Make Arkane PEP8 compliant

Arkane.py

@@ -54,7 +54,7 @@
 arkane = Arkane()
 
 # Parse and validate the command-line arguments
-arkane.parseCommandLineArguments()
+arkane.parse_command_line_arguments()
 
 # Execute the job
 arkane.execute()

arkane/common.py

@@ -42,7 +42,7 @@
 
 import rmgpy.constants as constants
 from rmgpy import __version__
-from rmgpy.molecule.element import element_list, get_element
+from rmgpy.molecule.element import get_element
 from rmgpy.molecule.translator import to_inchi, to_inchi_key
 from rmgpy.pdep.collision import SingleExponentialDown
 from rmgpy.quantity import ScalarQuantity, ArrayQuantity
@@ -58,8 +58,6 @@
 
 from arkane.pdep import PressureDependenceJob
 
-################################################################################
-
 
 # Add a custom string representer to use block literals for multiline strings
 def str_repr(dumper, data):
@@ -229,7 +227,7 @@ def save_yaml(self, path):
     def load_yaml(self, path, label=None, pdep=False):
         """
         Load the all statMech data from the .yml file in `path` into `species`
-        `pdep` is a boolean specifying whether or not jobList includes a pressureDependentJob.
+        `pdep` is a boolean specifying whether or not job_list includes a pressureDependentJob.
         """
         yml_file = os.path.basename(path)
         if label:
@@ -312,26 +310,26 @@ def load_yaml(self, path, label=None, pdep=False):
 ################################################################################
 
 
-def is_pdep(jobList):
+def is_pdep(job_list):
     """A helper function to determine whether a job is PressureDependenceJob or not"""
-    for job in jobList:
+    for job in job_list:
         if isinstance(job, PressureDependenceJob):
             return True
     return False
 
 
-def check_conformer_energy(Vlist, path):
+def check_conformer_energy(energies, path):
     """
     Check to see that the starting energy of the species in the potential energy scan calculation
     is not 0.5 kcal/mol (or more) higher than any other energies in the scan. If so, print and 
     log a warning message.  
     """
-    v_list = np.array(Vlist, np.float64)
-    v_diff = (v_list[0] - np.min(v_list)) * constants.E_h * constants.Na / 1000
-    if v_diff >= 2:  # we choose 2 kJ/mol to be the critical energy
+    energies = np.array(energies, np.float64)
+    e_diff = (energies[0] - np.min(energies)) * constants.E_h * constants.Na / 1000
+    if e_diff >= 2:  # we choose 2 kJ/mol to be the critical energy
         logging.warning('the species corresponding to {path} is different in energy from the lowest energy conformer '
                         'by {diff} kJ/mol. This can cause significant errors in your computed rate constants.'
-                        .format(path=os.path.basename(path), diff=v_diff))
+                        .format(path=os.path.basename(path), diff=e_diff))
 
 
 def get_element_mass(input_element, isotope=None):

arkane/commonTest.py

@@ -48,7 +48,7 @@
 
 from arkane import Arkane, input
 from arkane.common import ArkaneSpecies, get_element_mass
-from arkane.input import jobList
+from arkane.input import job_list
 from arkane.statmech import InputError, StatMechJob
 
 ################################################################################
@@ -81,11 +81,11 @@ class TestArkaneJob(unittest.TestCase):
     def setUp(cls):
         """A method that is run before each unit test in this class"""
         arkane = Arkane()
-        job_list = arkane.loadInputFile(os.path.join(os.path.dirname(os.path.abspath(__file__)),
-                                                     'data', 'methoxy.py'))
+        job_list = arkane.load_input_file(os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                                                       'data', 'methoxy.py'))
         pdepjob = job_list[-1]
         cls.kineticsjob = job_list[0]
-        pdepjob.activeJRotor = True
+        pdepjob.active_j_rotor = True
         network = pdepjob.network
         cls.Nisom = len(network.isomers)
         cls.Nreac = len(network.reactants)
@@ -99,9 +99,9 @@ def setUp(cls):
         cls.PminValue = pdepjob.Pmin.value
         cls.Pcount = pdepjob.Pcount
         cls.Tcount = pdepjob.Tcount
-        cls.GenTlist = pdepjob.generateTemperatureList()
+        cls.GenTlist = pdepjob.generate_T_list()
         cls.PlistValue = pdepjob.Plist.value
-        cls.maximumGrainSizeValue = pdepjob.maximumGrainSize.value
+        cls.maximum_grain_size_value = pdepjob.maximum_grain_size.value
         cls.method = pdepjob.method
         cls.rmgmode = pdepjob.rmgmode
 
@@ -189,7 +189,7 @@ def test_maximum_grain_size_value(self):
         """
         Test the max grain size value.
         """
-        self.assertEqual(self.maximumGrainSizeValue, 0.5)
+        self.assertEqual(self.maximum_grain_size_value, 0.5)
 
     def test_method(self):
         """
@@ -242,7 +242,7 @@ def test_species(self):
 
     def test_species_statmech(self):
         """Test loading of statmech job from species input file."""
-        job = jobList[-1]
+        job = job_list[-1]
         self.assertTrue(isinstance(job, StatMechJob))
         job.modelChemistry = self.modelChemistry
         job.frequencyScaleFactor = self.frequencyScaleFactor
@@ -256,7 +256,7 @@ def test_species_statmech(self):
     def test_species_thermo(self):
         """Test thermo job execution for species from separate input file."""
         input.thermo('C2H4', 'NASA')
-        job = jobList[-1]
+        job = job_list[-1]
         filepath = os.path.join(self.directory, 'reactions', 'H+C2H4=C2H5')
         job.execute(output_directory=filepath)
         self.assertTrue(os.path.isfile(os.path.join(filepath, 'output.py')))
@@ -271,7 +271,7 @@ def test_transition_state(self):
 
     def test_transition_state_statmech(self):
         """Test loading of statmech job from transition state input file."""
-        job = jobList[-1]
+        job = job_list[-1]
         self.assertTrue(isinstance(job, StatMechJob))
         job.modelChemistry = self.modelChemistry
         job.frequencyScaleFactor = self.frequencyScaleFactor
@@ -289,8 +289,8 @@ class TestStatmech(unittest.TestCase):
     def setUp(cls):
         """A method that is run before each unit test in this class"""
         arkane = Arkane()
-        cls.job_list = arkane.loadInputFile(os.path.join(os.path.dirname(os.path.abspath(__file__)),
-                                                         'data', 'Benzyl', 'input.py'))
+        cls.job_list = arkane.load_input_file(os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                                                           'data', 'Benzyl', 'input.py'))
 
     def test_gaussian_log_file_error(self):
         """Test that the proper error is raised if gaussian geometry and frequency file paths are the same"""
@@ -330,7 +330,7 @@ def test_dump_yaml(self):
         """
         Test properly dumping the ArkaneSpecies object and respective sub-objects
         """
-        job_list = self.arkane.loadInputFile(self.dump_input_path)
+        job_list = self.arkane.load_input_file(self.dump_input_path)
         for job in job_list:
             job.execute(output_directory=self.dump_path)
         self.assertTrue(os.path.isfile(self.dump_output_file))
@@ -340,7 +340,7 @@ def test_create_and_load_yaml(self):
         Test properly loading the ArkaneSpecies object and respective sub-objects
         """
         # Create YAML file by running Arkane
-        job_list = self.arkane.loadInputFile(self.dump_input_path)
+        job_list = self.arkane.load_input_file(self.dump_input_path)
         for job in job_list:
             job.execute(output_directory=self.dump_path)
 

arkane/data/methoxy.py

@@ -224,7 +224,7 @@
     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
     rmgmode=False,

arkane/data/methoxy_explore.py

@@ -231,7 +231,7 @@
     maximumGrainSize=(0.5, 'kcal/mol'),
     minimumGrainCount=500,
     method='modified strong collision',
-    interpolationModel=('pdeparrhenius'),
+    interpolationModel='pdeparrhenius',
     activeKRotor=True,
     rmgmode=False,
 )

arkane/encorr/corr.py

@@ -42,8 +42,6 @@
 import arkane.encorr.pbac as pbac
 from arkane.exceptions import AtomEnergyCorrectionError, BondAdditivityCorrectionError
 
-################################################################################
-
 
 def get_energy_correction(model_chemistry, atoms, bonds, coords, nums, multiplicity=1,
                           atom_energies=None, apply_atom_corrections=True,

arkane/encorr/mbac.py

@@ -85,7 +85,7 @@ def get_bac(model_chemistry, coords, nums, multiplicity=1, mol_corr=0.0):
 
     # Bond correction
     bac_bond = 0.0
-    for bond in mol.getAllEdges():
+    for bond in mol.get_all_edges():
         atom1 = bond.atom1
         atom2 = bond.atom2
         symbol1 = atom1.element.symbol