for dt in unique_dtypes])))
-        ntypes = int(nparams / nkeys)
-        out_file.write(
-            "{:d} dihedral types\n".format(
-                ntypes
+        nparams = len(
+            list(
+                _flatten(
+                    (
+                        map(
+                            lambda x: [
+                                val.tolist() for val in x.parameters.values()
+                            ],
+                            unique_dtypes,
+                        )
+                    )
+                )
             )
         )
+        # nparams = len(list(chain([dt.parameters.values() for dt in unique_dtypes])))
+        ntypes = int(nparams / nkeys)
+        out_file.write("{:d} dihedral types\n".format(ntypes))
     if top.n_impropers > 0 and atom_style in ["full", "molecular"]:
         out_file.write(
             "{:d} improper types\n".format(
@@ -933,9 +943,13 @@ def _write_dihedraltypes(out_file, top, base_unyts, parser, cfactorsDict):
     """Write out dihedrals to LAMMPS file."""
     test_dihedraltype = top.dihedrals[0].dihedral_type
     out_file.write(f"\nDihedral Coeffs #{test_dihedraltype.name}\n")
-    param_labels0 = parser(test_dihedraltype) # tuple (paramsList, params_namesList)
-
-    if isinstance(param_labels0[0][0], list): # check for parsing out multiple instances from the dihedral
+    param_labels0 = parser(
+        test_dihedraltype
+    )  # tuple (paramsList, params_namesList)
+
+    if isinstance(
+        param_labels0[0][0], list
+    ):  # check for parsing out multiple instances from the dihedral
         param_labels = [
             write_out_parameter_and_units(
                 name, convert_kelvin_to_energy_units(param, "kJ"), base_unyts
@@ -959,8 +973,10 @@ def _write_dihedraltypes(out_file, top, base_unyts, parser, cfactorsDict):
     # handle variable lengths for parameters
     base_msg = "{}\t"  # handles index
     end_msg = "# {}\t{}\t{}\t{}\n"
-
-    if parser.__name__ == "parse_opls_style_dihedral": # one opls parameter per dihedral type
+
+    if (
+        parser.__name__ == "parse_opls_style_dihedral"
+    ):  # one opls parameter per dihedral type
         for idx, (dihedral_type, members) in enumerate(index_membersList):
             param_labels = parser(dihedral_type)
             variable_msg = "{:8}\t" * len(param_labels[1])
@@ -975,18 +991,22 @@ def _write_dihedraltypes(out_file, top, base_unyts, parser, cfactorsDict):
                             n_decimals=6,
                             name=parameterStr,
                         )
-                        for parameter, parameterStr in zip(*parser(dihedral_type))
+                        for parameter, parameterStr in zip(
+                            *parser(dihedral_type)
+                        )
                     ],
                     *members,
                 )
             )
     elif parser.__name__ == "parse_charmm_style_dihedral":
-        ndecimalsDict = {"k":6, "n":0, "phi_eq":0, "weights":1}
+        ndecimalsDict = {"k": 6, "n": 0, "phi_eq": 0, "weights": 1}
         for idx, (dihedral_type, members) in enumerate(index_membersList):
             parameter_termList, parameterStrList = parser(dihedral_type)
             variable_msg = "{:8}\t" * len(parameterStrList)
             full_msg = base_msg + variable_msg + end_msg
-            for parameter_terms in parameter_termList: # list of params on each line
+            for (
+                parameter_terms
+            ) in parameter_termList:  # list of params on each line
                 out_file.write(
                     full_msg.format(
                         idx + 1,
@@ -997,7 +1017,9 @@ def _write_dihedraltypes(out_file, top, base_unyts, parser, cfactorsDict):
                                 n_decimals=ndecimalsDict[parameterStr],
                                 name=parameterStr,
                             )
-                            for parameter, parameterStr in zip(parameter_terms, parameterStrList)
+                            for parameter, parameterStr in zip(
+                                parameter_terms, parameterStrList
+                            )
                         ],
                         *members,
                     )
@@ -1022,8 +1044,8 @@ def parse_charmm_style_dihedral(dihedral_type, weightsArray=None):
     if not weightsArray:  # used for amber forcefield weights are 0
         weightsArray = np.zeros(kArray.size) * u.dimensionless
     allParamsList = []
-    for a,b,c,d in zip(kArray, nArray, phi_eqArray, weightsArray):
-        allParamsList.append([a,b,c,d])
+    for a, b, c, d in zip(kArray, nArray, phi_eqArray, weightsArray):
+        allParamsList.append([a, b, c, d])
     return allParamsList, ["k", "n", "phi_eq", "weights"]
 
 
@@ -1190,9 +1212,10 @@ def _default_lj_val(top, source):
             f"Provided {source} for default LJ cannot be found in the topology."
         )
 
+
 def _flatten(iterable):
     try:
         for item in iterable:
             yield from _flatten(item)
     except TypeError:
-        yield iterable
+        yield iterable