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ReactionMechanismGenerator / RMG-Py

Python version of the amazing Reaction Mechanism Generator (RMG).
http://reactionmechanismgenerator.github.io/RMG-Py/
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Conda build problems #472

Closed rwest closed 8 years ago

rwest commented 8 years ago

I just rebuilt PyDQED and PyDAS binaries with the latest conda on MacOS, and now can't build RMG-Py with it, getting ValueError: numpy.dtype has the wrong size, try recompiling.

It looks like PyDAS used numpy: 1.10.1-py27_0 but RMG-Py is using numpy: 1.9.3-py27_0. Not sure how these dependencies are resolved. Maybe temporarily we could force both to use numpy 1.9.3, or there might be something more intelligent to do.

Can someone look into this? Would be good to get working binaries out today, and I have a grant proposal due so shouldn't spend more time on it...

rwest commented 8 years ago

Think the issue is RDKit has these dependencies: boost ==1.56.0 numpy 1.9 python 2.7

so we must build PyDQED and PyDAS using numpy 1.9* too

rwest commented 8 years ago

That is now resolved. The new conda recipes for PyDQED and PyDAS require compatible numpy and python versions, and the OS X binaries on anaconda.org/rmg are updated accordingly.

It can build ok, but now dies in testing:

TEST START: rmg-1.0.1-py27_0
Fetching package metadata: ..............
Solving package specifications: .....................................
The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    rmg-1.0.1                  |           py27_0        92.6 MB

The following NEW packages will be INSTALLED:

    boost:           1.56.0-py27_1       
    bzip2:           1.0.6-0             
    cairo:           1.12.18-3           
    cairocffi:       0.6-py27_1          
    cffi:            1.2.1-py27_0        
    coverage:        4.0-py27_0          
    cython:          0.21-py27_1         
    eigen:           3.2.1-0             
    expat:           2.1.0-0             
    fontconfig:      2.11.1-py27_3       
    freetype:        2.5.2-2             
    gprof2dot:       2015.02.03-py27_0   
    graphviz:        2.38.0-3            
    guppy:           0.1.10-py27_0       
    jinja2:          2.8-py27_0          
    jpeg:            8d-2                
    libgcc:          4.8.5-1             
    libpng:          1.6.17-0            
    libtiff:         4.0.3-0             
    libxml2:         2.9.2-1             
    markupsafe:      0.23-py27_0         
    matplotlib:      1.4.3-np19py27_3    
    mopac:           2012-2              
    ncurses:         5.9-1               
    nose:            1.3.7-py27_0        
    numpy:           1.9.3-py27_0        
    openbabel:       2.3.2-py27_4        
    openssl:         1.0.1k-1            
    pip:             7.1.2-py27_0        
    pixman:          0.32.6-0            
    pkg-config:      0.28-1              
    psutil:          3.2.2-py27_0        
    pycparser:       2.14-py27_0         
    pydas:           1.0.1-np19py27_6    
    pydot:           2.0.1-py27_1        
    pydqed:          1.0.0-np19py27_3    
    pyparsing:       2.0.3-py27_0        
    pyqt:            4.11.4-py27_0       
    python:          2.7.10-1            
    python-dateutil: 2.4.2-py27_0        
    pytz:            2015.6-py27_0       
    qt:              4.8.7-1             
    quantities:      0.10.1-np19py27_0   
    rdkit:           2015.03.1-np19py27_0
    readline:        6.2.5-1             
    rmg:             1.0.1-py27_0        
    scipy:           0.16.0-np19py27_1   
    setuptools:      18.4-py27_0         
    sip:             4.16.9-py27_0       
    six:             1.10.0-py27_0       
    sqlite:          3.8.4.1-1           
    symmetry:        1.0.1-0             
    tk:              8.5.18-0            
    wheel:           0.26.0-py27_1       
    xlwt:            1.0.0-py27_0        
    zlib:            1.2.8-1             
===== testing package: rmg-1.0.1-py27_0 =====
import: u'rmgpy'
===== rmg-1.0.1-py27_0 OK =====
+ make -C /Users/rwest/anaconda/conda-bld/work test
mkdir -p testing/coverage
rm -rf testing/coverage/*
nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
test the checkConformerEnergy function with an list of energies. ... ok
Test the calculation of the high-pressure limit rate coef for one of the kinetics jobs at Tmin and Tmax. ... ok
Test the generated temperature list. ... ok
Test the master equation solution method chosen. ... ok
Test the number of isomers identified. ... ok
Test the whether or not RMG mode is turned on. ... ok
Test the number of products identified. ... ok
Test the number of reactants identified. ... ok
Test a path reaction label ... ok
Test the number pressures specified. ... ok
Test the minimum pressure value. ... ok
Test the pressure list. ... ok
Test the whether or not RMG mode is turned on. ... ok
Test the number temperatures specified. ... ok
Test the temperature list. ... ok
Test the Temperature Units. ... ok
Test the temperature value. ... ok
Test the whether or not tunneling has been included in a specific kinetics job. ... ok
Test the max grain size value. ... ok
Uses a Gaussian03 log file for ethylene (C2H4) to test that its ... SKIP: WIP test failed: -78.46694399999998 != -78.467452 within 4 places
Uses a Gaussian03 log file for ethylene (C2H4) to test that its ... SKIP: WIP test failed: -78.55632 != -78.562189 within 4 places
Uses a Gaussian03 log file for oxygen (O2) to test that its ... ok
Uses an optimum geometry for s-butanol (CCC(O)C) to test that the ... ok
Uses an optimum geometry for ethane (CC) to test that the ... ok
Test that a Geometry object can be successfully reconstructed ... ok
Test that a Geometry object can be successfully pickled and unpickled ... ok
Uses a Molepro log file for ethylene_dz (C2H4) to test that F12a ... ok
Uses a Molepro log file for ethylene_qz (C2H4) to test that F12b ... ok
Uses a Molepro log file for OH (C2H4) to test that radical ... ok
Uses a Qchem log files to test that ... ok
Uses a Qchem log file for CO to test that its ... ok
Uses a Qchem log file for npropyl to test that its ... ok
Uses a Qchem log files to test that ... ok
Uses a Qchem log files to test that ... ok
Uses a Qchem log file for npropyl to test that its ... ok
Test the value of the atomic mass unit. ... ok
Test the value of the Avogadro constant. ... ok
Test the value of the Bohr radius. ... ok
Test the value of the Boltzmann constant. ... ok
Test the value of the electron rest mass. ... ok
Test the value of the elementary charge constant. ... ok
Test the value of the gas law constant. ... ok
Test the value of the Hartree energy. ... ok
Test the value of the neutron rest mass. ... ok
Test the value of pi. ... ok
Test the value of the Planck constant. ... ok
Test the value of the proton rest mass. ... ok
Test the value of the reduced Planck constant. ... ok
Test the value of the speed of light in a vacuum. ... ok
Test that nodes can match other nodes. ... ok
Test that the MatchNodeToStructure family works properly. ... ok
Test that the loadFamilies function raises the correct exceptions ... ok
Test we can estimate solvation thermochemistry. ... ok
Test that for a given solvent viscosity and temperature we can calculate a solute's diffusivity ... ok
Test we can obtain solute parameters via group additivity for a molecule with lone pairs ... ok
Test we can calculate and set the McGowan volume for species containing H,C,O,N or S ... ok
Test we can obtain solute parameters via group additivity for a molecule with both lone ... ok
Test that we can obtain solute parameters via group additivity for an amide ... ok
Test we can obtain solute parameters via group additivity for ammonia ... ok
Test that we can obtain solute parameters via group additivity for CO. ... ok
Test we can estimate Abraham solute parameters correctly using group contributions ... ok
Test we can obtain solute parameters from a library ... ok
Test we can obtain solvent parameters from a library ... ok
Test we can calculate the solvent viscosity given a temperature and its A-E correlation parameters ... ok
Test that the new ThermoDatabase generates appropriate thermo data. ... SKIP: WIP test failed: Expected list, got rmgpy.molecule.molecule.Molecule
Test that the symmetry contribution is correctly added for radicals ... ERROR
Test we generate symmetry numbers correctly. ... SKIP: WIP test failed: Expected list, got rmgpy.molecule.molecule.Molecule
Test that the new ThermoDatabase generates appropriate thermo data. for Aromatics. ... SKIP: WIP test failed: Expected list, got rmgpy.molecule.molecule.Molecule
Test that the symmetry contribution is correctly added for radicals for Aromatics. ... ERROR
Test we generate symmetry numbers correctly. for Aromatics. ... SKIP: WIP test failed: Expected list, got rmgpy.molecule.molecule.Molecule
Test that the Arrhenius A property was properly set. ... ok
Test that the Arrhenius Ea property was properly set. ... ok
Test that the Arrhenius T0 property was properly set. ... ok
Test that the Arrhenius Tmax property was properly set. ... ok
Test that the Arrhenius Tmin property was properly set. ... ok
Test the Arrhenius.changeRate() method. ... ok
Test the Arrhenius.changeT0() method. ... ok
Test that the Arrhenius comment property was properly set. ... ok
Test the Arrhenius.fitToData() method. ... ok
Test the Arrhenius.getRateCoefficient() method. ... ok
Test the Arrhenius.isTemperatureValid() method. ... ok
Test that the Arrhenius n property was properly set. ... ok
Test that an Arrhenius object can be pickled and unpickled with no loss ... ok
Test that an Arrhenius object can be reconstructed from its repr() ... ok
Test that the ArrheniusEP A property was properly set. ... ok
Test that the ArrheniusEP E0 property was properly set. ... ok
Test that the ArrheniusEP Tmax property was properly set. ... ok
Test that the ArrheniusEP Tmin property was properly set. ... ok
Test that the ArrheniusEP alpha property was properly set. ... ok
Test the ArrheniusEP.changeRate() method. ... ok
Test that the ArrheniusEP comment property was properly set. ... ok
Test the ArrheniusEP.getRateCoefficient() method. ... ok
Test the ArrheniusEP.isTemperatureValid() method. ... ok
Test that the ArrheniusEP n property was properly set. ... ok
Test that an ArrheniusEP object can be pickled and unpickled with no loss ... ok
Test that an ArrheniusEP object can be reconstructed from its repr() ... ok
Test that the MultiArrhenius Tmax property was properly set. ... ok
Test that the MultiArrhenius Tmin property was properly set. ... ok
Test that the MultiArrhenius A property was properly set. ... ok
Test the MultiArrhenius.changeRate() method. ... ok
Test that the MultiArrhenius comment property was properly set. ... ok
Test the MultiArrhenius.getRateCoefficient() method. ... ok
Test the MultiArrhenius.isTemperatureValid() method. ... ok
Test that a MultiArrhenius object can be pickled and unpickled with no loss ... ok
Test that a MultiArrhenius object can be reconstructed from its repr() ... ok
Test that we can convert to an Arrhenius ... ok
Test the toArrhenius fitting multiple kinetics over a small range, see if we're within 5% at a few points ... ok
Test the toArrhenius temperature range is set correctly. ... ok
Test that the MultiPDepArrhenius Pmax property was properly set. ... ok
Test that the MultiPDepArrhenius Pmin property was properly set. ... ok
Test that the MultiPDepArrhenius Tmax property was properly set. ... ok
Test that the MultiPDepArrhenius Tmin property was properly set. ... ok
Test that the MultiPDepArrhenius arrhenius property was properly set. ... ok
Test the PDepMultiArrhenius.changeRate() method. ... ok
Test that the MultiPDepArrhenius comment property was properly set. ... ok
Test the MultiPDepArrhenius.getRateCoefficient() method. ... ok
Test the MultiPDepArrhenius.isPressureValid() method. ... ok
Test the MultiPDepArrhenius.isTemperatureValid() method. ... ok
Test that a MultiPDepArrhenius object can be pickled and unpickled with ... ok
Test that a MultiPDepArrhenius object can be reconstructed from its ... ok
Test that the PDepArrhenius Pmax property was properly set. ... ok
Test that the PDepArrhenius Pmin property was properly set. ... ok
Test that the PDepArrhenius Tmax property was properly set. ... ok
Test that the PDepArrhenius Tmin property was properly set. ... ok
Test that the PDepArrhenius arrhenius property was properly set. ... ok
Test the PDepArrhenius.changeRate() method. ... ok
Test that the PDepArrhenius comment property was properly set. ... ok
Test the PDepArrhenius.fitToData() method. ... ok
Test the PDepArrhenius.getRateCoefficient() method. ... ok
Test the PDepArrhenius.isPressureDependent() method. ... ok
Test that a PDepArrhenius object can be successfully pickled and ... ok
Test that the PDepArrhenius pressures property was properly set. ... ok
Test that a PDepArrhenius object can be successfully reconstructed ... ok
Test that the Chebyshev Pmax property was properly set. ... ok
Test that the Chebyshev Pmin property was properly set. ... ok
Test that the Chebyshev Tmax property was properly set. ... ok
Test that the Chebyshev Tmin property was properly set. ... ok
Test the Chebyshev.changeRate() method. ... ok
Test that the Chebyshev coeffs property was properly set. ... ok
Test that the Chebyshev comment property was properly set. ... ok
Test the Chebyshev.fitToData() method. ... ok
Test the Chebyshev.getRateCoefficient() method. ... ok
Test the Chebyshev.isPressureDependent() method. ... ok
Test that a Chebyshev object can be pickled and unpickled with no loss ... ok
Test that a Chebyshev object can be reconstructed from its repr() ... ok
Test that the Lindemann Pmax property was properly set. ... ok
Test that the Lindemann Pmin property was properly set. ... ok
Test that the Lindemann Tmax property was properly set. ... ok
Test that the Lindemann Tmin property was properly set. ... ok
Test that the Lindemann arrheniusHigh property was properly set. ... ok
Test that the Lindemann arrheniusLow property was properly set. ... ok
Test the Lindemann.changeRate() method. ... ok
Test that the Lindemann comment property was properly set. ... ok
Test the Lindemann.getRateCoefficient() method. ... ok
Test the Lindemann.isPressureDependent() method. ... ok
Test that a Lindemann object can be pickled and unpickled with no loss ... ok
Test that a Lindemann object can be reconstructed from its repr() ... ok
Test that the ThirdBody Pmax property was properly set. ... ok
Test that the ThirdBody Pmin property was properly set. ... ok
Test that the ThirdBody Tmax property was properly set. ... ok
Test that the ThirdBody Tmin property was properly set. ... ok
Test that the ThirdBody arrhenius property was properly set. ... ok
Test the ThirdBody.changeRate() method. ... ok
Test that the ThirdBody comment property was properly set. ... ok
Test the getEffectiveColliderEfficiencies() method ... ok
Test the ThirdBody.getEffectivePressure() method. ... ok
Test the ThirdBody.getRateCoefficient() method. ... ok
Test the ThirdBody.isPressureDependent() method. ... ok
Test that a ThirdBody object can be successfully pickled and ... ok
Test that a ThirdBody object can be successfully reconstructed ... ok
Test that the Troe Pmax property was properly set. ... ok
Test that the Troe Pmin property was properly set. ... ok
Test that the Troe T1 property was properly set. ... ok
Test that the Troe T2 property was properly set. ... ok
Test that the Troe T3 property was properly set. ... ok
Test that the Troe Tmax property was properly set. ... ok
Test that the Troe Tmin property was properly set. ... ok
Test that the Troe alpha property was properly set. ... ok
Test that the Troe arrheniusHigh property was properly set. ... ok
Test that the Troe arrheniusLow property was properly set. ... ok
Test the Troe.changeRate() method. ... ok
Test that the Troe comment property was properly set. ... ok
Test the Troe.getRateCoefficient() method. ... ok
Test the Troe.isPressureDependent() method. ... ok
Test that a Troe object can be pickled and unpickled with no loss of ... ok
Test that a Troe object can be reconstructed from its repr() output ... ok
Test that the KineticsData Tdata property was properly set. ... ok
Test that the KineticsData Tmax property was properly set. ... ok
Test that the KineticsData Tmin property was properly set. ... ok
Test that the KineticsData comment property was properly set. ... ok
Test the KineticsData.getRateCoefficient() method. ... ok
Test the KineticsData.isTemperatureValid() method. ... ok
Test that the KineticsData kdata property was properly set. ... ok
Test that a KineticsData object can be pickled and unpickled with no ... ok
Test that a KineticsData object can be reconstructed from its repr() ... ok
Test that the PDepKineticsData Pdata property was properly set. ... ok
Test that the PDepKineticsData Pmax property was properly set. ... ok
Test that the PDepKineticsData Pmin property was properly set. ... ok
Test that the PDepKineticsData Tdata property was properly set. ... ok
Test that the PDepKineticsData Tmax property was properly set. ... ok
Test that the PDepKineticsData Tmin property was properly set. ... ok
Test that the PDepKineticsData comment property was properly set. ... ok
Test the PDepKineticsData.getRateCoefficient() method. ... ok
Test the PDepKineticsData.isPressureValid() method. ... ok
Test the PDepKineticsData.isTemperatureValid() method. ... ok
Test that the PDepKineticsData kdata property was properly set. ... ok
Test that a PDepKineticsData object can be pickled and unpickled with no ... ok
Test that a PDepKineticsData object can be reconstructed from its repr() ... ok
Test the conversion of first-order rate coefficient units to an integer ... ok
Test the conversion of second-order rate coefficient units to an integer ... ok
Test the conversion of third-order rate coefficient units to an integer ... ok
Test the conversion of zeroth-order rate coefficient units to an integer ... ok
Test the conversion of a reaction order of one to rate coefficient ... ok
Test the conversion of a reaction order of two to rate coefficient ... ok
Test the conversion of a reaction order of three to rate coefficient ... ok
Test the conversion of a reaction order of zero to rate coefficient ... ok
Test that the Eckart E0_TS property was properly set. ... ok
Test that the Eckart E0_prod property was properly set. ... ok
Test that the Eckart E0_reac property was properly set. ... ok
Test the Eckart.calculateTunnelingFactor() method. ... ok
Test that the Eckart frequency property was properly set. ... ok
Test that an Eckart object can be successfully pickled and ... ok
Test that an Eckart object can be successfully reconstructed ... ok
Test the Wigner.calculateTunnelingFactor() method. ... ok
Test that the Wigner frequency property was properly set. ... ok
Test that a Wigner object can be successfully pickled and unpickled ... ok
Test that a Wigner object can be successfully reconstructed from its ... ok
test_check_hund_rule_fail (rmgpy.molecule.adjlistTest.TestConsistencyChecker) ... ok
test_check_hund_rule_success (rmgpy.molecule.adjlistTest.TestConsistencyChecker) ... ok
adjlist: Test the Group.fromAdjacencyList() method. ... ok
testFromAdjacencyList_multiplicity (rmgpy.molecule.adjlistTest.TestGroupAdjLists) ... ok
testFromAdjacencyList_multiplicity_list (rmgpy.molecule.adjlistTest.TestGroupAdjLists) ... ok
adjlist: Test the Group.fromAdjacencyList() method on an old style adjacency list. ... ok
adjlist: Test the Group.toAdjacencyList() method. ... ok
adjlist: Check the adjacency list read/write functions for a full molecule. ... ok
adjlist: Test the Molecule.fromAdjacencyList() method 1. ... ok
adjlist: Test the Molecule.fromAdjacencyList() method 2. ... ok
adjlist: Test the Molecule.fromAdjacencyList() method 3. ... ok
adjlist: Test the Molecule.fromAdjacencyList() method 4. ... ok
Test we can read an intermediate style adjacency list with implicit hydrogens 1 ... ok
Test we can read an old style adjacency list with implicit hydrogens 1 ... ok
Test we can read an old style adjacency list with implicit hydrogens 2 ... ok
Test we can read an old style adjacency list with implicit hydrogens 3 ... ok
Test we can read an old style adjacency list with implicit hydrogens 4 ... ok
Test we can read an old style adjacency list with implicit hydrogens 5 ... SKIP: WIP test failed: Non-neutral molecule encountered. Currently, RMG does not support ion chemistry.

        1 C 2S {2,T}
        2 O 2S {1,T}

Test we can read an old style adjacency list with implicit hydrogens 1 ... ok
adjlist: Check the adjacency list read/write functions for a full molecule. ... ok
adjlist: Test that the adjlist reading and writing works with Helium. ... ok
adjlist: Test that improperly formed adjlists raise an InvalidAdjacencyListError. ... ok
adjlist: Test the Molecule.toAdjacencyList() method. ... ok
adjlist: Check that we can convert back to old style adjacency list ... ok
adjlist: Test that molecules with old or intermediate adjacency list formats containing unusual ... ok
adjlist: Test that molecule adjlists containing wildcards raise an InvalidAdjacencyListError. ... ok
Test the AtomType.equivalent() method. ... ok
Test the AtomType.isSpecificCaseOf() method. ... ok
Test that we can reconstruct an AtomType object from its repr() ... ok
Test that an AtomType object can be successfully pickled and ... ok
Test the AtomType.setActions() method. ... ok
Test that getAtomType() returns appropriate carbon atom types. ... ok
Test that getAtomType() returns the hydrogen atom type. ... ok
Test that getAtomType() returns appropriate nitrogen atom types. ... ok
Test that getAtomType() returns appropriate types for other misc inerts. ... ok
Test that getAtomType() returns appropriate oxygen atom types. ... ok
Test that getAtomType() returns appropriate silicon atom types. ... multiplicity 10
1  S  u0 p2 c0 {2,D}
2  S  u0 p1 c0 {1,D} {3,S}
3  S  u0 p2 c0 {2,S} {6,S}
4  Si u1 p0 c0 {5,S} {11,D}
5  Si u2 p0 c0 {4,S} {7,S}
6  Si u2 p-2 c0 {3,S} {8,T}
7  Si u1 p0 c0 {5,S} {9,D}
8  Si u2 p-2 c0 {6,T} {10,S}
9  Si u0 p0 c0 {7,D} {10,D}
10 Si u1 p0 c0 {8,S} {9,D}
11 O  u0 p2 c0 {4,D}

ok
Test that getAtomType() returns appropriate sulfur atom types. ... ok
Test we can create PDF files from molecules. ... Oct 19 14:29:17 RichardsMacBookPro13.local python[23699] <Error>: The function ‘CGFontGetGlyphPath’ is obsolete and will be removed in an upcoming update. Unfortunately, this application, or a library it uses, is using this obsolete function, and is thereby contributing to an overall degradation of system performance.
Oct 19 14:29:17 RichardsMacBookPro13.local python[23699] <Error>: The function ‘CGFontGetGlyphPaths’ is obsolete and will be removed in an upcoming update. Unfortunately, this application, or a library it uses, is using this obsolete function, and is thereby contributing to an overall degradation of system performance.
ok
Test we can create PDF surface without a temporary file (newer versions of PyCairo?) ... ok
Test we can create PNG files from molecules. ... ok
Test we can draw a polycyclic molecule ... ok
Test the rmgpy.elements.getElement() method. ... ok
Test that we can reconstruct an Element object from its repr() ... ok
Test that an Element object can be successfully pickled and ... ok
Test the Graph.addEdge() method. ... ok
Test the Graph.addVertex() method. ... ok
Test the graph copy function to ensure a complete copy of the graph is ... ok
Test the Graph.getAllCycles() method. ... ok
test_getAllCyclicVertices (rmgpy.molecule.graphTest.TestGraph) ... ok
test_getAllPolycylicVertices (rmgpy.molecule.graphTest.TestGraph) ... ok
Test the Graph.getEdge() method. ... ok
Test the Graph.getEdges() method. ... ok
Test the Graph.getSmallestSetOfSmallestRings() method. ... ok
Test the Graph.hasEdge() method. ... ok
Test the Graph.hasVertex() method. ... ok
Test the Graph.isCyclic() method. ... ok
Test the Graph.isEdgeInCycle() method. ... ok
Test the Graph.isVertexInCycle() method. ... ok
Check the graph isomorphism functions. ... ok
Test the graph merge function to ensure a proper merging of the graph ... ok
Test that a Graph object can be successfully pickled and unpickled ... ok
Test the Graph.removeEdge() method. ... ok
Test the Graph.removeVertex() method. ... ok
Test the Graph.resetConnectivityValues() method. ... ok
Test the Graph.sortVertices() method. ... ok
Test the graph split function to ensure a proper splitting of the graph ... ok
Check the subgraph isomorphism functions. ... ok
Test the Graph.updateConnectivityValues() method. ... ok
Tests the vertex connectivity values as introduced by Morgan (1965). ... ok
Test the Group.clearLabeledAtoms() method. ... ok
Test the Group.containsLabeledAtom() method. ... ok
Test the Group.findIsomorphism() method. ... ok
Test the Group.findSubgraphIsomorphisms() method. ... ok
Test the Group.fromAdjacencyList() method. ... ok
Test the Group.getLabeledAtom() method. ... ok
Test the Group.getLabeledAtoms() method. ... ok
Test the Group.isIsomorphic() method. ... ok
Test the Group.isSubgraphIsomorphic() method. ... ok
Test that a Group object can be successfully pickled and ... ok
Test the Group.toAdjacencyList() method. ... ok
Test the GroupAtom.applyAction() method for a BREAK_BOND action. ... ok
Test the GroupAtom.applyAction() method for a CHANGE_BOND action. ... ok
Test the GroupAtom.applyAction() method for a FORM_BOND action. ... ok
Test the GroupAtom.applyAction() method for a GAIN_RADICAL action. ... ok
Test the GroupAtom.applyAction() method for a CHANGE_BOND action. ... ok
Test the GroupAtom.applyAction() method for a LOSE_RADICAL action. ... ok
Test the GroupAtom.copy() method. ... ok
Test the GroupAtom.equivalent() method. ... ok
Test the GroupAtom.isSpecificCaseOf() method. ... ok
Test that a GroupAtom object can be successfully pickled and ... ok
Test the GroupBond.applyAction() method for a BREAK_BOND action. ... ok
Test the GroupBond.applyAction() method for a CHANGE_BOND action. ... ok
Test the GroupBond.applyAction() method for a FORM_BOND action. ... ok
Test the GroupBond.applyAction() method for a GAIN_RADICAL action. ... ok
Test the GroupBond.applyAction() method for a CHANGE_BOND action. ... ok
Test the GroupBond.applyAction() method for a LOSE_RADICAL action. ... ok
Test the GroupBond.copy() method. ... ok
Test the GroupBond.equivalent() method. ... ok
Test the GroupBond.isSpecificCaseOf() method. ... ok
Test that a GroupBond object can be successfully pickled and ... ok
Test that default multiplicity equals 1. ... ok
testReduce (rmgpy.molecule.inchiTest.AugmentedInChITest) ... ok
test_compare (rmgpy.molecule.inchiTest.AugmentedInChITest) ... ok
test_constructor (rmgpy.molecule.inchiTest.AugmentedInChITest) ... ok
test_compose_aug_inchi (rmgpy.molecule.inchiTest.ComposeTest) ... ok
test_ignore (rmgpy.molecule.inchiTest.IgnorePrefixTest) ... ok
test_compare (rmgpy.molecule.inchiTest.InChITest) ... ok
test_constructor (rmgpy.molecule.inchiTest.InChITest) ... ok
testC2H2 (rmgpy.molecule.inchiparsingTest.InChITest) ... multiplicity 3
1 C u1 p0 c0 {2,D} {3,S}
2 C u1 p0 c0 {1,D} {4,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {2,S}

ok
testC2H3O3 (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
testC4H6O (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
.O-HC.-CH2CH=CH2 ... ok
testC5H6O (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
testC5H6O_2 (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
testC6H6 (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
testCO (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
testMethylene (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
testO2 (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
testQuadri2DoubleBondMult5 (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
testQuadriRadicalDoubleBondZwitterMult5 (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
testTriRadical2DoubleBondMult4 (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
testTriRadicalDoubleBondMult4 (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
testTriRadicalZwitterMult4 (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
test_C2H3_triradical_parsing (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
test_C2H4_biradical_parsing (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
test_C3H6_biradical_parsing (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
test_CH3_parsing (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
test_Ethane_parsing (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
test_Ethyl_parsing (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
test_H2_parsing (rmgpy.molecule.inchiparsingTest.InChITest) ... ok
Test isormophism check of a CS group vs. a sulfur containing molecule ... SKIP: WIP test failed: False is not true
rmgpy.molecule.isomorphismTest.run_parameter_tests ... ok
distinct multiplicity for both molecules set by user. ... ok
identical multiplicity for both molecules set by user. ... ok
Multiplicity not set for one of two molecules ... ok
Both multiplicities not set. ... ok
rmgpy.molecule.isomorphismTest.test_isomorphism_R ... ok
Testing multiplicities in mol and group that don't match ... ok
Testing multiplicities in group vs. group ... ok
Test the Atom.applyAction() method for a BREAK_BOND action. ... ok
Test the Atom.applyAction() method for a CHANGE_BOND action. ... ok
Test the Atom.applyAction() method for a FORM_BOND action. ... ok
Test the Atom.applyAction() method for a GAIN_RADICAL action. ... ok
Test the Atom.applyAction() method for a CHANGE_BOND action. ... ok
Test the Atom.applyAction() method for a LOSE_RADICAL action. ... ok
Test the Atom.copy() method. ... ok
Test the Atom.decrementRadical() method. ... ok
Test the Atom.equivalent() method. ... ok
Test the Atom.incrementRadical() method. ... ok
Test the Atom.isCarbon() method. ... ok
Test the Atom.isHydrogen() method. ... ok
Test the Atom.isNonHydrogen() method. ... ok
Test the Atom.isOxygen() method. ... ok
Test the Atom.isSpecificCaseOf() method. ... ok
Test the Atom.mass property. ... ok
Test the Atom.number property. ... ok
Test that a Atom object can be successfully pickled and ... ok
Test the Atom.symbol property. ... ok
Test the Bond.applyAction() method for a BREAK_BOND action. ... ok
Test the Bond.applyAction() method for a CHANGE_BOND action. ... ok
Test the Bond.applyAction() method for a FORM_BOND action. ... ok
Test the Bond.applyAction() method for a GAIN_RADICAL action. ... ok
Test the Bond.applyAction() method for a CHANGE_BOND action. ... ok
Test the Bond.applyAction() method for a LOSE_RADICAL action. ... ok
Test the Bond.copy() method. ... ok
Test the Bond.decrementOrder() method. ... ok
Test the GroupBond.equivalent() method. ... ok
Test the Bond.incrementOrder() method. ... ok
Test the Bond.isBenzene() method. ... ok
Test the Bond.isDouble() method. ... ok
Test the Bond.isSingle() method. ... ok
Test the Bond.isSpecificCaseOf() method. ... ok
Test the Bond.isTriple() method. ... ok
Test that a Bond object can be successfully pickled and ... ok
Check the adjacency list read/write functions for a full molecule. ... ok
Test the Molecule.isAromatic() method for Benzene. ... ok
Test the Molecule.isAromatic() method for Cyclohexane. ... ok
Test the Molecule.isAromatic() method for Naphthalene. ... ok
Test that Augmented InChI generation is printing the /mult layer ... ok
Test that Augmented InChI Key generation is printing the mult layer ... ok
Test that singlet carbene molecules, bearing an electron pair rather than unpaired electrons ... ok
Test the Molecule.clearLabeledAtoms() method. ... ok
Test the Molecule.containsLabeledAtom() method. ... ok
Test the Molecule.countInternalRotors() method. ... ok
Test the Molecule.countInternalRotors() method for dimethylacetylene. ... SKIP: WIP test failed: 2 != 1
Test the Molecule.countInternalRotors() method. ... ok
Test the Molecule.countInternalRotors() method. ... ok
Test the Molecule.countInternalRotors() method. ... ok
Test the Molecule.countInternalRotors() method. ... ok
Test the Molecule.countInternalRotors() method. ... ok
Test the Molecule.fromAdjacencyList() method. ... ok
Make sure that H radical is produced properly from its InChI ... ok
Make sure that H radical is produced properly from its SMILES ... ok
Test the Molecule.getLabeledAtoms() method. ... ok
Test the Molecule.getLabeledAtom() method. ... ok
Test the Molecule.getLabeledAtoms() method. ... ok
Test the Molecule.getMolecularWeight() method. ... ok
Test that the symmetry number getter works properly ... ERROR
Test that InChI Key generation is working properly. ... ok
Test the Molecule.isInCycle() method with ethane. ... ok
Test the Molecule.isInCycle() method with ethane. ... ok
Check the graph isomorphism functions. ... ok
Test that we can round-trip SMILES strings of Kekulized aromatics ... ok
Test that we can print SMILES strings of Kekulized structures ... ok
Tests that an aromatic molecule returns at least one Kekulized resonance isomer. ... ok
Test we can make aromatic and Kekulized resonance isomers of 2-methylanthracen-1-ol ... SKIP: WIP test failed: Expected a resonance form Molecule(SMILES="CC1C=CC2=CC3=CC=CC=C3C=C2C=1O") that was not generated.
Only generated these:
Molecule(SMILES="CC1=CC=C2C=C3C=CC=CC3=CC2=C1O")
Molecule(SMILES="Cc1ccc2cc3ccccc3cc2c1O")
Test the Molecule.isLinear() method. ... ok
Test the Molecule.isLinear() method. ... ok
Test the Molecule.isLinear() method. ... ok
Test the Molecule.isLinear() method. ... ok
Test the Molecule.isLinear() method. ... ok
Test the Molecule.isLinear() method. ... ok
Test the Molecule.isLinear() method. ... ok
Test the Molecule.isLinear() method. ... ok
Test the Molecule.isLinear() method. ... ok
Test that augmented inchi without InChI layer raises Exception. ... ok
Test that augmented inchi with wrong layer is caught. ... ==============================
*** Open Babel Error  in InChI code
  Reading InChI failed
[14:29:18] ERROR: 
ok
Test that augmented inchi with wrong layer is caught. ... ok
Test that augmented inchi with wrong layer is caught. ... ok
Test a key-value pair is added to the props attribute of Molecule. ... ok
Test that Molecule's props dictionaries are independent of each other. ... ok
Test we can make both Kekulized resonance isomers of 2-Hydroxy-1-methylbenzene ... SKIP: WIP test failed: Didn't generate 3 resonance isomers
Test that a Molecule object can be successfully pickled and ... ok
Test that the atom mapping returned by toRDKitMol contains the correct ... ok
Test that the species [CH] has three radical electrons and a spin multiplicity of 4. ... ok
Test that the species [CH2] has two radical electrons and a spin multiplicity of 3. ... ok
Test radical count on [CH2]C[CH2] ... ok
Test the Molecule.getRadicalCount() method. ... ok
Test that we can generate a few SMILES strings as expected ... ok
Test the Molecule.getSmallestSetOfSmallestRings() method with a complex ... ok
Test that the Molecule.saturate() method works properly for an indenyl radical ... ok
Check the graph isomorphism functions. ... ok
testSubgraphIsomorphismAgain (rmgpy.molecule.moleculeTest.TestMolecule) ... ok
testSubgraphIsomorphismManyLabels (rmgpy.molecule.moleculeTest.TestMolecule) ... ok
Test the Molecule.toAdjacencyList() method. ... ok
Test that multiplicity layer be optional in cases where the layer is not needed. ... ok
test_fromAugmentedInChI (rmgpy.molecule.parserTest.parserTest) ... ok
Test that toRDKitMol returns correct indices and atom mappings. ... ok
test_Benzene_aro (rmgpy.molecule.resonanceTest.ResonanceTest) ... ok
test_Benzene_kek (rmgpy.molecule.resonanceTest.ResonanceTest) ... ok
CyclobutylBenzene-radical ... ok
CyclopropylMethylBenzene ... ok
CyclopropylBenzene, generate aro resonance isomers ... ok
PropylBenzene-radical ... ok
CyclopropylBenzene-radical, aromatic bonds ... ok
CyclopropylBenzene-radical, kekulized bonds ... ok
Failure: ValueError (rmgpy.molecule.graph.Vertex has the wrong size, try recompiling) ... ERROR
Test the Molecule.calculateAtomSymmetryNumber() on CC ... ERROR
Test the Molecule.calculateAtomSymmetryNumber() on CC(C)C ... ERROR
Test the Molecule.calculateAtomSymmetryNumber() on CH4 ... ERROR
Test the Molecule.calculateAtomSymmetryNumber() on [CH3] ... ERROR
Test the Molecule.calculateAtomSymmetryNumber() on CCC ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on CC(C)=C=C(CC)CC ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on CC=C=[C] ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on C=C=CCCC ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on C=C=C(C(C(C(C=C=C)=C=C)=C=C)=C=C) ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on C=C=[C]C(C)(C)[C]=C=C ... SKIP: WIP test failed: Missing type object
Test the Molecule.calculateAxisSymmetryNumber() on C=C=C=O ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on CC=C=C=O ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on C=C=C=N ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on C=C=C=[N] ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on C=C=C=C ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on C=C=C=[CH] ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on C=C ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on C=C=C ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on C=C=[C] ... ERROR
Test the Molecule.calculateAxisSymmetryNumber() on O=O ... ERROR
Test the Molecule.calculateBondSymmetryNumber() on C#C ... ERROR
Test the Molecule.calculateBondSymmetryNumber() on CCCC ... ERROR
Test the Molecule.calculateBondSymmetryNumber() on CC ... ERROR
Test the Molecule.calculateBondSymmetryNumber() on C=C. ... ERROR
Test the Molecule.calculateBondSymmetryNumber() on CCC ... ERROR
Test the Molecule.calculateCyclicSymmetryNumber() on C1CCCCC1 ... ERROR
Test the Molecule.calculateSymmetryNumber() on C#C ... ERROR
Test the Molecule.calculateSymmetryNumber() on C#CC#C ... ERROR
Test the Molecule.calculateSymmetryNumber() on C1=C=C=1 ... ERROR
Test the Molecule.calculateSymmetryNumber() on [C]#[C] ... ERROR
Test the Molecule.calculateSymmetryNumber() on C=[CH]. ... ERROR
Test the Molecule.calculateSymmetryNumber() on C=C ... ERROR
Test the Molecule.calculateSymmetryNumber() on C=O ... ERROR
Test the Molecule.calculateSymmetryNumber() on [H][H] ... ERROR
Test the Molecule.calculateSymmetryNumber() on [OH] ... ERROR
Test the Molecule.calculateSymmetryNumber() on CH4 ... ERROR
Test the Molecule.calculateSymmetryNumber() on [CH3] ... ERROR
Test the Molecule.calculateSymmetryNumber() on O=O ... ERROR
Test the Molecule.calculateSymmetryNumber() on H2O ... ERROR
Test the Molecule.calculateSymmetryNumber() on C=C=[C]C(C)(C)[C]=C=C ... ERROR
Test the Species.getSymmetryNumber() (total symmetry) on Cc1ccccc1C ... ERROR
Test the Species.getSymmetryNumber() (total symmetry) on Cc1ccc(C)cc1 ... SKIP: WIP test failed: Missing type object
Test the Molecule.calculateSymmetryNumber() on C(=CC(c1ccccc1)C([CH]CCCCCC)C=Cc1ccccc1)[CH]CCCCCC ... SKIP: WIP test failed: Missing type object
Test the Species.getSymmetryNumber() (total symmetry) on c1ccccc1 ... ERROR
Test the Molecule.calculateSymmetryNumber() on CC ... ERROR
Test the Species.getSymmetryNumber() (total symmetry) on c1ccccc1C ... ERROR
Test the SingleExponentialDown.T0 attribute. ... ok
Test the SingleExponentialDown.sigma attribute. ... ok
Test the SingleExponentialDown.getAlpha() method. ... ok
Test the SingleExponentialDown.n attribute. ... ok
Test that a SingleExponentialDown object can be successfully pickled ... ok
Test that a SingleExponentialDown object can be successfully ... ok
Test that the network `bathGas` property was properly set. ... ok
Test that the Network.initialize() method. ... ok
Test that the network `isomers` property was properly set. ... ok
Test that the network `label` property was properly set. ... ok
Test that the network `netReactions` property was properly set. ... ok
Test that the network `pathReactions` property was properly set. ... ok
Test that the network `products` property was properly set. ... ok
Test that the network `reactants` property was properly set. ... ok
Test that generateThermoData() works correctly. ... SKIP: Gaussian not found. Try resetting your environment variables if you want to use it.
Test that generateThermoData() can load thermo from a previous run. ... SKIP: Gaussian not found. Try resetting your environment variables if you want to use it.
Test that generateThermoData() works correctly. ... SKIP: Gaussian not found. Try resetting your environment variables if you want to use it.
Test that generateThermoData() can load thermo from a previous run. ... SKIP: Gaussian not found. Try resetting your environment variables if you want to use it.
Test that getThermoData() fails when expected. ... ok
Test that getThermoData() works correctly. ... SKIP: If GAUSSIAN installed, try checking your environment variables.
Test that getThermoData() works correctly. ... SKIP: If MOPAC installed, try checking your environment variables.
Test that initialize() works correctly. ... ok
Test that setDefaultOutputDirectory() works correctly. ... ok
Test that checkAllSet() works correctly. ... ok
Test that generateThermoData() works correctly. ... SKIP: MOPAC not found. Try resetting your environment variables if you want to use it.
Test that generateThermoData() can load thermo from a previous run. ... SKIP: MOPAC not found. Try resetting your environment variables if you want to use it.
Test that generateThermoData() works correctly. ... SKIP: MOPAC not found. Try resetting your environment variables if you want to use it.
Test that generateThermoData() can load thermo from a previous run. ... SKIP: MOPAC not found. Try resetting your environment variables if you want to use it.
Test that generateThermoData() works correctly. ... SKIP: MOPAC not found. Try resetting your environment variables if you want to use it.
Test that generateThermoData() can load thermo from a previous run. ... SKIP: MOPAC not found. Try resetting your environment variables if you want to use it.
Test the creation of an acceleration quantity with units of cm/s^2. ... ok
Test the creation of an acceleration quantity with units of m/s^2. ... ok
Test the creation of an area quantity with units of m^2. ... ok
Test the creation of an area quantity with units of m^2. ... ok
Test the creation of an concentration quantity with units of molecules/m^3. ... ok
Test the creation of an concentration quantity with units of mol/m^3. ... ok
Test the creation of an concentration quantity with units of m^-3. ... ok
Test the creation of a dipole moment quantity with units of C*m. ... ok
Test the creation of a dipole moment quantity with units of J/mol. ... ok
Test the creation of an energy quantity with units of J. ... ok
Test the creation of an energy quantity with units of J/mol. ... ok
Test the creation of an energy quantity with units of K (not really an energy!). ... ok
Test the creation of an energy quantity with units of cal. ... ok
Test the creation of an energy quantity with units of cal/mol. ... ok
Test the creation of an energy quantity with units of kJ. ... ok
Test the creation of an energy quantity with units of kJ/mol. ... ok
Test the creation of an energy quantity with units of kcal. ... ok
Test the creation of an energy quantity with units of kcal/mol. ... ok
Test the creation of a flux quantity with units of molecules/(m^2*s). ... ok
Test the creation of a flux quantity with units of mol/(m^2*s). ... ok
Test the creation of a flux quantity with units of m^-2*s^-1. ... ok
Test the creation of an force quantity with units of N. ... ok
Test the creation of a frequency quantity with units of GHz. ... ok
Test the creation of a frequency quantity with units of Hz. ... ok
Test the creation of a frequency quantity with units of K. ... ok
Test the creation of a frequency quantity with units of MHz. ... ok
Test the creation of a frequency quantity with units of cm^-1. ... ok
Test the creation of a frequency quantity with units of eV. ... ok
Test the creation of a frequency quantity with units of kHz. ... ok
Test the creation of a frequency quantity with units of s^-1. ... ok
Test the creation of a heat capacity quantity with units of J/K. ... ok
Test the creation of a heat capacity quantity with units of J/(mol*K). ... ok
Test the creation of a heat capacity quantity with units of cal/K. ... ok
Test the creation of a heat capacity quantity with units of cal/(mol*K). ... ok
Test the creation of a heat capacity quantity with units of kJ/K. ... ok
Test the creation of a heat capacity quantity with units of kJ/(mol*K). ... ok
Test the creation of a heat capacity quantity with units of kcal/K. ... ok
Test the creation of a heat capacity quantity with units of kcal/(mol*K). ... ok
Test the creation of a moment of inertia quantity with units of amu*angstrom^2. ... ok
Test the creation of a moment of inertia quantity with units of kg*m^2. ... ok
Test the creation of a length quantity with units of cm. ... ok
Test the creation of a length quantity with units of km. ... ok
Test the creation of a length quantity with units of m. ... ok
Test the creation of a length quantity with units of mm. ... ok
Test the creation of a length quantity with units of nm. ... ok
Test the creation of a length quantity with units of pm. ... ok
Test the creation of a length quantity with units of um. ... ok
Test the creation of a mass quantity with units of amu. ... ok
Test the creation of a mass quantity with units of g/mol. Note that ... ok
Test the creation of a mass quantity with units of kg. ... ok
Test the creation of a mass quantity with units of kg/mol. Note that ... ok
Test the creation of a momentum quantity with units of kg*m/s^2. ... ok
Test the creation of a power quantity with units of W. ... ok
Test the creation of a pressure quantity with units of Pa. ... ok
Test the creation of a pressure quantity with units of atm. ... ok
Test the creation of a pressure quantity with units of bar. ... ok
Test the creation of a pressure quantity with units of psi. ... ok
Test the creation of a pressure quantity with units of torr. ... ok
Test the creation of a rate coefficient quantity with units of cm^3/(molecule*s). ... ok
Test the creation of a rate coefficient quantity with units of cm^3/(mol*s). ... ok
Test the creation of a rate coefficient quantity with units of cm^6/(mol^2*s). ... ok
Test the creation of a rate coefficient quantity with units of cm^6/(molecule^2*s). ... ok
Test the creation of a rate coefficient quantity with units of cm^9/(mol^3*s). ... ok
Test the creation of a rate coefficient quantity with units of cm^9/(molecule^3*s). ... ok
Test the creation of a rate coefficient quantity with units of m^3/(mol*s). ... ok
Test the creation of a rate coefficient quantity with units of m^6/(mol^2*s). ... ok
Test the creation of a rate coefficient quantity with units of m^9/(mol^3*s). ... ok
Test the creation of a rate coefficient quantity with units of s^-1. ... ok
Test the creation of a temperature quantity with units of K. ... ok
Test the creation of a temperature quantity with units of degrees C. ... ok
Test the creation of a temperature quantity with units of degrees F. ... ok
Test the creation of a temperature quantity with units of degrees R. ... ok
Test the creation of a time quantity with units of fs. ... ok
Test the creation of a time quantity with units of hr. ... ok
Test the creation of a time quantity with units of min. ... ok
Test the creation of a time quantity with units of ms. ... ok
Test the creation of a time quantity with units of ns. ... ok
Test the creation of a time quantity with units of ps. ... ok
Test the creation of a time quantity with units of s. ... ok
Test the creation of a time quantity with units of us. ... ok
Test the creation of an velocity quantity with units of m/s. ... ok
Test the creation of an velocity quantity with units of m/s. ... ok
Test the creation of an volume quantity with units of L. ... ok
Test the creation of an volume quantity with units of m^3. ... ok
Test the Reaction.getEnthalpyOfReaction() method. ... ok
Test the Reaction.getEntropyOfReaction() method. ... ok
Test the Reaction.getEquilibriumConstant() method. ... ok
Test the Reaction.getEquilibriumConstant() method. ... ok
Test the Reaction.getEquilibriumConstant() method. ... ok
Test the Reaction.getFreeEnergyOfReaction() method. ... ok
Test the Reaction.generateReverseRateCoefficient() method. ... ok
Test the Reaction.hasTemplate() method. ... ok
Test the Reaction.isAssociation() method. ... ok
Test the Reaction.isDissociation() method. ... ok
Test the Reaction.isIsomerization() method. ... ok
Test that a Reaction object can be successfully reconstructed ... ok
Test that a Reaction object can be successfully pickled and ... ok
Test the Reaction.getRateCoefficient() method. ... ok
Test the Reaction.getStoichiometricCoefficient() method. ... ok
A test of the transition state theory k(T) calculation function, ... ok
test1to1 (rmgpy.reactionTest.TestReactionIsomorphism) ... ok
test1to2 (rmgpy.reactionTest.TestReactionIsomorphism) ... ok
test2to2 (rmgpy.reactionTest.TestReactionIsomorphism) ... ok
test2to3 (rmgpy.reactionTest.TestReactionIsomorphism) ... ok
test_attach_detach (rmgpy.solver.baseTest.ListenerTest) ... ok
test_listen (rmgpy.solver.baseTest.ListenerTest) ... ok
Test the solver's ability to simulate a model with collision efficiencies. ... ok
Test the simple batch reactor with a simple kinetic model. Here we ... ok
Test that a Species object can be reconstructed from its repr(). ... ok
Test that a Species object can be pickled and unpickled. ... ok
Test that both resonance forms of 1-penten-3-yl are printed by __repr__ ... ok
Test that 1-penten-3-yl makes 2-penten-1-yl resonance isomer ... ok
Test a key-value pair is added to the props attribute of Species. ... ok
Test that Species's props dictionaries are independent of each other. ... ok
Test that toAdjacencyList() works as expected. ... ok
Test the Conformer.getCenterOfMass() method. ... ok
Test the StatMech.getDensityOfStates() method for ethylene. ... ok
Test the StatMech.getDensityOfStates() method for oxygen. ... ok
Test the StatMech.getEnthalpy() method for ethylene. ... ok
Test the StatMech.getEnthalpy() method for oxygen. ... ok
Test the StatMech.getEntropy() method for ethylene. ... ok
Test the StatMech.getEntropy() method for oxygen. ... ok
Test the StatMech.getHeatCapacity() method for ethylene. ... ok
Test the StatMech.getHeatCapacity() method for oxygen. ... ok
Test the Conformer.getInternalReducedMomentOfInertia() method. ... ok
Test the Conformer.getMomentOfInertiaTensor() method. ... ok
Test the Conformer.getNumberDegreesOfFreedom() method. ... ok
Test the StatMech.getPartitionFunction() method for ethylene. ... ok
Test the StatMech.getPartitionFunction() method for oxygen. ... ok
Test the Conformer.getPrincipalMomentsOfInertia() method. ... ok
Test the StatMech.getSumOfStates() method for ethylene. ... ok
Test the StatMech.getSumOfStates() method for oxygen. ... ok
Test the Conformer.getTotalMass() method. ... ok
Test the KRotor.getDensityOfStates() method using a classical ... ok
Test the KRotor.getDensityOfStates() method using a quantum rotor. ... ok
Test the KRotor.getEnthalpy() method using a classical rotor. ... ok
Test the KRotor.getEnthalpy() method using a quantum rotor. ... ok
Test the KRotor.getEntropy() method using a classical rotor. ... ok
Test the KRotor.getEntropy() method using a quantum rotor. ... ok
Test the KRotor.getHeatCapacity() method using a classical rotor. ... ok
Test the KRotor.getHeatCapacity() method using a quantum rotor. ... ok
Test the KRotor.getLevelDegeneracy() method. ... ok
Test the KRotor.getLevelEnergy() method. ... ok
Test the KRotor.getPartitionFunction() method for a classical ... ok
Test the KRotor.getPartitionFunction() method for a quantum ... ok
Test getting the KRotor.rotationalConstant property. ... ok
Test the KRotor.getSumOfStates() method using a classical rotor. ... ok
Test the KRotor.getSumOfStates() method using a quantum rotor. ... ok
Test that a KRotor object can be pickled and unpickled with no loss ... ok
Test that a KRotor object can be reconstructed from its repr() output ... ok
Test setting the KRotor.rotationalConstant property. ... ok
Test the LinearRotor.getDensityOfStates() method using a classical ... ok
Test the LinearRotor.getDensityOfStates() method using a quantum rotor. ... ok
Test the LinearRotor.getEnthalpy() method using a classical rotor. ... ok
Test the LinearRotor.getEnthalpy() method using a quantum rotor. ... ok
Test the LinearRotor.getEntropy() method using a classical rotor. ... ok
Test the LinearRotor.getEntropy() method using a quantum rotor. ... ok
Test the LinearRotor.getHeatCapacity() method using a classical rotor. ... ok
Test the LinearRotor.getHeatCapacity() method using a quantum rotor. ... ok
Test the LinearRotor.getLevelDegeneracy() method. ... ok
Test the LinearRotor.getLevelEnergy() method. ... ok
Test the LinearRotor.getPartitionFunction() method for a classical ... ok
Test the LinearRotor.getPartitionFunction() method for a quantum ... ok
Test getting the LinearRotor.rotationalConstant property. ... ok
Test the LinearRotor.getSumOfStates() method using a classical rotor. ... ok
Test the LinearRotor.getSumOfStates() method using a quantum rotor. ... ok
Test that a LinearRotor object can be pickled and unpickled with no ... ok
Test that a LinearRotor object can be reconstructed from its repr() ... ok
Test setting the LinearRotor.rotationalConstant property. ... ok
Test the NonlinearRotor.getDensityOfStates() method using a classical ... ok
Test the NonlinearRotor.getEnthalpy() method using a classical rotor. ... ok
Test the NonlinearRotor.getEntropy() method using a classical rotor. ... ok
Test the NonlinearRotor.getHeatCapacity() method using a classical ... ok
Test the NonlinearRotor.getPartitionFunction() method for a classical ... ok
Test getting the NonlinearRotor.rotationalConstant property. ... ok
Test the NonlinearRotor.getSumOfStates() method using a classical rotor. ... ok
Test that a NonlinearRotor object can be pickled and unpickled with ... ok
Test that a NonlinearRotor object can be reconstructed from its ... ok
Test setting the NonlinearRotor.rotationalConstant property. ... ok
Test the SphericalTopRotor.getDensityOfStates() method using a classical ... ok
Test the SphericalTopRotor.getDensityOfStates() method using a quantum rotor. ... ok
Test the SphericalTopRotor.getEnthalpy() method using a classical rotor. ... ok
Test the SphericalTopRotor.getEnthalpy() method using a quantum rotor. ... ok
Test the SphericalTopRotor.getEntropy() method using a classical rotor. ... ok
Test the SphericalTopRotor.getEntropy() method using a quantum rotor. ... ok
Test the SphericalTopRotor.getHeatCapacity() method using a classical rotor. ... ok
Test the SphericalTopRotor.getHeatCapacity() method using a quantum rotor. ... ok
Test the SphericalTopRotor.getLevelDegeneracy() method. ... ok
Test the SphericalTopRotor.getLevelEnergy() method. ... ok
Test the SphericalTopRotor.getPartitionFunction() method for a classical ... ok
Test the SphericalTopRotor.getPartitionFunction() method for a quantum ... ok
Test getting the SphericalTopRotor.rotationalConstant property. ... ok
Test the SphericalTopRotor.getSumOfStates() method using a classical rotor. ... ok
Test the SphericalTopRotor.getSumOfStates() method using a quantum rotor. ... ok
Test that a SphericalTopRotor object can be pickled and unpickled ... ok
Test that a SphericalTopRotor object can be reconstructed from its ... ok
Test setting the SphericalTopRotor.rotationalConstant property. ... ok
Test the getDensityOfStates() method. ... ok
Test the getEnthalpy() method. ... ok
Test the getEntropy() method. ... ok
Test the getHeatCapacity() method. ... ok
Test the getPartitionFunction() method. ... ok
Test the HinderedRotor.getDensityOfStates() method using a classical ... ok
Test the HinderedRotor.getDensityOfStates() method using a Fourier ... ok
Test the HinderedRotor.getDensityOfStates() method using a classical ... ok
Test the HinderedRotor.getDensityOfStates() method using a Fourier ... ok
Test the HinderedRotor.getEnthalpy() method using a cosine potential ... ok
Test the HinderedRotor.getEnthalpy() method using a Fourier series ... ok
Test the HinderedRotor.getEnthalpy() method using a cosine potential ... ok
Test the HinderedRotor.getEnthalpy() method using a Fourier series ... ok
Test the HinderedRotor.getEntropy() method using a cosine potential ... ok
Test the HinderedRotor.getEntropy() method using a Fourier series ... ok
Test the HinderedRotor.getEntropy() method using a cosine potential ... ok
Test the HinderedRotor.getEntropy() method using a Fourier series ... ok
Test the HinderedRotor.getHeatCapacity() method using a cosine ... ok
Test the HinderedRotor.getHeatCapacity() method using a Fourier series ... ok
Test the HinderedRotor.getHeatCapacity() method using a cosine ... ok
Test the HinderedRotor.getHeatCapacity() method using a Fourier series ... ok
Test the HinderedRotor.getPartitionFunction() method for a cosine ... ok
Test the HinderedRotor.getPartitionFunction() method for a Fourier ... ok
Test the HinderedRotor.getPartitionFunction() method for a cosine ... ok
Test the HinderedRotor.getPartitionFunction() method for a Fourier ... ok
Test the HinderedRotor.getPotential() method for a cosine potential. ... ok
Test the HinderedRotor.getPotential() method for a Fourier series ... ok
Test getting the HinderedRotor.rotationalConstant property. ... ok
Test the HinderedRotor.getSumOfStates() method using a cosine potential ... ok
Test the HinderedRotor.getSumOfStates() method using a Fourier series ... ok
Test the HinderedRotor.getSumOfStates() method using a cosine potential ... ok
Test the HinderedRotor.getSumOfStates() method using a Fourier series ... ok
Test that a HinderedRotor object can be pickled and unpickled with no ... ok
Test that a HinderedRotor object can be reconstructed from its repr() ... ok
Test setting the HinderedRotor.rotationalConstant property. ... ok
Test the IdealGasTranslation.getDensityOfStates() method using a ... ok
Test the IdealGasTranslation.getEnthalpy() method using a classical ... ok
Test the IdealGasTranslation.getEntropy() method using a classical ... ok
Test the IdealGasTranslation.getHeatCapacity() method using a classical ... ok
Test the IdealGasTranslation.getPartitionFunction() method for a ... ok
Test the IdealGasTranslation.getSumOfStates() method using a classical ... ok
Test that a IdealGasTranslation object can be pickled and unpickled ... ok
Test that an IdealGasTranslation object can be reconstructed from its ... ok
Test the HarmonicOscillator.getDensityOfStates() method using a set of ... ok
Test the HarmonicOscillator.getDensityOfStates() method using a set of ... ok
Test the HarmonicOscillator.getEnthalpy() method using a set of ... ok
Test the HarmonicOscillator.getEnthalpy() method using a set of quantum ... ok
Test the HarmonicOscillator.getEntropy() method using a set of ... ok
Test the HarmonicOscillator.getEntropy() method using a set of quantum ... ok
Test the HarmonicOscillator.getHeatCapacity() method using a set of ... ok
Test the HarmonicOscillator.getHeatCapacity() method using a set of ... ok
Test the HarmonicOscillator.getPartitionFunction() method for a set of ... ok
Test the HarmonicOscillator.getPartitionFunction() method for a set of ... ok
Test the HarmonicOscillator.getSumOfStates() method using a set of ... ok
Test the HarmonicOscillator.getSumOfStates() method using a set of ... ok
Test that a HarmonicOscillator object can be pickled and unpickled ... ok
Test that a HarmonicOscillator object can be reconstructed from its ... ok
Test round-trip conversion from Wilhoit to NASA and back ... ok
Test round-trip conversion from Wilhoit to ThermoData and back ... ok
Test the conversion of a NASA model to a ThermoData model. ... ok
Test the conversion of a NASA model to a Wilhoit model. ... ok
Test the conversion of a ThermoData model to a NASA model. ... ok
Test the conversion of a ThermoData model to a Wilhoit model. ... ok
Test the conversion of a Wilhoit model to a NASA model. ... ok
Test the conversion of a Wilhoit model to a ThermoData model. ... ok
Test that the NASA comment property was properly set. ... ok
Test that the NASA E0 property was properly set. ... ok
Test that the NASA Tmax property was properly set. ... ok
Test that the NASA Tmin property was properly set. ... ok
Test the NASA.getEnthalpy() method. ... ok
Test the NASA.getEntropy() method. ... ok
Test the NASA.getFreeEnergy() method. ... ok
Test the NASA.getHeatCapacity() method. ... ok
Test the NASA.isTemperatureValid() method. ... ok
Test that a NASA object can be pickled and unpickled with no loss of ... ok
Test that the NASA high-temperature polynomial was properly set. ... ok
Test that the NASA low-temperature polynomial was properly set. ... ok
Test that a NASA object can be reconstructed from its repr() output ... ok
Test that the ThermoData comment property was properly set. ... ok
Test that the ThermoData Cp0 property was properly set. ... ok
Test that the ThermoData CpInf property was properly set. ... ok
Test that the ThermoData Cpdata property was properly set. ... ok
Test that the ThermoData E0 property was properly set. ... ok
Test that the ThermoData H298 property was properly set. ... ok
Test that the ThermoData S298 property was properly set. ... ok
Test that the ThermoData Tdata property was properly set. ... ok
Test that the ThermoData Tmax property was properly set. ... ok
Test that the ThermoData Tmin property was properly set. ... ok
Test the ThermoData.getEnthalpy() method. ... ok
Test the ThermoData.getEntropy() method. ... ok
Test the ThermoData.getFreeEnergy() method. ... ok
Test the ThermoData.getHeatCapacity() method. ... ok
Test the ThermoData.isTemperatureValid() method. ... ok
Test that a ThermoData object can be successfully pickled and ... ok
Test that a ThermoData object can be successfully reconstructed from its ... ok
Test that the Wilhoit B property was properly set. ... ok
Test that the Wilhoit Cp0 property was properly set. ... ok
Test that the Wilhoit CpInf property was properly set. ... ok
Test that the Wilhoit E0 property is properly calculated from Enthalpy at 0.001 K ... ok
Test that the Wilhoit H0 property was properly set. ... ok
Test that the Wilhoit S0 property was properly set. ... ok
Test that the Wilhoit Tmax property was properly set. ... ok
Test that the Wilhoit Tmin property was properly set. ... ok
Test that the Wilhoit a0 property was properly set. ... ok
Test that the Wilhoit a1 property was properly set. ... ok
Test that the Wilhoit a2 property was properly set. ... ok
Test that the Wilhoit a3 property was properly set. ... ok
Test that the Wilhoit comment property was properly set. ... ok
Test the Wilhoit.fitToData() method. ... ok
Test the Wilhoit.getEnthalpy() method. ... ok
Test the Wilhoit.getEntropy() method. ... ok
Test the Wilhoit.getFreeEnergy() method. ... ok
Test the Wilhoit.getHeatCapacity() method. ... ok
Test the Wilhoit.isTemperatureValid() method. ... ok
Test that a Wilhoit object can be pickled and unpickled with no loss ... ok
Test that a Wilhoit object can be reconstructed from its repr() output ... ok
Test that the CriticalPointGroupContribution Pc property was properly set. ... ok
Test that the CriticalPointGroupContribution Tb property was properly set. ... ok
Test that the CriticalPointGroupContribution Tc property was properly set. ... ok
Test that the CriticalPointGroupContribution Vc property was properly set. ... ok
Test that a CriticalPointGroupContribution object can be pickled and unpickled with no loss of information. ... ok
Test that a CriticalPointGroupContribution object can be reconstructed from its repr() output with no loss of information ... ok
Test that the CriticalPointGroupContribution structureIndex property was properly set. ... ok
Test that the TransportData comment property was properly set. ... ok
Test that the TransportData dipoleMoment property was properly set. ... ok
Test that the TransportData epsilon property was properly set. ... ok
Test the LennardJones.getCollisionFrequency() method. ... ok
Test that a TransportData object can be pickled and unpickled with no loss of information. ... ok
Test that the TransportData polarizability property was properly set. ... ok
Test that a TransportData object can be reconstructed from its repr() output with no loss of information ... ok
Test that the TransportData rotrelaxcollnum property was properly set. ... ok
Test that the TransportData shapeIndex property was properly set. ... ok
Test that the TransportData sigma property was properly set. ... ok
testJoback (rmgpy.transportDataTest.TestTransportDatabase) ... ok
Test Joback doesn't crash on Cb desription of beneze ... ok

======================================================================
ERROR: Test that the symmetry contribution is correctly added for radicals
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/data/thermoTest.py", line 96, in testSymmetryContributionRadicals
    thermoData_ga = self.database.getThermoDataFromGroups(spc)
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/data/thermo.py", line 901, in getThermoDataFromGroups
    tdata = self.estimateThermoViaGroupAdditivity(molecule)
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/data/thermo.py", line 999, in estimateThermoViaGroupAdditivity
    thermoData = self.estimateRadicalThermoViaHBI(molecule, self.computeGroupAdditivityThermo)
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/data/thermo.py", line 955, in estimateRadicalThermoViaHBI
    thermoData.S298.value_si -= constants.R * math.log(molecule.getSymmetryNumber())
  File "rmgpy/molecule/molecule.py", line 1453, in rmgpy.molecule.molecule.Molecule.getSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:26987)
    self.calculateSymmetryNumber()
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test that the symmetry contribution is correctly added for radicals for Aromatics.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/data/thermoTest.py", line 96, in testSymmetryContributionRadicals
    thermoData_ga = self.database.getThermoDataFromGroups(spc)
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/data/thermo.py", line 901, in getThermoDataFromGroups
    tdata = self.estimateThermoViaGroupAdditivity(molecule)
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/data/thermo.py", line 999, in estimateThermoViaGroupAdditivity
    thermoData = self.estimateRadicalThermoViaHBI(molecule, self.computeGroupAdditivityThermo)
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/data/thermo.py", line 955, in estimateRadicalThermoViaHBI
    thermoData.S298.value_si -= constants.R * math.log(molecule.getSymmetryNumber())
  File "rmgpy/molecule/molecule.py", line 1453, in rmgpy.molecule.molecule.Molecule.getSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:26987)
    self.calculateSymmetryNumber()
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test that the symmetry number getter works properly
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/moleculeTest.py", line 1184, in testGetSymmetryNumber
    self.assertEquals(12, mol.getSymmetryNumber())
  File "rmgpy/molecule/molecule.py", line 1453, in rmgpy.molecule.molecule.Molecule.getSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:26987)
    self.calculateSymmetryNumber()
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Failure: ValueError (rmgpy.molecule.graph.Vertex has the wrong size, try recompiling)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/envs/_test/lib/python2.7/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/Users/rwest/anaconda/envs/_test/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/Users/rwest/anaconda/envs/_test/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "rmgpy/molecule/graph.pxd", line 27, in init rmgpy.molecule.symmetry (build/pyrex/rmgpy/molecule/symmetry.c:12534)
    cdef class Vertex(object):
ValueError: rmgpy.molecule.graph.Vertex has the wrong size, try recompiling

======================================================================
ERROR: Test the Molecule.calculateAtomSymmetryNumber() on CC
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 49, in testAtomSymmetryNumberEthane
    symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAtomSymmetryNumber() on CC(C)C
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 71, in testAtomSymmetryNumberIsobutane
    symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAtomSymmetryNumber() on CH4
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 27, in testAtomSymmetryNumberMethane
    symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAtomSymmetryNumber() on [CH3]
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 38, in testAtomSymmetryNumberMethyl
    symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAtomSymmetryNumber() on CCC
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 60, in testAtomSymmetryNumberPropane
    symmetryNumber *= calculateAtomSymmetryNumber(molecule, atom)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on CC(C)=C=C(CC)CC
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 188, in testAxisSymmetryNumber1
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 2)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on CC=C=[C]
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 174, in testAxisSymmetryNumber12Butadienyl
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 1)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on C=C=CCCC
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 181, in testAxisSymmetryNumber12Hexadienyl
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 1)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on C=C=C(C(C(C(C=C=C)=C=C)=C=C)=C=C)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 195, in testAxisSymmetryNumber2
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 2)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on C=C=C=O
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 210, in testAxisSymmetryNumber4
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 2)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on CC=C=C=O
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 217, in testAxisSymmetryNumber5
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 1)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on C=C=C=N
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 224, in testAxisSymmetryNumber6
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 1)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on C=C=C=[N]
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 231, in testAxisSymmetryNumber7
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 2)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on C=C=C=C
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 153, in testAxisSymmetryNumberButatriene
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 2)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on C=C=C=[CH]
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 160, in testAxisSymmetryNumberButatrienyl
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 1)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on C=C
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 139, in testAxisSymmetryNumberEthylene
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 2)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on C=C=C
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 146, in testAxisSymmetryNumberPropadiene
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 2)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on C=C=[C]
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 167, in testAxisSymmetryNumberPropadienyl
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 2)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateAxisSymmetryNumber() on O=O
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 238, in testAxisSymmetryOxygenSinglet
    self.assertEqual(calculateAxisSymmetryNumber(molecule), 1)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateBondSymmetryNumber() on C#C
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 131, in testBondSymmetryNumberAcetylene
    symmetryNumber *= calculateBondSymmetryNumber(molecule, atom1, atom2)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateBondSymmetryNumber() on CCCC
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 107, in testBondSymmetryNumberButane
    symmetryNumber *= calculateBondSymmetryNumber(molecule, atom1, atom2)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateBondSymmetryNumber() on CC
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 83, in testBondSymmetryNumberEthane
    symmetryNumber *= calculateBondSymmetryNumber(molecule, atom1, atom2)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateBondSymmetryNumber() on C=C.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 119, in testBondSymmetryNumberEthylene
    symmetryNumber *= calculateBondSymmetryNumber(molecule, atom1, atom2)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateBondSymmetryNumber() on CCC
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 95, in testBondSymmetryNumberPropane
    symmetryNumber *= calculateBondSymmetryNumber(molecule, atom1, atom2)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateCyclicSymmetryNumber() on C1CCCCC1
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 245, in testCyclicSymmetryNumberCyclohexane
    symmetryNumber = calculateCyclicSymmetryNumber(molecule)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on C#C
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 336, in testSymmetryNumberAcetylene
    self.assertEqual(Molecule().fromSMILES('C#C').calculateSymmetryNumber(), 2)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on C#CC#C
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 342, in testSymmetryNumberButadiyne
    self.assertEqual(Molecule().fromSMILES('C#CC#C').calculateSymmetryNumber(), 2)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on C1=C=C=1
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 384, in testSymmetryNumberCyclic
    self.assertEqual(Molecule().fromSMILES('C1=C=C=1').calculateSymmetryNumber(), 6)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on [C]#[C]
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 324, in testSymmetryNumberDicarbon
    self.assertEqual(Molecule().fromSMILES('[C]#[C]').calculateSymmetryNumber(), 2)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on C=[CH].
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 378, in testSymmetryNumberEthenyl
    self.assertEqual(Molecule().fromSMILES('C=[CH]').calculateSymmetryNumber(), 1)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on C=C
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 372, in testSymmetryNumberEthylene
    self.assertEqual(Molecule().fromSMILES('C=C').calculateSymmetryNumber(), 4)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on C=O
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 354, in testSymmetryNumberFormaldehyde
    self.assertEqual(Molecule().fromSMILES('C=O').calculateSymmetryNumber(), 2)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on [H][H]
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 330, in testSymmetryNumberHydrogen
    self.assertEqual(Molecule().fromSMILES('[H][H]').calculateSymmetryNumber(), 2)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on [OH]
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 312, in testSymmetryNumberHydroxyl
    self.assertEqual(Molecule().fromSMILES('[OH]').calculateSymmetryNumber(), 1)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on CH4
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 348, in testSymmetryNumberMethane
    self.assertEqual(Molecule().fromSMILES('C').calculateSymmetryNumber(), 12)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on [CH3]
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 360, in testSymmetryNumberMethyl
    self.assertEqual(Molecule().fromSMILES('[CH3]').calculateSymmetryNumber(), 6)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on O=O
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 318, in testSymmetryNumberOxygen
    self.assertEqual(Molecule().fromSMILES('O=O').calculateSymmetryNumber(), 2)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on H2O
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 366, in testSymmetryNumberWater
    self.assertEqual(Molecule().fromSMILES('O').calculateSymmetryNumber(), 2)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on C=C=[C]C(C)(C)[C]=C=C
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 299, in testTotalSymmetryNumber1
    self.assertEqual(Molecule().fromSMILES('C=C=[C]C(C)(C)[C]=C=C').calculateSymmetryNumber(), 18)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Species.getSymmetryNumber() (total symmetry) on Cc1ccccc1C
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 275, in testTotalSymmetryNumber12Dimethylbenzene
    symmetryNumber = species.getSymmetryNumber()
  File "rmgpy/species.py", line 362, in rmgpy.species.Species.getSymmetryNumber (build/pyrex/rmgpy/species.c:8007)
    symmetryNumber = numpy.max([mol.getSymmetryNumber() for mol in self.molecule])
  File "rmgpy/molecule/molecule.py", line 1453, in rmgpy.molecule.molecule.Molecule.getSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:26987)
    self.calculateSymmetryNumber()
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Species.getSymmetryNumber() (total symmetry) on c1ccccc1
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 255, in testTotalSymmetryNumberBenzene
    symmetryNumber = species.getSymmetryNumber()
  File "rmgpy/species.py", line 362, in rmgpy.species.Species.getSymmetryNumber (build/pyrex/rmgpy/species.c:8007)
    symmetryNumber = numpy.max([mol.getSymmetryNumber() for mol in self.molecule])
  File "rmgpy/molecule/molecule.py", line 1453, in rmgpy.molecule.molecule.Molecule.getSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:26987)
    self.calculateSymmetryNumber()
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Molecule.calculateSymmetryNumber() on CC
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 293, in testTotalSymmetryNumberEthane
    self.assertEqual(Molecule().fromSMILES('CC').calculateSymmetryNumber(), 18)
  File "rmgpy/molecule/molecule.py", line 1457, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27197)
    def calculateSymmetryNumber(self):
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object

======================================================================
ERROR: Test the Species.getSymmetryNumber() (total symmetry) on c1ccccc1C
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/rwest/anaconda/conda-bld/work/rmgpy/molecule/symmetryTest.py", line 265, in testTotalSymmetryNumberToluene
    symmetryNumber = species.getSymmetryNumber()
  File "rmgpy/species.py", line 362, in rmgpy.species.Species.getSymmetryNumber (build/pyrex/rmgpy/species.c:8007)
    symmetryNumber = numpy.max([mol.getSymmetryNumber() for mol in self.molecule])
  File "rmgpy/molecule/molecule.py", line 1453, in rmgpy.molecule.molecule.Molecule.getSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:26987)
    self.calculateSymmetryNumber()
  File "rmgpy/molecule/molecule.py", line 1463, in rmgpy.molecule.molecule.Molecule.calculateSymmetryNumber (build/pyrex/rmgpy/molecule/molecule.c:27123)
    self.symmetryNumber = calculateSymmetryNumber(self)
SystemError: Missing type object
Name                                 Stmts   Miss Branch BrPart  Cover   Missing
--------------------------------------------------------------------------------
rmgpy.py                                57     13     18      4    69%   73, 81-84, 106-109, 115, 118-122, 70->73, 103->106, 114->115, 116->118
rmgpy/cantherm.py                        5      0      0      0   100%   
rmgpy/cantherm/common.py                 9      4      2      0    45%   43-46
rmgpy/cantherm/gaussian.py             219    124    112      4    42%   57-72, 85-111, 120-162, 299, 303, 310-337, 345-399, 407-423, 187->247, 227->244, 298->299, 301->303
rmgpy/cantherm/geometry.py              74     25     14      2    67%   93, 102-103, 130-148, 156-159, 191, 193, 190->191, 192->193
rmgpy/cantherm/input.py                232     56    100     22    71%   82, 90-92, 122-125, 139, 146-148, 169, 180-182, 188, 190, 193-194, 206, 212, 219-221, 235, 237, 241, 245-249, 273-274, 280-287, 291-296, 321, 381-383, 387, 396-400, 81->82, 88->90, 94->134, 120->122, 138->139, 144->146, 150->174, 166->169, 179->180, 187->188, 189->190, 191->193, 205->206, 211->212, 215->219, 223->245, 234->235, 236->237, 240->241, 305->307, 386->387, 395->396
rmgpy/cantherm/kinetics.py             126     93     32      4    23%   61, 66, 73-76, 80-85, 95, 98, 103, 106, 111, 114, 122-129, 136-160, 167-217, 227-248, 60->61, 65->66, 72->73, 78->80
rmgpy/cantherm/main.py                  94     67     10      0    26%   45-46, 89-130, 139-168, 174-187, 193-194, 214-238
rmgpy/cantherm/molepro.py               33      2     18      4    88%   64, 87, 57->64, 68->81, 75->81, 84->87
rmgpy/cantherm/output.py                77     66     22      0    11%   47-49, 56-75, 81-94, 101-121, 127-141, 147-149, 155-158, 168-173
rmgpy/cantherm/pdep.py                 408    323    158      3    16%   117, 128, 179, 204, 224-238, 255-266, 270-301, 313-330, 334-366, 370-386, 390-486, 491-555, 568-580, 587-700, 111->117, 122->128, 253->255
rmgpy/cantherm/qchem.py                229    129    108      6    43%   82-107, 116-181, 223, 230, 311, 318-343, 350-384, 392-406, 201->272, 209->272, 222->223, 224->226, 229->230, 308->311
rmgpy/cantherm/statmech.py             532    498    238      0     4%   90, 97-128, 136-153, 158, 168-173, 180-182, 191-411, 415-421, 430-461, 469-499, 516-686, 697-897
rmgpy/cantherm/thermo.py               161    140     32      0    11%   63-64, 71-75, 83-130, 137-213, 225-277
rmgpy/chemkin.py                      1064    648    534     59    35%   92-103, 108-109, 116-117, 120-121, 124-125, 142-145, 157, 204-218, 220-246, 260-269, 274, 277, 297-307, 322-323, 325-326, 342-343, 347, 357-358, 362-365, 376-377, 402, 416-421, 436-437, 446-447, 456-479, 483-486, 494-500, 508-511, 515-520, 554-666, 704, 706-707, 731, 735-739, 751-766, 805, 808-812, 830-839, 854, 861-904, 908, 911, 917, 963-967, 976, 979, 987-988, 1013-1014, 1019-1024, 1042-1044, 1050-1052, 1054-1057, 1059-1062, 1065-1066, 1072, 1074-1078, 1115-1132, 1135, 1145, 1151-1158, 1210, 1215-1231, 1238-1243, 1254-1264, 1274-1326, 1337-1406, 1414-1462, 1479-1649, 1659-1679, 1689-1692, 1702-1716, 1740-1763, 1782-1828, 1837-1868, 104->87, 107->108, 156->157, 203->204, 219->220, 256->260, 273->274, 276->277, 296->297, 321->322, 324->325, 339->342, 346->347, 354->357, 361->362, 400->402, 414->416, 445->446, 454->456, 482->483, 493->494, 512->515, 551->554, 668->679, 703->704, 705->706, 730->731, 782->785, 802->810, 804->805, 807->808, 829->830, 853->854, 859->861, 905->908, 910->911, 916->917, 962->963, 974->-938, 975->976, 978->979, 983->987, 1012->1013, 1041->1042, 1053->1054, 1058->1059, 1064->1065, 1071->1072, 1105->1117, 1112->1115, 1134->1135, 1144->1145, 1146->1148, 1149->1151, 1177->1204, 1204->1208, 1208->1210, 1211->1215, 1466->-1466
rmgpy/data.py                            0      0      0      0   100%   
rmgpy/data/base.py                     698    470    306     22    30%   43-45, 121, 124-127, 130, 133-136, 230-232, 249-270, 276-293, 300-319, 325-351, 362-380, 393-449, 458, 470, 477, 487-488, 491, 511-521, 528-558, 567-622, 629-637, 645-742, 749-755, 762-774, 781-815, 825, 831-837, 843-848, 857-861, 870-883, 922-923, 928, 930, 941-946, 985, 996, 1001, 1016, 1023-1027, 1047, 1058-1064, 1071-1080, 1094-1101, 1119, 1129, 1151-1154, 1167, 1177-1181, 1193-1197, 1219-1238, 1244-1245, 1251, 1259-1272, 1286-1307, 457->458, 469->470, 476->477, 481->484, 490->491, 855->857, 920->922, 927->928, 929->930, 937->942, 940->941, 984->985, 994->1001, 995->996, 1015->1016, 1046->1047, 1118->1119, 1121->1124, 1128->1129, 1145->1147, 1149->1151, 1166->1167
rmgpy/data/kinetics.py                   7      0      0      0   100%   
rmgpy/data/kinetics/common.py          130    117     72      0     6%   107-108, 117-229, 241-287
rmgpy/data/kinetics/database.py        279    221    128      9    18%   82-87, 93-95, 102-104, 114-129, 143-153, 157-159, 161-163, 170-172, 178, 186-191, 201-227, 234-238, 245-259, 266-270, 277-284, 291-310, 317-352, 360-363, 371-376, 384-400, 413-422, 443-536, 138->142, 139->138, 142->143, 155->157, 160->161, 169->170, 177->178, 179->186, 180->179
rmgpy/data/kinetics/depository.py       56     42     16      0    19%   63-76, 82, 101, 114, 117, 123-158, 189-204, 210
rmgpy/data/kinetics/family.py          884    818    486      0     5%   93-106, 112, 131, 159, 167, 175-191, 202-284, 291, 298, 344-355, 365-425, 432-467, 473-484, 490-513, 526-605, 613-614, 621-625, 631-633, 639, 645-648, 655-656, 662-709, 720-804, 811, 818-821, 828-928, 937-940, 947-950, 963-1073, 1088-1131, 1138-1143, 1153-1179, 1188-1197, 1210-1245, 1252-1261, 1275-1475, 1483-1562, 1570, 1579-1584, 1594-1602, 1610-1613, 1626-1676, 1684-1692, 1699-1701, 1709-1714
rmgpy/data/kinetics/groups.py          291    274    174      0     4%   68-69, 75-82, 101-165, 175-201, 210-262, 275-542
rmgpy/data/kinetics/library.py         263    233    142      0     7%   89, 107, 120, 130-137, 147-162, 169-224, 228-262, 286-291, 306, 312-346, 356-360, 370-531
rmgpy/data/kinetics/rules.py           304    277    133      0     6%   59, 78-93, 99, 107-155, 162-188, 196-244, 252-319, 326-333, 340, 347, 354-367, 374-391, 397-459, 470-496, 503-567
rmgpy/data/reference.py                138    114     48      0    13%   89-95, 102-108, 114-132, 158-162, 169-183, 190-200, 226-231, 238-251, 258-269, 292-294, 301-311, 318-326
rmgpy/data/rmg.py                       87     66     14      0    21%   56-71, 92-104, 111-112, 119-120, 127-128, 141-156, 167-168, 175-176, 183-193, 201-208, 214-219
rmgpy/data/solvation.py                423    148    110      6    65%   50-122, 175, 246, 296, 324-329, 352, 359, 366, 407, 415, 422, 446-451, 457-459, 501-504, 511-513, 520-522, 530-545, 561-574, 612-624, 704-707, 710-713, 715-719, 739-741, 799-803, 838-842, 243->246, 703->704, 709->710, 714->715, 738->739, 837->838
rmgpy/data/statmech.py                 298    247    104      0    13%   48-86, 93-96, 103-111, 122, 135-137, 152, 162, 174, 189, 196, 203, 214, 226-234, 249, 256, 263, 270-277, 286-301, 311-347, 356-437, 447-459, 465-471, 477-480, 487-492, 499-500, 507-519, 526-528, 535-539, 546-548, 555-557, 564-566, 574-591, 608-621, 634-642, 650-655, 663-666, 675, 688-689, 697-704
rmgpy/data/statmechfit.py              248    213     70      0    11%   95-137, 151-193, 207-244, 260-307, 316-319, 327-330, 338-343, 352-355, 364-366, 378-381, 384-407, 419-422, 425-457, 469-472, 475-506
rmgpy/data/thermo.py                   506    318    200     24    34%   61-129, 136-154, 174, 193-204, 210, 237, 241-242, 259, 266, 273, 314, 322, 329, 355-361, 367-370, 380, 410, 432-436, 443-445, 452-454, 461-463, 471-538, 553-564, 574-617, 634-744, 765-783, 793, 798, 807-808, 827-843, 853-864, 902-911, 930-934, 939, 944, 950, 960-983, 1000-1007, 1043-1047, 1052, 1058, 1064-1088, 1098, 1127, 1129, 1133-1137, 1148, 236->237, 240->241, 377->380, 402->400, 409->410, 764->765, 788->798, 792->793, 806->807, 809->812, 812->-800, 898->904, 928->930, 937->939, 943->944, 947->950, 998->1003, 1049->1053, 1063->1064, 1097->1098, 1126->1127, 1128->1129, 1132->1133, 1147->1148
rmgpy/data/transport.py                267    133     72      9    45%   51-107, 159, 166, 173, 194, 212, 219, 226, 247-252, 258-260, 304-307, 314-316, 323-325, 335-349, 357-369, 380-384, 411, 443-464, 486-487, 514, 522, 524, 528-532, 549-582, 193->194, 279->277, 286->-270, 410->411, 440->443, 513->514, 521->522, 523->524, 527->528
rmgpy/display.py                        12      6      2      0    43%   37, 45-49
rmgpy/kinetics.py                        6      0      0      0   100%   
rmgpy/kinetics/diffusionLimited.py      56     43     12      0    19%   16-19, 22, 34-61, 70-86
rmgpy/molecule.py                        5      0      0      0   100%   
rmgpy/molecule/adjlist.py              593    100    385     57    80%   74-75, 84, 131, 175, 179-181, 191, 233, 240-244, 250-254, 260-265, 272-275, 295, 303, 341, 354, 356, 358, 376, 390-391, 416-418, 451, 456-457, 471, 479-480, 494, 503, 543, 561, 564, 572, 590, 597, 616, 618, 624, 626, 631, 661, 674, 676, 678, 696, 737-738, 746, 776-779, 787, 791, 872-896, 909, 914, 919-920, 937, 978-981, 83->84, 130->131, 174->175, 178->179, 190->191, 202->186, 232->233, 239->240, 249->250, 259->260, 270->272, 294->295, 302->303, 340->341, 353->354, 355->356, 357->358, 373->376, 450->451, 455->456, 470->471, 478->479, 493->494, 502->503, 514->498, 541->564, 542->543, 557->561, 571->572, 586->590, 587->575, 596->597, 615->616, 617->618, 623->624, 625->626, 627->631, 628->608, 660->661, 673->674, 675->676, 677->678, 693->696, 702->707, 743->746, 756->755, 774->776, 784->787, 790->791, 818->817, 841->840, 870->872, 908->909, 911->917, 913->914, 936->937, 977->978
rmgpy/molecule/atomtypedatabase.py      82      6     12      0    94%   17-18, 22-23, 27-28
rmgpy/molecule/draw.py                 952    591    448     59    36%   73-74, 79, 82-85, 144-149, 176-178, 187-192, 200-202, 205-208, 211-213, 216-218, 221-224, 273-281, 294-295, 303-355, 380-382, 391-396, 405-436, 444-454, 461-586, 593-647, 654-726, 739-833, 857-858, 866-867, 882-883, 893, 915-936, 949-951, 965-966, 990-991, 1009-1012, 1018-1019, 1021-1023, 1035-1036, 1065-1066, 1113-1121, 1143-1144, 1157-1160, 1179-1184, 1190-1191, 1220-1221, 1229-1231, 1234-1235, 1243-1245, 1251-1258, 1263-1266, 1275-1278, 1283-1300, 1310-1313, 1317-1320, 1324-1341, 1369-1373, 1387-1510, 78->79, 80->82, 161->172, 174->176, 198->200, 203->205, 209->211, 214->216, 219->221, 270->273, 293->294, 300->303, 379->380, 849->846, 856->857, 892->893, 914->915, 947->949, 1007->1009, 1017->1018, 1020->1021, 1059->1065, 1083->1089, 1110->1124, 1111->1124, 1112->1113, 1142->1143, 1150->1157, 1153->1193, 1177->1193, 1178->1179, 1188->1193, 1189->1190, 1206->1213, 1219->1220, 1224->1228, 1225->1228, 1226->1228, 1228->1229, 1232->1247, 1233->1234, 1238->1242, 1239->1242, 1240->1242, 1242->1243, 1250->1251, 1262->1263, 1270->1274, 1271->1274, 1272->1274, 1274->1275, 1282->1283, 1302->1344, 1305->1309, 1306->1309, 1307->1309, 1309->1310, 1316->1317, 1323->1324
rmgpy/pdep.py                            5      0      0      0   100%   
rmgpy/pdep/draw.py                     297    283     86      0     4%   57-70, 73-79, 87-107, 116-125, 131-145, 151-162, 168-184, 188-216, 224-484
rmgpy/pdep/network.py                  532    408    230      9    19%   51-53, 60, 130, 137-149, 161, 181, 194-261, 272-345, 358, 361, 364, 396, 460-464, 473, 495-515, 529-688, 699-716, 724-738, 745-748, 755-758, 768-771, 774-775, 789-860, 871-925, 938-954, 160->161, 180->181, 356->358, 359->361, 362->364, 395->396, 459->460, 467->475, 469->473
rmgpy/qm.py                              0      0      0      0   100%   
rmgpy/qm/gaussian.py                   141    109     54      2    18%   27-28, 30-31, 51-52, 56-61, 80-139, 145-150, 166-169, 176-201, 209-232, 238, 26->27, 29->30
rmgpy/qm/main.py                        82     25     32      9    63%   69, 76-79, 83, 166-175, 187, 189, 191, 194-205, 68->69, 75->76, 82->83, 141->-133, 165->166, 185->195, 186->187, 188->189, 190->191
rmgpy/qm/molecule.py                   223    163     48      4    24%   10-11, 50, 55-56, 62-63, 66-67, 77, 84, 88, 97-105, 118-139, 143-145, 161-194, 221-225, 236, 244, 249, 253, 258, 263, 269, 275-276, 282-287, 293-295, 301-306, 313, 321-346, 352-360, 366-384, 391, 400-403, 411-413, 419-422, 431-476, 46->50, 54->55, 61->62, 65->66
rmgpy/qm/mopac.py                      147    108     54      3    21%   25, 27, 29, 66-67, 70-75, 94-157, 163, 187-213, 225-248, 266-289, 24->25, 26->27, 28->29
rmgpy/qm/qmdata.py                      35     27      2      0    22%   23-38, 41, 75-101
rmgpy/qm/qmverifier.py                  26     20      6      0    19%   18-24, 40-61, 71
rmgpy/qm/symmetry.py                    81     52     18      0    33%   128-130, 133, 163-169, 174, 180-189, 195-204, 210-222, 231-255
rmgpy/rmg.py                             2      0      0      0   100%   
rmgpy/rmg/input.py                     315    208     99     13    30%   77, 79, 82, 88-90, 96, 101, 107, 110, 125, 128-130, 142, 146-148, 161-182, 192-194, 201, 203, 220-221, 240-278, 290-305, 319-322, 356-359, 379-419, 429-577, 76->77, 78->79, 81->82, 85->88, 95->96, 124->125, 127->128, 136->139, 139->141, 141->142, 145->146, 200->201, 202->203
rmgpy/rmg/main.py                      780    672    308      3    10%   46-47, 194-195, 200-201, 208-216, 222-228, 239-262, 270-272, 276-306, 315-460, 468-658, 669-689, 696-697, 700-710, 716-732, 739-743, 750-816, 822-829, 835-856, 865-878, 891-938, 949-982, 993-1142, 1149-1158, 1169-1211, 1222, 1224-1225, 1228-1243, 1256-1326, 191->193, 193->194, 199->200
rmgpy/rmg/model.py                     935    817    524      9     9%   81, 99-101, 111-173, 181-189, 196-200, 248, 255-318, 346, 350, 383-387, 395-401, 410-412, 433, 439, 448, 466-536, 554-608, 626-637, 643-654, 666-822, 831-898, 905-991, 1000-1036, 1046-1072, 1078, 1086-1171, 1179-1233, 1242-1245, 1255-1256, 1264-1268, 1275-1281, 1289-1299, 1311-1359, 1374-1414, 1428-1453, 1466-1519, 1534-1612, 1623-1626, 1636-1658, 1665-1700, 343->346, 347->350, 382->383, 409->410, 420->427, 422->-403, 427->433, 435->439, 447->448
rmgpy/rmg/output.py                    160    152     68      0     4%   62-363, 371-956
rmgpy/rmg/pdep.py                      312    285    182      0     5%   71-83, 89, 106, 128-131, 134, 140, 143, 150, 156-176, 185-206, 215-237, 244-263, 271-295, 303-313, 320-375, 385-446, 453-631
rmgpy/solver.py                          2      0      0      0   100%   
rmgpy/statmech.py                        5      0      0      0   100%   
rmgpy/thermo.py                          3      0      0      0   100%   
rmgpy/transport.py                      28      5      0      0    82%   33-36, 71
--------------------------------------------------------------------------------
TOTAL                                14016   9959   6043    346    26%   
----------------------------------------------------------------------
Ran 883 tests in 19.362s

FAILED (SKIP=26, errors=47)
make: *** [test] Error 1
TESTS FAILED: rmg-1.0.1-py27_0
rwest commented 8 years ago

Now fixed. See PR #474