[fmt] Format converters modules and tests (#4850)

Author: RMeli

package/MDAnalysis/converters/OpenMM.py

@@ -77,13 +77,17 @@ class OpenMMSimulationReader(base.SingleFrameReaderBase):
     """
 
     format = "OPENMMSIMULATION"
-    units = {"time": "ps", "length": "nm", "velocity": "nm/ps",
-             "force": "kJ/(mol*nm)", "energy": "kJ/mol"}
+    units = {
+        "time": "ps",
+        "length": "nm",
+        "velocity": "nm/ps",
+        "force": "kJ/(mol*nm)",
+        "energy": "kJ/mol",
+    }
 
     @staticmethod
     def _format_hint(thing):
-        """Can this reader read *thing*?
-        """
+        """Can this reader read *thing*?"""
         try:
             from openmm.app import Simulation
         except ImportError:
@@ -104,34 +108,38 @@ def _read_first_frame(self):
             self.ts.triclinic_dimensions = self.convert_pos_from_native(
                 self.ts.triclinic_dimensions, inplace=False
             )
-            self.ts.dimensions[3:] = _sanitize_box_angles(self.ts.dimensions[3:])
+            self.ts.dimensions[3:] = _sanitize_box_angles(
+                self.ts.dimensions[3:]
+            )
             self.convert_velocities_from_native(self.ts._velocities)
             self.convert_forces_from_native(self.ts._forces)
             self.convert_time_from_native(self.ts.dt)
 
     def _mda_timestep_from_omm_context(self):
-        """ Construct Timestep object from OpenMM context """
+        """Construct Timestep object from OpenMM context"""
         try:
             import openmm.unit as u
         except ImportError:  # pragma: no cover
             import simtk.unit as u
 
-        state = self.filename.context.getState(-1, getVelocities=True,
-                getForces=True, getEnergy=True)
+        state = self.filename.context.getState(
+            -1, getVelocities=True, getForces=True, getEnergy=True
+        )
 
         n_atoms = self.filename.context.getSystem().getNumParticles()
 
         ts = self._Timestep(n_atoms, **self._ts_kwargs)
         ts.frame = 0
         ts.data["time"] = state.getTime()._value
         ts.data["potential_energy"] = (
-            state.getPotentialEnergy().in_units_of(u.kilojoule/u.mole)._value
+            state.getPotentialEnergy().in_units_of(u.kilojoule / u.mole)._value
         )
         ts.data["kinetic_energy"] = (
-            state.getKineticEnergy().in_units_of(u.kilojoule/u.mole)._value
+            state.getKineticEnergy().in_units_of(u.kilojoule / u.mole)._value
         )
         ts.triclinic_dimensions = state.getPeriodicBoxVectors(
-                asNumpy=True)._value
+            asNumpy=True
+        )._value
         ts.dimensions[3:] = _sanitize_box_angles(ts.dimensions[3:])
         ts.positions = state.getPositions(asNumpy=True)._value
         ts.velocities = state.getVelocities(asNumpy=True)._value
@@ -153,8 +161,7 @@ class OpenMMAppReader(base.SingleFrameReaderBase):
 
     @staticmethod
     def _format_hint(thing):
-        """Can this reader read *thing*?
-        """
+        """Can this reader read *thing*?"""
         try:
             from openmm import app
         except ImportError:
@@ -163,8 +170,7 @@ def _format_hint(thing):
             except ImportError:
                 return False
         else:
-            return isinstance(thing, (app.PDBFile, app.Modeller,
-                app.PDBxFile))
+            return isinstance(thing, (app.PDBFile, app.Modeller, app.PDBxFile))
 
     def _read_first_frame(self):
         self.n_atoms = self.filename.topology.getNumAtoms()
@@ -177,10 +183,12 @@ def _read_first_frame(self):
                 self.ts.triclinic_dimensions = self.convert_pos_from_native(
                     self.ts.triclinic_dimensions, inplace=False
                 )
-                self.ts.dimensions[3:] = _sanitize_box_angles(self.ts.dimensions[3:])
+                self.ts.dimensions[3:] = _sanitize_box_angles(
+                    self.ts.dimensions[3:]
+                )
 
     def _mda_timestep_from_omm_app(self):
-        """ Construct Timestep object from OpenMM Application object """
+        """Construct Timestep object from OpenMM Application object"""
 
         omm_object = self.filename
         n_atoms = omm_object.topology.getNumAtoms()
@@ -198,7 +206,7 @@ def _mda_timestep_from_omm_app(self):
 
 
 def _sanitize_box_angles(angles):
-    """ Ensure box angles correspond to first quadrant
+    """Ensure box angles correspond to first quadrant
 
     See `discussion on unitcell angles <https://github.com/MDAnalysis/mdanalysis/pull/2917/files#r620558575>`_
     """

package/MDAnalysis/converters/OpenMMParser.py

@@ -84,9 +84,7 @@ class OpenMMTopologyParser(TopologyReaderBase):
 
     @staticmethod
     def _format_hint(thing):
-        """Can this Parser read object *thing*?
-
-        """
+        """Can this Parser read object *thing*?"""
         try:
             from openmm import app
         except ImportError:
@@ -98,7 +96,7 @@ def _format_hint(thing):
             return isinstance(thing, app.Topology)
 
     def _mda_topology_from_omm_topology(self, omm_topology):
-        """ Construct mda topology from omm topology
+        """Construct mda topology from omm topology
 
         Can be used for any openmm object that contains a topology object
 
@@ -130,9 +128,11 @@ def _mda_topology_from_omm_topology(self, omm_topology):
             try:
                 from simtk.unit import daltons
             except ImportError:
-                msg = ("OpenMM is required for the OpenMMParser but "
-                       "it's not installed. Try installing it with \n"
-                       "conda install -c conda-forge openmm")
+                msg = (
+                    "OpenMM is required for the OpenMMParser but "
+                    "it's not installed. Try installing it with \n"
+                    "conda install -c conda-forge openmm"
+                )
                 raise ImportError(msg)
 
         atom_resindex = [a.residue.index for a in omm_topology.atoms()]
@@ -168,19 +168,21 @@ def _mda_topology_from_omm_topology(self, omm_topology):
                 if elem.symbol.capitalize() in SYMB2Z:
                     validated_elements.append(elem.symbol)
                 else:
-                    validated_elements.append('')
+                    validated_elements.append("")
                 atomtypes.append(elem.symbol)
                 masses.append(elem.mass.value_in_unit(daltons))
             else:
-                validated_elements.append('')
+                validated_elements.append("")
                 masses.append(0.0)
-                atomtypes.append('X')
+                atomtypes.append("X")
 
         if not all(validated_elements):
             if any(validated_elements):
-                warnings.warn("Element information missing for some atoms. "
-                              "These have been given an empty element record ")
-                if any(i == 'X' for i in atomtypes):
+                warnings.warn(
+                    "Element information missing for some atoms. "
+                    "These have been given an empty element record "
+                )
+                if any(i == "X" for i in atomtypes):
                     warnings.warn(
                         "For absent elements, atomtype has been  "
                         "set to 'X' and mass has been set to 0.0. "
@@ -189,10 +191,12 @@ def _mda_topology_from_omm_topology(self, omm_topology):
                         "to_guess=['masses', 'types']). "
                         "(for MDAnalysis version 2.x "
                         "this is done automatically,"
-                        " but it will be removed in 3.0).")
+                        " but it will be removed in 3.0)."
+                    )
 
-                attrs.append(Elements(np.array(validated_elements,
-                                               dtype=object)))
+                attrs.append(
+                    Elements(np.array(validated_elements, dtype=object))
+                )
 
             else:
                 wmsg = (
@@ -205,7 +209,8 @@ def _mda_topology_from_omm_topology(self, omm_topology):
                     "These can be guessed using "
                     "universe.guess_TopologyAttrs("
                     "to_guess=['masses', 'types']) "
-                    "See MDAnalysis.guessers.")
+                    "See MDAnalysis.guessers."
+                )
 
                 warnings.warn(wmsg)
         else:
@@ -239,9 +244,7 @@ class OpenMMAppTopologyParser(OpenMMTopologyParser):
 
     @staticmethod
     def _format_hint(thing):
-        """Can this Parser read object *thing*?
-
-        """
+        """Can this Parser read object *thing*?"""
         try:
             from openmm import app
         except ImportError:
@@ -252,10 +255,7 @@ def _format_hint(thing):
         else:
             return isinstance(
                 thing,
-                (
-                    app.PDBFile, app.Modeller,
-                    app.Simulation, app.PDBxFile
-                )
+                (app.PDBFile, app.Modeller, app.Simulation, app.PDBxFile),
             )
 
     def parse(self, **kwargs):