Autoformat. [ci skip]

Author: lohedges

src/BioSimSpace/Align/_align.py

@@ -1447,14 +1447,14 @@ def _roiMatch(
                 after_roi_atom_idx_molecule1 = []
             else:
                 after_roi_molecule0 = molecule0.search(
-                    f"residue[{res_idx+1}:{roi[i+1]}]"
+                    f"residue[{res_idx + 1}:{roi[i + 1]}]"
                 )
                 after_roi_atom_idx_molecule0 = [
                     a.index() for a in after_roi_molecule0.atoms()
                 ]
 
                 after_roi_molecule1 = molecule1.search(
-                    f"residue[{res_idx+1}:{roi[i+1]}]"
+                    f"residue[{res_idx + 1}:{roi[i + 1]}]"
                 )
                 after_roi_atom_idx_molecule1 = [
                     b.index() for b in after_roi_molecule1.atoms()
@@ -1476,12 +1476,12 @@ def _roiMatch(
             }
         else:
             # Get all of the remaining atoms after the last ROI
-            after_roi_molecule0 = molecule0.search(f"residue[{res_idx+1}:]")
+            after_roi_molecule0 = molecule0.search(f"residue[{res_idx + 1}:]")
             after_roi_atom_idx_molecule0 = [
                 a.index() for a in after_roi_molecule0.atoms()
             ]
 
-            after_roi_molecule1 = molecule1.search(f"residue[{res_idx+1}:]")
+            after_roi_molecule1 = molecule1.search(f"residue[{res_idx + 1}:]")
             after_roi_atom_idx_molecule1 = [
                 b.index() for b in after_roi_molecule1.atoms()
             ]

src/BioSimSpace/Gateway/_node.py

@@ -119,7 +119,7 @@ def __call__(self, parser, namespace, values, option_string=None):
             output_type = type(value)
             if output_type not in [_File, _FileSet]:
                 raise TypeError(
-                    "We currently only support File and " "FileSet outputs with CWL."
+                    "We currently only support File and FileSet outputs with CWL."
                 )
 
         # Store the absolute path of the Python interpreter used to run the node.

src/BioSimSpace/Metadynamics/CollectiveVariable/_distance.py

@@ -652,7 +652,7 @@ def _validate(self):
         if self._weights0 is not None:
             if not isinstance(self._atom0, list):
                 raise ValueError(
-                    "'weights0' only valid when 'atom0' is a " "list of atom indices."
+                    "'weights0' only valid when 'atom0' is a list of atom indices."
                 )
             elif len(self._weights0) != len(self._atom0):
                 raise ValueError(
@@ -664,7 +664,7 @@ def _validate(self):
         if self._weights1 is not None:
             if not isinstance(self._atom1, list):
                 raise ValueError(
-                    "'weights1' only valid when 'atom1' is a " "list of atom indices."
+                    "'weights1' only valid when 'atom1' is a list of atom indices."
                 )
             elif len(self._weights1) != len(self._atom1):
                 raise ValueError(

src/BioSimSpace/Process/_amber.py

@@ -265,8 +265,7 @@ def _setup(self, **kwargs):
             # Check that the system contains a perturbable molecule.
             if self._system.nPerturbableMolecules() == 0:
                 raise ValueError(
-                    "'BioSimSpace.Protocol.FreeEnergy' requires a "
-                    "perturbable molecule!"
+                    "'BioSimSpace.Protocol.FreeEnergy' requires a perturbable molecule!"
                 )
 
             # Make sure the protocol is valid.

src/BioSimSpace/Process/_atm_utils.py

@@ -610,7 +610,7 @@ def createLoopWithReporting(
         output = ""
         output += "# Reporting for MBAR:\n"
         # round master lambda to 4 d.p. to avoid floating point errors
-        output += f"master_lambda_list = {[round(i,4) for i in self.protocol._get_lambda_values()]}\n"
+        output += f"master_lambda_list = {[round(i, 4) for i in self.protocol._get_lambda_values()]}\n"
         output += "master_lambda = master_lambda_list[window_index]\n"
 
         output += "if is_restart:\n"
@@ -810,7 +810,7 @@ def createReportingBoth(
 
         output += "# Reporting for MBAR:\n"
         # round master lambda to 4 d.p. to avoid floating point errors
-        output += f"master_lambda_list = {[round(i,4) for i in self.protocol._get_lambda_values()]}\n"
+        output += f"master_lambda_list = {[round(i, 4) for i in self.protocol._get_lambda_values()]}\n"
         output += "master_lambda = master_lambda_list[window_index]\n"
         output += "if is_restart:\n"
         output += "    try:\n"
@@ -945,7 +945,7 @@ def createSinglePointTest(
         """Create a single point test for the ATM force"""
         output = ""
         output += "# Create the dictionary which will hold the energies\n"
-        output += f"master_lambda_list = {[round(i,4) for i in self.protocol._get_lambda_values()]}\n"
+        output += f"master_lambda_list = {[round(i, 4) for i in self.protocol._get_lambda_values()]}\n"
         output += "energies = {}\n"
         output += f"for i in master_lambda_list[:{inflex_point}]:\n"
         output += "    energies[i] = []\n"

src/BioSimSpace/Process/_gromacs.py

@@ -232,8 +232,7 @@ def _setup(self, **kwargs):
             # Check that the system contains a perturbable molecule.
             if self._system.nPerturbableMolecules() == 0:
                 raise ValueError(
-                    "'BioSimSpace.Protocol.FreeEnergy' requires a "
-                    "perturbable molecule!"
+                    "'BioSimSpace.Protocol.FreeEnergy' requires a perturbable molecule!"
                 )
 
             # Check that the perturbation type is supported..
@@ -2201,7 +2200,7 @@ def _add_position_restraints(self):
                                 # Write restraints for each atom.
                                 for atom_idx in restrained_atoms:
                                     file.write(
-                                        f"{atom_idx+1:4}    1       {force_constant}       {force_constant}       {force_constant}       {force_constant}       {force_constant}       {force_constant}\n"
+                                        f"{atom_idx + 1:4}    1       {force_constant}       {force_constant}       {force_constant}       {force_constant}       {force_constant}       {force_constant}\n"
                                     )
 
                             else:
@@ -2214,7 +2213,7 @@ def _add_position_restraints(self):
                                 # Write restraints for each atom.
                                 for atom_idx in restrained_atoms:
                                     file.write(
-                                        f"{atom_idx+1:4}    1       {force_constant}       {force_constant}       {force_constant}\n"
+                                        f"{atom_idx + 1:4}    1       {force_constant}       {force_constant}       {force_constant}\n"
                                     )
 
                         # Work out the offset.
@@ -2300,7 +2299,7 @@ def _add_position_restraints(self):
                             # Write restraints for each atom.
                             for atom_idx in atom_idxs:
                                 file.write(
-                                    f"{atom_idx+1:4}    1       {force_constant}       {force_constant}       {force_constant}\n"
+                                    f"{atom_idx + 1:4}    1       {force_constant}       {force_constant}       {force_constant}\n"
                                 )
 
                         # Work out the offset.
@@ -2671,8 +2670,7 @@ def _getFinalFrame(self):
             # Locate the coordinate file.
             if not _os.path.isfile(self._crd_file):
                 _warnings.warn(
-                    "Invalid coordinate file! "
-                    "%s gro file not found." % (self._crd_file)
+                    "Invalid coordinate file! %s gro file not found." % (self._crd_file)
                 )
                 return None
 

src/BioSimSpace/Process/_openmm.py

@@ -894,7 +894,7 @@ def _generate_config(self):
                 lower_wall = colvar.getLowerBound().getValue().nanometers().value()
                 upper_wall = colvar.getUpperBound().getValue().nanometers().value()
             self.addToConfig(
-                f"proj = BiasVariable(projection, {lower_wall-0.2}, {upper_wall+0.2}, {sigma_proj}, False, gridWidth=200)"
+                f"proj = BiasVariable(projection, {lower_wall - 0.2}, {upper_wall + 0.2}, {sigma_proj}, False, gridWidth=200)"
             )
 
             sigma_ext = colvar.getHillWidth()[1].nanometers().value()

src/BioSimSpace/Process/_plumed.py

@@ -1513,8 +1513,7 @@ def getFreeEnergy(self, index=None, stride=None, kt=_Types.Energy(1.0, "kt")):
 
             if proc.returncode != 0:
                 raise RuntimeError(
-                    "Failed to generate free energy estimate.\n"
-                    "Error: %s" % proc.stderr
+                    "Failed to generate free energy estimate.\nError: %s" % proc.stderr
                 )
 
             # Get a sorted list of all the fes*.dat files.

src/BioSimSpace/Process/_process_runner.py

@@ -269,7 +269,7 @@ def removeProcess(self, index):
 
         if index < -num_processes or index > num_processes - 1:
             raise IndexError(
-                f"'index' is out of range: [-{num_processes}:{num_processes-1}]"
+                f"'index' is out of range: [-{num_processes}:{num_processes - 1}]"
             )
 
         # Map negative indices back into positive range.
@@ -503,7 +503,7 @@ def start(self, index):
 
         if index < -num_processes or index > num_processes - 1:
             raise IndexError(
-                f"'index' is out of range: [-{num_processes}:{num_processes-1}]"
+                f"'index' is out of range: [-{num_processes}:{num_processes - 1}]"
             )
 
         # Map negative indices back into positive range.
@@ -766,7 +766,7 @@ def kill(self, index):
 
         if index < -num_processes or index > num_processes - 1:
             raise IndexError(
-                f"'index' is out of range: [-{num_processes}:{num_processes-1}]"
+                f"'index' is out of range: [-{num_processes}:{num_processes - 1}]"
             )
 
         # Map negative indices back into positive range.

src/BioSimSpace/Process/_somd.py

@@ -1711,7 +1711,7 @@ def sort_bonds(bonds, idx):
                 # Cannot have a bond with a dummy in both states.
                 if initial_dummy and final_dummy:
                     raise _IncompatibleError(
-                        "Dummy atoms are present in both the initial " "and final bond?"
+                        "Dummy atoms are present in both the initial and final bond?"
                     )
 
                 # Set the bond parameters of the dummy state to those of the non-dummy end state.