fixup! Make Arkane PEP8 compliant

arkane/input.py

@@ -70,7 +70,7 @@
 from arkane.thermo import ThermoJob
 
 
-species_dict, transition_state_dict, reaction_dict, networkDict = dict(), dict(), dict(), dict()
+species_dict, transition_state_dict, reaction_dict, network_dict = dict(), dict(), dict(), dict()
 job_list = list()
 
 
@@ -339,7 +339,7 @@ def reaction(label, reactants, products, transitionState=None, kinetics=None, tu
 
 def network(label, isomers=None, reactants=None, products=None, pathReactions=None, bathGas=None):
     """Load a network from an input file"""
-    global networkDict, species_dict, reaction_dict
+    global network_dict, species_dict, reaction_dict
     logging.info('Loading network {0}...'.format(label))
     isomers0 = isomers or []
     isomers = []
@@ -423,7 +423,7 @@ def network(label, isomers=None, reactants=None, products=None, pathReactions=No
         path_reactions=path_reactions,
         bath_gas=bath_gas,
     )
-    networkDict[label] = network
+    network_dict[label] = network
 
 
 def kinetics(label, Tmin=None, Tmax=None, Tlist=None, Tcount=0, sensitivity_conditions=None):
@@ -466,14 +466,14 @@ def pressureDependence(label, Tmin=None, Tmax=None, Tcount=0, Tlist=None, Pmin=N
                        maximumGrainSize=None, minimumGrainCount=0, method=None, interpolationModel=None,
                        activeKRotor=True, activeJRotor=True, rmgmode=False, sensitivity_conditions=None):
     """Generate a pressure dependent job"""
-    global job_list, networkDict
+    global job_list, network_dict
 
     if isinstance(interpolationModel, str):
         interpolationModel = (interpolationModel,)
 
     nwk = None
-    if label in list(networkDict.keys()):
-        nwk = networkDict[label]
+    if label in list(network_dict.keys()):
+        nwk = network_dict[label]
 
     job = PressureDependenceJob(network=nwk, Tmin=Tmin, Tmax=Tmax, Tcount=Tcount, Tlist=Tlist,
                                 Pmin=Pmin, Pmax=Pmax, Pcount=Pcount, Plist=Plist,
@@ -548,13 +548,10 @@ def load_input_file(path):
     Load the Arkane input file located at `path` on disk, and return a list of
     the jobs defined in that file.
     """
-    global species_dict, transition_state_dict, reaction_dict, networkDict, job_list
+    global species_dict, transition_state_dict, reaction_dict, network_dict, job_list
 
     # Clear module-level variables
-    species_dict = {}
-    transition_state_dict = {}
-    reaction_dict = {}
-    networkDict = {}
+    species_dict, transition_state_dict, reaction_dict, network_dict = dict(), dict(), dict(), dict()
     job_list = []
 
     global_context = {'__builtins__': None}
@@ -649,7 +646,7 @@ def load_input_file(path):
             if atom_energies is not None:
                 job.arkane_species.atom_energies = atom_energies
 
-    return job_list, reaction_dict, species_dict, transition_state_dict, networkDict
+    return job_list, reaction_dict, species_dict, transition_state_dict, network_dict
 
 
 def process_model_chemistry(model_chemistry):

arkane/kinetics.py

@@ -419,7 +419,7 @@ def clear(self):
         self.surface = None
         self.cr = None
 
-    def __get_energy_range(self):
+    def _get_energy_range(self):
         """
         Return the minimum and maximum energy in J/mol on the potential energy surface.
         """
@@ -434,7 +434,7 @@ def __get_energy_range(self):
                                              self.reaction.transition_state.conformer.E0.value_si / 1000.))
         return e0_min, e0_max
 
-    def __use_structure_for_label(self, configuration):
+    def _use_structure_for_label(self, configuration):
         """
         Return ``True`` if the configuration should use molecular structures
         for its labels or ``False`` otherwise.
@@ -452,7 +452,7 @@ def __use_structure_for_label(self, configuration):
 
         return use_structures
 
-    def __get_text_size(self, text, padding=2, file_format='pdf'):
+    def _get_text_size(self, text, padding=2, file_format='pdf'):
         try:
             import cairocffi as cairo
         except ImportError:
@@ -467,7 +467,7 @@ def __get_text_size(self, text, padding=2, file_format='pdf'):
         height = extents[3] + 2 * padding
         return [0, 0, width, height]
 
-    def __draw_text(self, text, cr, x0, y0, padding=2):
+    def _draw_text(self, text, cr, x0, y0, padding=2):
         cr.save()
         cr.set_font_size(self.options['fontSizeNormal'])
         extents = cr.text_extents(text)
@@ -479,19 +479,19 @@ def __draw_text(self, text, cr, x0, y0, padding=2):
         height = extents[3] + 2 * padding
         return [0, 0, width, height]
 
-    def __get_label_size(self, configuration, file_format='pdf'):
+    def _get_label_size(self, configuration, file_format='pdf'):
         width = 0
         height = 0
         bounding_rects = []
-        if self.__use_structure_for_label(configuration):
+        if self._use_structure_for_label(configuration):
             for spec in configuration.species_list:
                 rect = MoleculeDrawer().draw(spec.molecule[0], file_format=file_format)[2]
                 bounding_rects.append(list(rect))
         else:
             for spec in configuration.species_list:
-                bounding_rects.append(self.__get_text_size(spec.label, file_format=file_format))
+                bounding_rects.append(self._get_text_size(spec.label, file_format=file_format))
 
-        plus_rect = self.__get_text_size('+', file_format=file_format)
+        plus_rect = self._get_text_size('+', file_format=file_format)
 
         for rect in bounding_rects:
             if width < rect[2]:
@@ -501,18 +501,18 @@ def __get_label_size(self, configuration, file_format='pdf'):
 
         return [0, 0, width, height]
 
-    def __draw_label(self, configuration, cr, x0, y0, file_format='pdf'):
+    def _draw_label(self, configuration, cr, x0, y0, file_format='pdf'):
 
-        bounding_rect = self.__get_label_size(configuration, file_format=file_format)
+        bounding_rect = self._get_label_size(configuration, file_format=file_format)
         padding = 2
 
-        use_structures = self.__use_structure_for_label(configuration)
+        use_structures = self._use_structure_for_label(configuration)
         y = y0
         for i, spec in enumerate(configuration.species_list):
             if i > 0:
-                rect = self.__get_text_size('+', padding=padding, file_format=file_format)
+                rect = self._get_text_size('+', padding=padding, file_format=file_format)
                 x = x0 - 0.5 * (rect[2] - bounding_rect[2]) + 2 * padding
-                self.__draw_text('+', cr, x, y)
+                self._draw_text('+', cr, x, y)
                 y += rect[3]
 
             if use_structures:
@@ -526,9 +526,9 @@ def __draw_label(self, configuration, cr, x0, y0, file_format='pdf'):
                 cr.restore()
                 y += rect[3]
             else:
-                rect = self.__get_text_size(spec.label, padding=padding, file_format=file_format)
+                rect = self._get_text_size(spec.label, padding=padding, file_format=file_format)
                 x = x0 - 0.5 * (rect[2] - bounding_rect[2]) + 2 * padding
-                self.__draw_text(spec.label, cr, x, y)
+                self._draw_text(spec.label, cr, x, y)
                 y += rect[3]
 
         return bounding_rect
@@ -554,10 +554,10 @@ def draw(self, reaction, file_format, path=None):
         # Generate the bounding rectangles for each configuration label
         label_rects = []
         for well in self.wells:
-            label_rects.append(self.__get_label_size(well, file_format=file_format))
+            label_rects.append(self._get_label_size(well, file_format=file_format))
 
         # Get energy range (use kJ/mol internally)
-        e0_min, e0_max = self.__get_energy_range()
+        e0_min, e0_max = self._get_energy_range()
         e0_min *= 0.001
         e0_max *= 0.001
 
@@ -579,7 +579,7 @@ def draw(self, reaction, file_format, path=None):
             raise InputError('Invalid value "{0}" for Eunits parameter.'.format(e_units))
 
         # Determine height required for drawing
-        e_height = self.__get_text_size('0.0', file_format=file_format)[3] + 6
+        e_height = self._get_text_size('0.0', file_format=file_format)[3] + 6
         y_e0 = (e0_max - 0.0) * e_slope + padding + e_height
         height = (e0_max - e0_min) * e_slope + 2 * padding + e_height + 6
         for i in range(len(self.wells)):
@@ -684,7 +684,7 @@ def draw(self, reaction, file_format, path=None):
         # Fill the background with white
         cr.set_source_rgba(1.0, 1.0, 1.0, 1.0)
         cr.paint()
-        self.__draw_text('E0 ({0})'.format(e_units), cr, 15, 10, padding=2)  # write units
+        self._draw_text('E0 ({0})'.format(e_units), cr, 15, 10, padding=2)  # write units
 
         # Draw reactions
         e0_reac = self.wells[0].E0 * 0.001 - e0_offset
@@ -771,7 +771,7 @@ def draw(self, reaction, file_format, path=None):
             cr.rectangle(x, y, label_rects[i][2], label_rects[i][3])
             cr.set_source_rgba(1.0, 1.0, 1.0, 0.75)
             cr.fill()
-            self.__draw_label(well, cr, x, y, file_format=file_format)
+            self._draw_label(well, cr, x, y, file_format=file_format)
 
         # Finish Cairo drawing
         if file_format == 'png':

arkane/main.py

@@ -153,7 +153,7 @@ def load_input_file(self, input_file):
         loaded set of jobs as a list.
         """
         self.input_file = input_file
-        self.job_list, self.reaction_dict, self.species_dict, self.transition_state_dict, self.networkDict = \
+        self.job_list, self.reaction_dict, self.species_dict, self.transition_state_dict, self.network_dict = \
             load_input_file(self.input_file)
         logging.info('')
         return self.job_list

examples/arkane/explorer/methoxy/input.py

@@ -198,9 +198,9 @@
     minimumGrainCount = 500, 
     method = 'modified strong collision',
     #Other methods include: 'reservoir state', 'chemically-significant eigenvalues', 
-    interpolationModel = ('pdeparrhenius'), 
+    interpolationModel = 'pdeparrhenius',
     activeKRotor = True,
-#    active_j_rotor = False,  # causes Arkane to crash
+#    active_J_rotor = False,  # causes Arkane to crash
     rmgmode = False, 
 )
 
@@ -209,6 +209,6 @@
     explore_tol=0.01,
     energy_tol=8e1,
     flux_tol=1e-6,
-     bathGas={'He':1.0},
-     maximumRadicalElectrons=2,
+    bathGas={'He':1.0},
+    maximumRadicalElectrons=2,
 )