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'rmgpy.species.Species' has no 'clearLabeledAtoms' in makeNewSpecies #35

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rwest opened this issue Jun 10, 2011 · 0 comments
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'rmgpy.species.Species' has no 'clearLabeledAtoms' in makeNewSpecies #35

rwest opened this issue Jun 10, 2011 · 0 comments

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@rwest
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rwest commented Jun 10, 2011

When I run with:

# Data sources
database(
    '../RMG-database/input',
    thermoLibraries = ['primaryThermoLibrary', 'GRI-Mech3.0'],
    reactionLibraries = ['GRI-Mech3.0'],
    seedMechanisms = [],
)

it fails with:

Adding seed mechanism GRI-Mech3.0 to model core...
Traceback (most recent call last):
  File "rmg.py", line 673, in <module>
    execute(args)
  File "rmg.py", line 262, in execute
    reactionModel.addSeedMechanismToCore(database, seedMechanism, react=False)
  File "/Users/rwest/XCodeProjects/RMGpy/RMG-Py/rmgpy/rmg/model.py", line 1305, in addSeedMechanismToCore
    r, isNew = self.makeNewReaction(rxn)
  File "/Users/rwest/XCodeProjects/RMGpy/RMG-Py/rmgpy/rmg/model.py", line 748, in makeNewReaction
    forward.reactants = [self.makeNewSpecies(molecule)[0] for molecule in forward.reactants]
  File "/Users/rwest/XCodeProjects/RMGpy/RMG-Py/rmgpy/rmg/model.py", line 641, in makeNewSpecies
    molecule.clearLabeledAtoms()
AttributeError: 'rmgpy.species.Species' object has no attribute 'clearLabeledAtoms'
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