I'm getting the following errors while trying to get a TS object.
Action Error for this reaction CC1=C[CH]C=CC1=O+CCCCO_CC1=CC=CC=C1O+CCC[CH]O1
ActionError Traceback (most recent call last)
<ipython-input-160-bddd08767730> in <module>
----> 1 rxn.get_labeled_reaction()
~/Code/RMG-Py3/AutoTST/autotst/reaction.py in get_labeled_reaction(self)
337 try:
338 labeled_r, labeled_p = family.get_labeled_reactants_and_products(
--> 339 test_reaction.reactants, test_reaction.products)
340 except ValueError:
341 continue
~/Code/RMG-Py3/RMG-Py/rmgpy/data/kinetics/family.py in get_labeled_reactants_and_products(self, reactants, products)
2672 # raise exception
2673 if num_mappings > 0:
-> 2674 raise ActionError('Something wrong with products that RMG cannot find a match!')
2675
2676 return None, None
ActionError: Something wrong with products that RMG cannot find a match!
while IndexError for this reaction
C1=CC=C(C=CC2=CC=CC=C2)C=C1+[O]O_C(=CC1=CC=CC=C1)=C1C=C[CH]C=C1+OO
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-164-a9a69e534d3e> in <module>
----> 1 rxn.ts
~/Code/RMG-Py3/AutoTST/autotst/reaction.py in ts(self)
116 if self._ts is None:
117 ts_dict = {}
--> 118 for direction, complex in self.get_rmg_complexes().items():
119 ts = TS(
120 reaction_label=self.label,
~/Code/RMG-Py3/AutoTST/autotst/reaction.py in get_rmg_complexes(self)
521
522 if self.rmg_reaction is None:
--> 523 self.get_labeled_reaction()
524
525 reactant_complex = RMGMolecule()
~/Code/RMG-Py3/AutoTST/autotst/reaction.py in get_labeled_reaction(self)
337 try:
338 labeled_r, labeled_p = family.get_labeled_reactants_and_products(
--> 339 test_reaction.reactants, test_reaction.products)
340 except ValueError:
341 continue
~/Code/RMG-Py3/RMG-Py/rmgpy/data/kinetics/family.py in get_labeled_reactants_and_products(self, reactants, products)
2631 # get mappings in forward direction
2632 mappings_a = self._match_reactant_to_template(molecule_a, template.reactants[0].item)
-> 2633 mappings_b = self._match_reactant_to_template(molecule_b, template.reactants[1].item)
2634 mappings = list(itertools.product(mappings_a, mappings_b))
2635 # get
mappings in the reverse direction
IndexError: list index out of range
Both of these errors can be traced back to family.py in rmgpy. The reactions in question are scraped from importer project and were able to make a transition state in py2. I'm seeing these errors after we updated to py3.
I'm getting the following errors while trying to get a TS object. Action Error for this reaction
CC1=C[CH]C=CC1=O+CCCCO_CC1=CC=CC=C1O+CCC[CH]O1
while IndexError for this reaction
C1=CC=C(C=CC2=CC=CC=C2)C=C1+[O]O_C(=CC1=CC=CC=C1)=C1C=C[CH]C=C1+OO
Both of these errors can be traced back to
family.py
in rmgpy. The reactions in question are scraped from importer project and were able to make a transition state in py2. I'm seeing these errors after we updated to py3.