Merge pull request #1168 from ReactionMechanismGenerator/GetRidofUnusedCode

Remove unused code

Author: goldmanm

rmgpy/cantherm/gaussian.py

@@ -260,9 +260,7 @@ def loadEnergy(self,frequencyScaleFactor=1.):
         CBS-QB3 value.
         """
 
-        modes = []
         E0 = None; E0_cbs = None; scaledZPE = None
-        spinMultiplicity = 1
 
         f = open(self.path, 'r')
         line = f.readline()
@@ -307,9 +305,7 @@ def loadZeroPointEnergy(self):
         Load the unscaled zero-point energy in J/mol from a Gaussian log file.
         """
 
-        modes = []
         ZPE = None
-        spinMultiplicity = 1
 
         f = open(self.path, 'r')
         line = f.readline()

rmgpy/cantherm/gaussianTest.py

@@ -33,7 +33,7 @@
 import os
 
 from rmgpy.cantherm.gaussian import GaussianLog
-from rmgpy.statmech import Conformer, IdealGasTranslation, LinearRotor, NonlinearRotor, HarmonicOscillator, HinderedRotor
+from rmgpy.statmech import IdealGasTranslation, LinearRotor, NonlinearRotor, HarmonicOscillator, HinderedRotor
 import rmgpy.constants as constants
 from external.wip import work_in_progress
 ################################################################################

rmgpy/cantherm/qchem.py

@@ -114,11 +114,8 @@ def loadGeometry(self):
         last is returned.
         """
         atom = []; coord = []; number = []; 
-        try:
-            f = open(self.path, 'r')
-        except IndexError:
-            print('File not found')
-        f = open(self.path, 'r')  
+
+        f = open(self.path, 'r')
         line = f.readline()
         while line != '':
             if 'Final energy is' in line:
@@ -202,8 +199,7 @@ def loadConformer(self, symmetry=None, spinMultiplicity=None, opticalIsomers=1):
             # The rest of the data we want is in the Thermochemistry section of the output
             elif 'VIBRATIONAL ANALYSIS' in line:
                 modes = []
-                
-                inPartitionFunctions = False
+
                 line = f.readline()
                 while line != '':
 
@@ -254,7 +250,6 @@ def loadConformer(self, symmetry=None, spinMultiplicity=None, opticalIsomers=1):
                         else:
                             for i in range(3):
                                 inertia[i] *= (constants.a0/1e-10)**2
-                                pass
                                 rotation = NonlinearRotor(inertia=(inertia,"amu*angstrom^2"), symmetry=symmetry)
                                 #modes.append(rotation)
                             rot.append(rotation) 
@@ -281,9 +276,7 @@ def loadEnergy(self,frequencyScaleFactor=1.):
         in the file is returned. The zero-point energy is *not* included in 
         the returned value.
         """
-        modes = []
-        E0 = None 
-        spinMultiplicity = 1
+        E0 = None
 
         f = open(self.path, 'r')
         line = f.readline()
@@ -314,9 +307,7 @@ def loadZeroPointEnergy(self,frequencyScaleFactor=1.):
         Load the unscaled zero-point energy in J/mol from a Qchem output file.
         """
 
-        modes = []
         ZPE = None
-        spinMultiplicity = 1
 
         f = open(self.path, 'r')
         line = f.readline()

rmgpy/constraints.py

@@ -43,7 +43,7 @@ def failsSpeciesConstraints(species):
 
     try:
         speciesConstraints = getInput('speciesConstraints')
-    except Exception, e:
+    except Exception:
         logging.debug('Species constraints could not be found.')
         speciesConstraints = {}
 

rmgpy/data/base.py

@@ -222,7 +222,7 @@ def load(self, path, local_context=None, global_context=None):
         f = open(path, 'r')
         try:
             exec f in global_context, local_context
-        except Exception, e:
+        except Exception:
             logging.error('Error while reading database {0!r}.'.format(path))
             raise
         f.close()

rmgpy/data/kinetics/family.py

@@ -36,14 +36,12 @@
 import logging
 import codecs
 from copy import deepcopy
-import itertools
-import numpy as np
 
 from rmgpy.constraints import failsSpeciesConstraints
 from rmgpy.data.base import Database, Entry, LogicNode, LogicOr, ForbiddenStructures,\
                             getAllCombinations
 from rmgpy.reaction import Reaction
-from rmgpy.kinetics import Arrhenius, ArrheniusEP
+from rmgpy.kinetics import Arrhenius
 from rmgpy.molecule import Bond, GroupBond, Group, Molecule
 from rmgpy.species import Species
 

rmgpy/data/kinetics/library.py

@@ -45,8 +45,7 @@
 
 from rmgpy.reaction import Reaction
 from rmgpy.kinetics import Arrhenius, ThirdBody, Lindemann, Troe, \
-                           PDepArrhenius, MultiArrhenius, MultiPDepArrhenius, \
-                           PDepKineticsModel
+                           PDepArrhenius, MultiArrhenius, MultiPDepArrhenius
 from rmgpy.molecule import Molecule
 from rmgpy.species import Species
 from .common import saveEntry
@@ -302,7 +301,7 @@ def load(self, path, local_context=None, global_context=None):
         f = open(path, 'r')
         try:
             exec f in global_context, local_context
-        except Exception, e:
+        except Exception:
             logging.error('Error while reading database {0!r}.'.format(path))
             raise
         f.close()

rmgpy/data/thermo.py

@@ -45,12 +45,10 @@
 
 import rmgpy.constants as constants
 from rmgpy.thermo import NASAPolynomial, NASA, ThermoData, Wilhoit
-from rmgpy.molecule import Molecule, Atom, Bond, Group
+from rmgpy.molecule import Molecule, Bond, Group
 import rmgpy.molecule
 from rmgpy.species import Species
 
-from rmgpy.scoop_framework.util import get
-
 #: This dictionary is used to add multiplicity to species label
 _multiplicity_labels = {1:'S',2:'D',3:'T',4:'Q',5:'V',}
 
@@ -250,8 +248,7 @@ def averageThermoData(thermoDataList=None):
     """
     if thermoDataList is None:
         thermoDataList = []
-        
-    import copy
+
     numValues = len(thermoDataList)
 
     if numValues == 0:
@@ -260,10 +257,10 @@ def averageThermoData(thermoDataList=None):
         logging.debug('Averaging thermo data over {0} value(s).'.format(numValues))
 
         if numValues == 1:
-            return copy.deepcopy(thermoDataList[0])
+            return deepcopy(thermoDataList[0])
 
         else:
-            averagedThermoData = copy.deepcopy(thermoDataList[0])
+            averagedThermoData = deepcopy(thermoDataList[0])
             for thermoData in thermoDataList[1:]:
                 averagedThermoData = addThermoData(averagedThermoData, thermoData)
 
@@ -337,7 +334,6 @@ def convertRingToSubMolecule(ring):
     This function takes a ring structure (can either be monoring or polyring) to create a new 
     submolecule with newly deep copied atoms
     """
-    from rmgpy.molecule.molecule import Molecule, Bond
 
     atomsMapping = {}
     for atom in ring:
@@ -359,8 +355,6 @@ def combineTwoRingsIntoSubMolecule(ring1, ring2):
     submolecule with newly deep copied atoms
     """
 
-    from rmgpy.molecule.molecule import Molecule, Bond
-
     assert len(commonAtoms(ring1, ring2))>0, "The two input rings don't have common atoms."
 
     atomsMapping = {}
@@ -680,7 +674,7 @@ def removeGroup(self, groupToRemove):
         parentR = groupToRemove.parent
 
         #look for other pointers that point toward entry
-        for entryName, entry in self.entries.iteritems():
+        for entry in self.entries.itervalues():
             if isinstance(entry.data, basestring):
                 if entry.data == groupToRemove.label:
                     #if the entryToRemove.data is also a pointer, then copy
@@ -1051,7 +1045,7 @@ def getThermoData(self, species, trainingSet=None):
 
         try:
             quantumMechanics = getInput('quantumMechanics')
-        except Exception, e:
+        except Exception:
             logging.debug('Quantum Mechanics DB could not be found.')
             quantumMechanics = None
 
@@ -1239,12 +1233,12 @@ def getThermoDataFromDepository(self, species):
         Returns: a list of tuples (thermoData, depository, entry) without any Cp0 or CpInf data.
         """
         items = []
-        for label, entry in self.depository['stable'].entries.iteritems():
+        for entry in self.depository['stable'].entries.itervalues():
             for molecule in species.molecule:
                 if molecule.isIsomorphic(entry.item):
                     items.append((deepcopy(entry.data), self.depository['stable'], entry))
                     break
-        for label, entry in self.depository['radical'].entries.iteritems():
+        for entry in self.depository['radical'].entries.itervalues():
             for molecule in species.molecule:
                 if molecule.isIsomorphic(entry.item):
                     items.append((deepcopy(entry.data), self.depository['radical'], entry))
@@ -1263,7 +1257,7 @@ def getThermoDataFromLibrary(self, species, library):
         Returns a tuple: (ThermoData, library, entry)  or None.
         """
         match = None
-        for label, entry in library.entries.iteritems():
+        for entry in library.entries.itervalues():
             for molecule in species.molecule:
                 if molecule.isIsomorphic(entry.item) and entry.data is not None:
                     thermoData = deepcopy(entry.data)
@@ -1685,8 +1679,7 @@ def __addRingCorrectionThermoDataFromTree(self, thermoData, ring_database, molec
         if thermoData is None:
             return data, node, isPartialMatch
         else:
-            return addThermoData(thermoData, data, groupAdditivity=True, verbose = True), node, isPartialMatch
-            return addThermoData(thermoData, data, groupAdditivity=True, verbose=True), node
+            return addThermoData(thermoData, data, groupAdditivity=True, verbose=True), node, isPartialMatch
             # By setting verbose=True, we turn on the comments of ring correction to pass the unittest.
             # Typically this comment is very short and also very helpful to check if the ring correction is calculated correctly.
 

rmgpy/kinetics/modelTest.py

@@ -36,7 +36,6 @@
 
 from rmgpy.kinetics.model import getReactionOrderFromRateCoefficientUnits, \
                                  getRateCoefficientUnitsFromReactionOrder
-import rmgpy.constants as constants
 
 ################################################################################
 

rmgpy/molecule/group.py

@@ -209,7 +209,6 @@ def __loseRadical(self, radical):
         or 3 radical electrons.
         """
         radicalElectrons = []
-        pairs = set()
         if any([len(atomType.decrementRadical) == 0 for atomType in self.atomType]):
             raise ActionError('Unable to update GroupAtom due to LOSE_RADICAL action: Unknown atom type produced from set "{0}".'.format(self.atomType))
 
@@ -1282,7 +1281,7 @@ def standardizeAtomType(self):
 
         #list of :class:AtomType which are elements with more sub-divided atomtypes beneath them
         specifics= [elementLabel for elementLabel in allElements if elementLabel not in nonSpecifics]
-        for index, atom in enumerate(self.atoms):
+        for atom in self.atoms:
             claimedAtomType = atom.atomType[0]
             newAtomType = None
             element = None
@@ -1366,7 +1365,7 @@ def addExplicitLigands(self):
             #Do not perform is this atom has wildCards
             if atom.hasWildCards: continue
             elif claimedAtomType is atomTypes['CO'] or claimedAtomType is atomTypes['CS']:
-                for atom2, bond12 in atom.bonds.iteritems():
+                for bond12 in atom.bonds.itervalues():
                     if bond12.isDouble():
                         break
                 else: atomsToAddTo.append(index)
@@ -1392,9 +1391,7 @@ def standardizeGroup(self):
         Returns a 'True' if the group was modified otherwise returns 'False'
         """
 
-        modified = False
-
-        #If viable then we apply current conventions:
+        # If viable then we apply current conventions:
         checkList=[]
         checkList.append(self.standardizeAtomType())
         checkList.append(self.addExplicitLigands())