def __init__(self, smiles=None, rmg_molecule=None, index=0):
self.energy = None
self.index = index
if (smiles or rmg_molecule):
if smiles and rmg_molecule:
assert rmg_molecule.isIsomorphic(
RMGMolecule(SMILES=smiles)
), "SMILES string did not match RMG Molecule object"
self.smiles = smiles
self.rmg_molecule = rmg_molecule
elif rmg_molecule:
self.rmg_molecule = rmg_molecule
self.smiles = rmg_molecule.toSMILES()
else:
self.smiles = smiles
self.rmg_molecule = RMGMolecule(SMILES=smiles)
self.rmg_molecule.updateMultiplicity()
self.get_mols()
self.get_geometries()
else:
self.smiles = None
self.rmg_molecule = None
self.rdkit_molecule = None
self.ase_molecule = None
self.bonds = []
self.angles = []
self.torsions = []
self.cistrans = []
self.chiral_centers = []
def setUp(self):
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.reaction2 = Reaction(rmg_reaction=RMGReaction(
reactants=[RMGMolecule(smiles="CC"),
RMGMolecule(smiles="[O]O")],
products=[RMGMolecule(smiles="[CH2]C"),
RMGMolecule(smiles="OO")]))
def check_isomorphic(conformer):
"""
Compares whatever is in the log file 'f'
to the SMILES of the passed in 'conformer'
"""
starting_molecule = RMGMolecule(smiles=conformer.smiles)
starting_molecule = starting_molecule.to_single_bonds()
atoms = self.read_log(
os.path.join(scratch_dir, f)
)
test_molecule = RMGMolecule()
test_molecule.from_xyz(
atoms.arrays["numbers"],
atoms.arrays["positions"]
)
if not starting_molecule.is_isomorphic(test_molecule):
logging.info(
"Output geometry of {} is not isomorphic with input geometry".format(calc.label))
return False
else:
logging.info(
"{} was successful and was validated!".format(calc.label))
return True
def get_complexes(self, rmg_reaction=None):
"""
A method to create a forward and reverse TS complexes used to initialize transition state geometries
"""
if not rmg_reaction:
rmg_reaction = self.rmg_reaction
reactant_complex = RMGMolecule()
for react in rmg_reaction.reactants:
if isinstance(react, RMGMolecule):
reactant_complex = reactant_complex.merge(react)
elif isinstance(react, RMGSpecies):
reactant_complex = reactant_complex.merge(react.molecule[0])
product_complex = RMGMolecule()
for prod in rmg_reaction.products:
if isinstance(prod, RMGMolecule):
product_complex = product_complex.merge(prod)
elif isinstance(prod, RMGSpecies):
product_complex = product_complex.merge(prod.molecule[0])
reactant_complex.updateMultiplicity()
product_complex.updateMultiplicity()
self.complexes = {
"forward": reactant_complex,
"reverse": product_complex
}
return self.complexes
def __init__(
self,
smiles=None,
reaction_label=None,
direction='forward',
rmg_molecule=None,
reaction_family="H_Abstraction",
distance_data=None,
index=0):
self.energy = None
#####################################################
#####################################################
assert reaction_label, "A reaction label needs to be provided in addition to a smiles or rmg_molecule"
assert direction in ["forward",
"reverse"], "Please provide a valid direction"
self.reaction_label = reaction_label
self.direction = direction.lower()
self._rdkit_molecule = None
self._ase_molecule = None
self.reaction_family = reaction_family
self.distance_data = distance_data
self.index = index
if (smiles or rmg_molecule):
if smiles and rmg_molecule:
assert rmg_molecule.isIsomorphic(RMGMolecule(
SMILES=smiles)), "SMILES string did not match RMG Molecule object"
self.smiles = smiles
self.rmg_molecule = rmg_molecule
elif rmg_molecule:
self.rmg_molecule = rmg_molecule
self.smiles = rmg_molecule.toSMILES()
else:
self.smiles = smiles
self.rmg_molecule = RMGMolecule(SMILES=smiles)
self.rmg_molecule.updateMultiplicity()
self.get_mols()
self.get_geometries()
self._symmetry_number = None
else:
self.smiles = None
self.rmg_molecule = None
self.rdkit_molecule = None
self._pseudo_geometry = None
self.ase_molecule = None
self.bonds = []
self.angles = []
self.torsions = []
self.cistrans = []
self.chiral_centers = []
self._symmetry_number = None
def test_rmg_reaction(self):
test_reaction = RMGReaction(
reactants=[RMGMolecule(smiles="CC"),
RMGMolecule(smiles="[O]O")],
products=[RMGMolecule(smiles="[CH2]C"),
RMGMolecule(smiles="OO")])
self.assertTrue(
test_reaction.is_isomorphic(self.reaction.get_rmg_reaction()))
self.assertTrue(
test_reaction.is_isomorphic(self.reaction2.get_rmg_reaction()))
def setUp(self):
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.reaction2 = Reaction(rmg_reaction=RMGReaction(
reactants=[RMGMolecule(smiles="CC"),
RMGMolecule(smiles="[O]O")],
products=[RMGMolecule(smiles="[CH2]C"),
RMGMolecule(smiles="OO")]))
self.ts = self.reaction.ts["forward"][0]
self.ts2 = self.reaction.ts["forward"][0]
self.ts.get_molecules()
self.ts2.get_molecules()
def get_rmg_reaction(self):
if self.rmg_reaction:
return self.rmg_reaction
r, p = self.label.split("_")
reactants = []
products = []
for react in r.split("+"):
reactants.append(RMGMolecule(SMILES=react))
for prod in p.split("+"):
products.append(RMGMolecule(SMILES=prod))
self.rmg_reaction = RMGReaction(reactants=reactants, products=products)
return self.rmg_reaction
def __init__(self,
smiles=None,
reaction_label=None,
rmg_molecule=None,
reaction_family="H_Abstraction",
distance_data=None):
self.energy = None
#####################################################
#####################################################
assert reaction_label, "A reaction label needs to be provided in addition to a smiles or rmg_molecule"
self.reaction_label = reaction_label
self._rdkit_molecule = None
self._ase_molecule = None
self.reaction_family = reaction_family
self.distance_data = distance_data
if (smiles or rmg_molecule):
if smiles and rmg_molecule:
assert rmg_molecule.isIsomorphic(
RMGMolecule(SMILES=smiles)
), "SMILES string did not match RMG Molecule object"
self.smiles = smiles
self.rmg_molecule = rmg_molecule
elif rmg_molecule:
self.rmg_molecule = rmg_molecule
self.smiles = rmg_molecule.toSMILES()
else:
self.smiles = smiles
self.rmg_molecule = RMGMolecule(SMILES=smiles)
self.rmg_molecule.updateMultiplicity()
self.get_mols()
self.get_geometries()
else:
self.smiles = None
self.rmg_molecule = None
self.rdkit_molecule = None
self._pseudo_geometry = None
self.ase_molecule = None
self.bonds = []
self.angles = []
self.torsions = []
self.cistrans = []
self.chiral_centers = []
def get_rmg_complexes(self):
"""
A method to create a forward and reverse TS complexes used to initialize transition state geometries
Variables:
- rmg_reaction (RMGReaction): The RMGReaction of interest
Returns:
- complexes (dict): a dictionary containing RMGMolecules of the forward and reverse reaction complexes
"""
if self.rmg_reaction is None:
self.get_labeled_reaction()
reactant_complex = RMGMolecule()
for react in self.rmg_reaction.reactants:
if isinstance(react, RMGMolecule):
reactant_complex = reactant_complex.merge(react)
elif isinstance(react, RMGSpecies):
for mol in react.molecule:
if len(mol.getLabeledAtoms()) > 0:
reactant_complex = reactant_complex.merge(mol)
product_complex = RMGMolecule()
for prod in self.rmg_reaction.products:
if isinstance(prod, RMGMolecule):
product_complex = product_complex.merge(prod)
elif isinstance(prod, RMGSpecies):
for mol in prod.molecule:
if len(mol.getLabeledAtoms()) > 0:
product_complex = product_complex.merge(mol)
reactant_complex.updateMultiplicity()
product_complex.updateMultiplicity()
if len(reactant_complex.getLabeledAtoms()) == 0 or len(
product_complex.getLabeledAtoms()) == 0:
logging.warning(
"REACTING ATOMS LABELES NOT PROVIDED. Please call `Reaction.get_labeled_reaction` to generate labeled complexes"
)
self.complexes = {
"forward": reactant_complex,
"reverse": product_complex
}
return self.complexes
def get_molecules(self):
if not self.rmg_molecule:
self.rmg_molecule = RMGMolecule(SMILES=self.smiles)
self.rdkit_molecule = self.get_rdkit_mol()
self.ase_molecule = self.get_ase_mol()
self.get_geometries()
return self.rdkit_molecule, self.ase_molecule
def test_molecule(self):
"""
Test that a Molecule contains the `id` attribute.
"""
rmg_mol = RMGMolecule(smiles='C')
mol = Molecule(smiles='C')
self.assertIsInstance(mol, RMGMolecule)
self.assertTrue(hasattr(mol, 'id'))
self.assertFalse(hasattr(rmg_mol, 'id'))
def test_labeled_reaction(self):
test_reaction = RMGReaction(
reactants=[RMGMolecule(smiles="CC"),
RMGMolecule(smiles="[O]O")],
products=[RMGMolecule(smiles="[CH2]C"),
RMGMolecule(smiles="OO")])
labeled_reaction, reaction_family = self.reaction.get_labeled_reaction(
)
self.assertEquals(reaction_family.lower(), "h_abstraction")
self.assertTrue(test_reaction.is_isomorphic(labeled_reaction))
merged = labeled_reaction.reactants[0].merge(
labeled_reaction.reactants[1])
self.assertTrue(merged.get_labeled_atoms("*1")[0].is_carbon())
self.assertTrue(merged.get_labeled_atoms("*2")[0].is_hydrogen())
self.assertTrue(merged.get_labeled_atoms("*3")[0].is_oxygen)
merged = labeled_reaction.products[0].merge(
labeled_reaction.products[1])
self.assertTrue(merged.get_labeled_atoms("*3")[0].is_carbon())
self.assertTrue(merged.get_labeled_atoms("*2")[0].is_hydrogen())
self.assertTrue(merged.get_labeled_atoms("*1")[0].is_oxygen)
labeled_reaction, reaction_family = self.reaction2.get_labeled_reaction(
)
self.assertEquals(reaction_family.lower(), "h_abstraction")
self.assertTrue(test_reaction.is_isomorphic(labeled_reaction))
merged = labeled_reaction.reactants[0].merge(
labeled_reaction.reactants[1])
self.assertTrue(merged.get_labeled_atoms("*1")[0].is_carbon())
self.assertTrue(merged.get_labeled_atoms("*2")[0].is_hydrogen())
self.assertTrue(merged.get_labeled_atoms("*3")[0].is_oxygen)
merged = labeled_reaction.products[0].merge(
labeled_reaction.products[1])
self.assertTrue(merged.get_labeled_atoms("*3")[0].is_carbon())
self.assertTrue(merged.get_labeled_atoms("*2")[0].is_hydrogen())
self.assertTrue(merged.get_labeled_atoms("*1")[0].is_oxygen)
def test_labeled_reaction(self):
test_reaction = RMGReaction(
reactants=[RMGMolecule(SMILES="CC"),
RMGMolecule(SMILES="[O]O")],
products=[RMGMolecule(SMILES="[CH2]C"),
RMGMolecule(SMILES="OO")])
labeled_reaction, reaction_family = self.reaction.get_labeled_reaction(
)
self.assertEquals(reaction_family.lower(), "h_abstraction")
self.assertTrue(test_reaction.isIsomorphic(labeled_reaction))
merged = labeled_reaction.reactants[0].merge(
labeled_reaction.reactants[1])
self.assertTrue(merged.getLabeledAtom("*1").isCarbon())
self.assertTrue(merged.getLabeledAtom("*2").isHydrogen())
self.assertTrue(merged.getLabeledAtom("*3").isOxygen)
merged = labeled_reaction.products[0].merge(
labeled_reaction.products[1])
self.assertTrue(merged.getLabeledAtom("*3").isCarbon())
self.assertTrue(merged.getLabeledAtom("*2").isHydrogen())
self.assertTrue(merged.getLabeledAtom("*1").isOxygen)
labeled_reaction, reaction_family = self.reaction2.get_labeled_reaction(
)
self.assertEquals(reaction_family.lower(), "h_abstraction")
self.assertTrue(test_reaction.isIsomorphic(labeled_reaction))
merged = labeled_reaction.reactants[0].merge(
labeled_reaction.reactants[1])
self.assertTrue(merged.getLabeledAtom("*1").isCarbon())
self.assertTrue(merged.getLabeledAtom("*2").isHydrogen())
self.assertTrue(merged.getLabeledAtom("*3").isOxygen)
merged = labeled_reaction.products[0].merge(
labeled_reaction.products[1])
self.assertTrue(merged.getLabeledAtom("*3").isCarbon())
self.assertTrue(merged.getLabeledAtom("*2").isHydrogen())
self.assertTrue(merged.getLabeledAtom("*1").isOxygen)
def get_complexes(self, rmg_reaction=None):
"""
A method to create a forward and reverse TS complexes used to initialize transition state geometries
Variables:
- rmg_reaction (RMGReaction): The RMGReaction of interest
Returns:
- complexes (dict): a dictionary containing RMGMolecules of the forward and reverse reaction complexes
"""
if not rmg_reaction:
rmg_reaction = self.rmg_reaction
reactant_complex = RMGMolecule()
for react in rmg_reaction.reactants:
if isinstance(react, RMGMolecule):
reactant_complex = reactant_complex.merge(react)
elif isinstance(react, RMGSpecies):
for mol in react.molecule:
if len(mol.getLabeledAtoms()) > 0:
reactant_complex = reactant_complex.merge(mol)
product_complex = RMGMolecule()
for prod in rmg_reaction.products:
if isinstance(prod, RMGMolecule):
product_complex = product_complex.merge(prod)
elif isinstance(prod, RMGSpecies):
for mol in prod.molecule:
if len(mol.getLabeledAtoms()) > 0:
product_complex = product_complex.merge(mol)
reactant_complex.updateMultiplicity()
product_complex.updateMultiplicity()
self.complexes = {
"forward": reactant_complex,
"reverse": product_complex}
return self.complexes
def calculate_symmetry_number(self):
numbers = self.ase_molecule.numbers
positions = self.ase_molecule.positions
mol = RMGMolecule()
mol.from_xyz(numbers, positions)
try:
species = RMGSpecies(molecule=[mol])
self._symmetry_number = species.get_symmetry_number()
except ValueError:
self._symmetry_number = mol.get_symmetry_number()
return self._symmetry_number
def validate_irc(self, calc=None):
"""
A method to verify an IRC calc
"""
assert "irc" in calc.label, "The calculator provided is not an IRC calculator"
reaction_label = calc.label.split("_irc")[0]
logging.info("Validating IRC file...")
irc_path = os.path.join(calc.scratch, calc.label + ".log")
if not os.path.exists(irc_path):
logging.info("It seems that the IRC claculation has not been run.")
return False
f = open(irc_path, "r")
file_lines = f.readlines()[-5:]
completed = False
for file_line in file_lines:
if "Normal termination" in file_line:
logging.info("IRC successfully ran")
completed = True
if not completed:
logging.info("IRC failed... could not be validated...")
return False
pth1 = list()
steps = list()
with open(irc_path) as outputFile:
for line in outputFile:
line = line.strip()
if line.startswith('Point Number:'):
if int(line.split()[2]) > 0:
if int(line.split()[-1]) == 1:
ptNum = int(line.split()[2])
pth1.append(ptNum)
else:
pass
elif line.startswith('# OF STEPS ='):
numStp = int(line.split()[-1])
steps.append(numStp)
# This indexes the coordinate to be used from the parsing
if steps == []:
logging.error('No steps taken in the IRC calculation!')
return False
else:
pth1End = sum(steps[:pth1[-1]])
# Compare the reactants and products
ircParse = ccread(irc_path)
# cf.
# http://cclib.sourceforge.net/wiki/index.php/Using_cclib#Additional_information
atomcoords = ircParse.atomcoords
atomnos = ircParse.atomnos
# Convert the IRC geometries into RMG molecules
# We don't know which is reactant or product, so take the two at the end of the
# paths and compare to the reactants and products
mol1 = RMGMolecule()
mol1.fromXYZ(atomnos, atomcoords[pth1End])
mol2 = RMGMolecule()
mol2.fromXYZ(atomnos, atomcoords[-1])
testReaction = RMGReaction(
reactants=mol1.split(),
products=mol2.split(),
)
r, p = reaction_label.split("_")
reactants = []
products = []
for react in r.split("+"):
react = RMGMolecule(SMILES=react)
reactants.append(react)
for prod in p.split("+"):
prod = RMGMolecule(SMILES=prod)
products.append(prod)
possible_reactants = []
possible_products = []
for reactant in reactants:
possible_reactants.append(
reactant.generate_resonance_structures())
for product in products:
possible_products.append(
product.generate_resonance_structures())
possible_reactants = list(itertools.product(*possible_reactants))
possible_products = list(itertools.product(*possible_products))
for possible_reactant in possible_reactants:
reactant_list = []
for react in possible_reactant:
reactant_list.append(react.toSingleBonds())
for possible_product in possible_products:
product_list = []
for prod in possible_product:
product_list.append(prod.toSingleBonds())
targetReaction = RMGReaction(reactants=list(reactant_list),
products=list(product_list))
if targetReaction.isIsomorphic(testReaction):
logging.info("IRC calculation was successful!")
return True
logging.info("IRC calculation failed for {} :(".format(calc.label))
return False
def __init__(self,
label=None,
rmg_reaction=None,
reaction_family="H_Abstraction",
calculator=None):
self.possible_families = [ # These families (and only these) will be loaded from both RMG and AutoTST databases
"R_Addition_MultipleBond", "H_Abstraction", "intra_H_migration"
]
self.load_databases()
self.calculator = calculator
if rmg_reaction:
self.rmg_reaction, self.reaction_family = self.get_labeled_reaction(
rmg_reaction=rmg_reaction)
if label:
try:
reactants = []
products = []
r, p = label.split("_")
for react in r.split("+"):
reactants.append(RMGMolecule(SMILES=react))
for prod in p.split("+"):
products.append(RMGMolecule(SMILES=prod))
test_reaction = RMGReaction(reactants=reactants,
products=products)
if self.rmg_reaction.isIsomorphic(test_reaction):
self.label = label
self.generate_reactants_and_products()
else:
logging.info(
"Label provided doesn't match the RMGReaction, creating a new label"
)
self.label = self.get_reaction_label(self.rmg_reaction)
self.generate_reactants_and_products()
except BaseException:
logging.info(
"Label provided doesn't match the RMGReaction, creating a new label"
)
self.label = self.get_reaction_label(self.rmg_reaction)
self.generate_reactants_and_products()
else:
self.label = self.get_reaction_label(self.rmg_reaction)
self.generate_reactants_and_products()
elif label:
try:
self.rmg_reaction, self.reaction_family = self.get_labeled_reaction(
label=label)
self.label = label
self.generate_reactants_and_products(self.rmg_reaction)
except BaseException:
logging.info(
"Label provided is not valid... setting everything to None"
)
self.rmg_reaction = None
self.label = None
self.reaction_family = reaction_family
else:
self.rmg_reaction = None
self.reaction_family = reaction_family
self.label = label
# a bit clumsy, but saves refactoring code for now.
self.ts_database = self.ts_databases[reaction_family]
self._ts = None
self._distance_data = None
def get_labeled_reaction(self, label=None, rmg_reaction=None):
"""
A method that will return a labeled reaction given a reaction label or rmg_reaction
"""
assert (
label
or rmg_reaction), "You must provide a reaction or a reaction label"
label_reaction = None
rmg_reaction_reaction = None
if label:
rmg_reactants = []
rmg_products = []
r, p = label.split("_")
for react in r.split("+"):
s = RMGMolecule(SMILES=react)
rmg_reactants.append(s)
for prod in p.split("+"):
s = RMGMolecule(SMILES=prod)
rmg_products.append(s)
label_reaction = RMGReaction(reactants=rmg_reactants,
products=rmg_products)
if rmg_reaction:
assert rmg_reaction.isIsomorphic(label_reaction)
test_reaction = label_reaction
else:
test_reaction = label_reaction
elif rmg_reaction:
rmg_reactants = []
rmg_products = []
for react in rmg_reaction.reactants:
if isinstance(react, RMGSpecies):
rmg_reactants.append(react.molecule)
elif isinstance(react, RMGMolecule):
rmg_reactants.append([react])
for prod in rmg_reaction.products:
if isinstance(prod, RMGSpecies):
rmg_products.append(prod.molecule)
elif isinstance(prod, RMGMolecule):
rmg_products.append([prod])
test_reactants = []
test_products = []
if len(rmg_reactants) == 1:
test_reactants = rmg_reactants
elif len(rmg_reactants) == 2:
l1, l2 = rmg_reactants
for i in l1:
for j in l2:
test_reactants.append([i, j])
if len(rmg_products) == 1:
test_reactants = rmg_products
elif len(rmg_products) == 2:
l1, l2 = rmg_products
for i in l1:
for j in l2:
test_products.append([i, j])
for test_reactant in test_reactants:
for test_products in test_products:
test_reaction = RMGReaction(reactants=test_reactant,
products=test_products)
if rmg_reaction.isIsomorphic(test_reaction):
break
got_one = False
for name, family in self.rmg_database.kinetics.families.items():
try:
labeled_r, labeled_p = family.getLabeledReactantsAndProducts(
test_reaction.reactants, test_reaction.products)
if not (labeled_r and labeled_p):
continue
got_one = True
except BaseException:
logging.info("Couldn't match {} family...".format(family))
if got_one:
break
assert got_one, "Couldn't find a match"
reaction_list = self.rmg_database.kinetics.generate_reactions_from_families(
test_reaction.reactants,
test_reaction.products,
only_families=[name])
assert reaction_list, "Could not match a reaction to a reaction family..."
for reaction in reaction_list:
if reaction.isIsomorphic(test_reaction):
reaction.reactants = labeled_r
reaction.products = labeled_p
break
return reaction, name
def __init__(self, smiles=[], rmg_species=None):
assert isinstance(smiles, list)
self._conformers = None
if ((len(smiles) != 0) and rmg_species):
# Provide both a list of smiles and an rmg_species
assert isinstance(rmg_species,
(rmgpy.molecule.Molecule, rmgpy.species.Species))
if isinstance(rmg_species, rmgpy.molecule.Molecule):
rmg_species = RMGSpecies(molecule=[rmg_species])
rmg_species.generate_resonance_structures()
else:
rmg_species.generate_resonance_structures()
smiles_list = []
for rmg_mol in rmg_species.molecule:
smiles_list.append(rmg_mol.toSMILES())
for s in smiles_list:
if s in smiles:
continue
if not (s in smiles):
smiles.append(s)
assert len(smiles) == len(
smiles_list
), "The list of smiles presented does not match the possible species provided"
self.smiles = smiles
self.rmg_species = rmg_species
elif (rmg_species and (len(smiles) == 0)):
# RMG species provided, but not smiles
assert isinstance(rmg_species,
(rmgpy.molecule.Molecule, rmgpy.species.Species))
if isinstance(rmg_species, rmgpy.molecule.Molecule):
rmg_species = RMGSpecies(molecule=[rmg_species])
rmg_species.generate_resonance_structures()
else:
rmg_species.generate_resonance_structures()
smiles = []
for rmg_mol in rmg_species.molecule:
smiles.append(rmg_mol.toSMILES())
self.smiles = smiles
self.rmg_species = rmg_species
elif ((not rmg_species) and (len(smiles) != 0)):
# smiles provided but not species
species_list = []
for smile in smiles:
molecule = RMGMolecule(SMILES=smile)
s = RMGSpecies(molecule=[molecule])
s.generate_resonance_structures()
species_list.append(s)
for s1 in species_list:
for s2 in species_list:
assert s1.isIsomorphic(
s2), "SMILESs provided describe different species"
self.smiles = smiles
self.rmg_species = species_list[0]
else:
self.smiles = []
self.rmg_species = rmg_species
def validate_irc(self):
"""
A method to verify an IRC calc
"""
logging.info("Validating IRC file...")
irc_path = os.path.join(
self.directory, "ts", self.conformer.reaction_label, "irc",
self.conformer.reaction_label + "_irc_" +
self.conformer.direction + "_" + str(self.conformer.index) +
".log")
complete, converged = self.verify_output_file(irc_path)
if not complete:
logging.info("It seems that the IRC claculation did not complete")
return False
if not converged:
logging.info("The IRC calculation did not converge...")
return False
pth1 = list()
steps = list()
with open(irc_path) as outputFile:
for line in outputFile:
line = line.strip()
if line.startswith('Point Number:'):
if int(line.split()[2]) > 0:
if int(line.split()[-1]) == 1:
ptNum = int(line.split()[2])
pth1.append(ptNum)
else:
pass
elif line.startswith('# OF STEPS ='):
numStp = int(line.split()[-1])
steps.append(numStp)
# This indexes the coordinate to be used from the parsing
if steps == []:
logging.error('No steps taken in the IRC calculation!')
return False
else:
pth1End = sum(steps[:pth1[-1]])
# Compare the reactants and products
ircParse = ccread(irc_path)
atomcoords = ircParse.atomcoords
atomnos = ircParse.atomnos
mol1 = RMGMolecule()
mol1.fromXYZ(atomnos, atomcoords[pth1End])
mol2 = RMGMolecule()
mol2.fromXYZ(atomnos, atomcoords[-1])
testReaction = RMGReaction(
reactants=mol1.split(),
products=mol2.split(),
)
r, p = self.conformer.reaction_label.split("_")
reactants = []
products = []
for react in r.split("+"):
react = RMGMolecule(SMILES=react)
reactants.append(react)
for prod in p.split("+"):
prod = RMGMolecule(SMILES=prod)
products.append(prod)
possible_reactants = []
possible_products = []
for reactant in reactants:
possible_reactants.append(
reactant.generate_resonance_structures())
for product in products:
possible_products.append(
product.generate_resonance_structures())
possible_reactants = list(itertools.product(*possible_reactants))
possible_products = list(itertools.product(*possible_products))
for possible_reactant in possible_reactants:
reactant_list = []
for react in possible_reactant:
reactant_list.append(react.toSingleBonds())
for possible_product in possible_products:
product_list = []
for prod in possible_product:
product_list.append(prod.toSingleBonds())
targetReaction = RMGReaction(reactants=list(reactant_list),
products=list(product_list))
if targetReaction.isIsomorphic(testReaction):
logging.info("IRC calculation was successful!")
return True
logging.info("IRC calculation failed for {} :(".format(calc.label))
return False
def get_labeled_reaction(self):
"""
A method that will return a labeled reaction given a reaction label or rmg_reaction
A label or an rmg_reaction needs to be provided in order for this method to work.
If both are provided, we assert that the label matches the reaction.
Variables:
- label (str): the reaction label of interest
- rmg_reaction (RMGReaction): the reaction of interest
Returns:
- reaction (RMGReaction): An RMGReaction with labeled reactants and products
- name (str): The string corresponding to the reaction family matched to the reaction of interest
"""
if not (self.rmg_database or self.ts_databases):
self.rmg_database, self.ts_databases = self.load_databases()
assert (self.label or self.rmg_reaction
), "You must provide a reaction or a reaction label"
match = False
if self.label:
rmg_reactants = []
rmg_products = []
r, p = self.label.split("_")
for react in r.split("+"):
s = RMGMolecule(SMILES=react)
rmg_reactants.append(s)
for prod in p.split("+"):
s = RMGMolecule(SMILES=prod)
rmg_products.append(s)
test_reaction = RMGReaction(reactants=rmg_reactants,
products=rmg_products)
if self.rmg_reaction:
assert self.rmg_reaction.isIsomorphic(
test_reaction
), "The reaction label provided does not match the RMGReaction provided..."
for name, family in list(
self.rmg_database.kinetics.families.items()):
if match:
break
try:
labeled_r, labeled_p = family.getLabeledReactantsAndProducts(
test_reaction.reactants, test_reaction.products)
except ValueError:
continue
if not (labeled_r and labeled_p):
continue
if ((len(labeled_r) > 0) and (len(labeled_p) > 0)):
logging.info("Matched reaction to {} family".format(name))
labeled_reactants = deepcopy(labeled_r)
labeled_products = deepcopy(labeled_p)
test_reaction.reactants = labeled_r[:]
test_reaction.products = labeled_p[:]
match = True
final_family = family
final_name = name
break
elif self.rmg_reaction: #RMGReaction but no label
rmg_reactants = []
rmg_products = []
for react in self.rmg_reaction.reactants:
if isinstance(react, RMGSpecies):
rmg_reactants.append(react.molecule)
elif isinstance(react, RMGMolecule):
rmg_reactants.append([react])
for prod in self.rmg_reaction.products:
if isinstance(prod, RMGSpecies):
rmg_products.append(prod.molecule)
elif isinstance(prod, RMGMolecule):
rmg_products.append([prod])
test_reactants = []
test_products = []
if len(rmg_reactants) == 1:
for l1 in rmg_reactants[0]:
test_reactants.append([l1])
elif len(rmg_reactants) == 2:
l1, l2 = rmg_reactants
for i in l1:
for j in l2:
test_reactants.append([i, j])
if len(rmg_products) == 1:
for l1 in rmg_products[0]:
test_products.append([l1])
elif len(rmg_products) == 2:
l1, l2 = rmg_products
for i in l1:
for j in l2:
test_products.append([i, j])
reacts = test_reactants[:]
prods = test_products[:]
for name, family in list(
self.rmg_database.kinetics.families.items()):
logging.info("Trying to match {} to {}".format(
self.rmg_reaction, family))
if match:
continue
test_reactants = reacts[:]
test_products = prods[:]
for test_reactant in test_reactants:
for test_product in test_products:
if match:
continue
test_reaction = RMGReaction(reactants=test_reactant,
products=test_product)
try:
labeled_r, labeled_p = family.getLabeledReactantsAndProducts(
test_reaction.reactants,
test_reaction.products)
if not (labeled_r and labeled_p):
logging.info(
"Unable to determine a reaction for the forward direction. Trying the reverse direction."
)
raise ActionError
except (ValueError, ActionError, IndexError):
try:
# Trying the reverse reaction if the forward reaction doesn't work
# This is useful for R_Addition reactions
labeled_r, labeled_p = family.getLabeledReactantsAndProducts(
test_reaction.products,
test_reaction.reactants)
except (ValueError, ActionError, IndexError):
continue
if not (labeled_r and labeled_p):
labeled_r, labeled_p = family.getLabeledReactantsAndProducts(
test_reaction.products,
test_reaction.reactants)
continue
if ((len(labeled_r) > 0) and
(len(labeled_p) > 0)) and (
self.rmg_reaction.isIsomorphic(test_reaction)):
logging.info(
"Matched reaction to {} family".format(name))
labeled_reactants = deepcopy(labeled_r)
labeled_products = deepcopy(labeled_p)
test_reaction.reactants = labeled_r[:]
test_reaction.products = labeled_p[:]
logging.info("{}".format(labeled_r))
logging.info("{}".format(labeled_p))
match = True
final_family = family
print final_family
final_name = name
assert match, "Could not idetify labeled reactants and products"
#try:
reaction_list = final_family.generateReactions(test_reaction.reactants,
test_reaction.products)
#except KeyError:
# reaction_list = None
# logging.info("For some reason, RMG is having trouble generating reactions for {}".format(test_reaction))
assert reaction_list, "Could not match a reaction to a reaction family..."
for reaction in reaction_list:
if test_reaction.isIsomorphic(reaction):
reaction.reactants = labeled_reactants
reaction.products = labeled_products
break
self.rmg_reaction = reaction
self.reaction_family = final_name
return self.rmg_reaction, self.reaction_family
def get_labeled_reaction(self, label=None, rmg_reaction=None):
"""
A method that will return a labeled reaction given a reaction label or rmg_reaction
A label or an rmg_reaction needs to be provided in order for this method to work.
If both are provided, we assert that the label matches the reaction.
Variables:
- label (str): the reaction label of interest
- rmg_reaction (RMGReaction): the reaction of interest
Returns:
- reaction (RMGReaction): An RMGReaction with labeled reactants and products
- name (str): The string corresponding to the reaction family matched to the reaction of interest
"""
assert (
label or rmg_reaction), "You must provide a reaction or a reaction label"
label_reaction = None
rmg_reaction_reaction = None
test_reactions = []
match = False
if label:
rmg_reactants = []
rmg_products = []
r, p = label.split("_")
for react in r.split("+"):
s = RMGMolecule(SMILES=react)
rmg_reactants.append(s)
for prod in p.split("+"):
s = RMGMolecule(SMILES=prod)
rmg_products.append(s)
test_reaction = RMGReaction(
reactants=rmg_reactants, products=rmg_products)
if rmg_reaction:
assert rmg_reaction.isIsomorphic(
test_reaction), "The reaction label provided does not match the RMGReaction provided..."
for name, family in list(self.rmg_database.kinetics.families.items()):
if match:
break
labeled_r, labeled_p = family.getLabeledReactantsAndProducts(
test_reaction.reactants, test_reaction.products)
if not (labeled_r and labeled_p):
continue
if ((len(labeled_r) > 0) and (len(labeled_p) > 0)):
logging.info("Matched reaction to {} family".format(name))
labeled_reactants = deepcopy(labeled_r)
labeled_products = deepcopy(labeled_p)
test_reaction.reactants = labeled_r[:]
test_reaction.products = labeled_p[:]
match = True
final_name = name
break
elif rmg_reaction:
rmg_reactants = []
rmg_products = []
for react in rmg_reaction.reactants:
if isinstance(react, RMGSpecies):
rmg_reactants.append(react.molecule)
elif isinstance(react, RMGMolecule):
rmg_reactants.append([react])
for prod in rmg_reaction.products:
if isinstance(prod, RMGSpecies):
rmg_products.append(prod.molecule)
elif isinstance(prod, RMGMolecule):
rmg_products.append([prod])
test_reactants = []
test_products = []
if len(rmg_reactants) == 1:
test_reactants = rmg_reactants
elif len(rmg_reactants) == 2:
l1, l2 = rmg_reactants
for i in l1:
for j in l2:
test_reactants.append([i, j])
if len(rmg_products) == 1:
test_reactants = rmg_products
elif len(rmg_products) == 2:
l1, l2 = rmg_products
for i in l1:
for j in l2:
test_products.append([i, j])
for name, family in list(self.rmg_database.kinetics.families.items()):
if match:
break
for test_reactant in test_reactants:
for test_products in test_products:
if match:
continue
test_reaction = RMGReaction(
reactants=test_reactant, products=test_products)
labeled_r, labeled_p = family.getLabeledReactantsAndProducts(
test_reaction.reactants, test_reaction.products)
if not (labeled_r and labeled_p):
continue
if ((len(labeled_r) > 0) and (len(labeled_p) > 0)):
logging.info(
"Matched reaction to {} family".format(name))
labeled_reactants = deepcopy(labeled_r)
labeled_products = deepcopy(labeled_p)
test_reaction.reactants = labeled_r[:]
test_reaction.products = labeled_p[:]
logging.info("\n{}".format(labeled_r))
logging.info("\n{}".format(labeled_p))
match = True
final_name = name
break
assert match, "Could not idetify labeled reactants and products"
reaction_list = self.rmg_database.kinetics.generate_reactions_from_families(
test_reaction.reactants, test_reaction.products, only_families=[final_name])
assert reaction_list, "Could not match a reaction to a reaction family..."
for reaction in reaction_list:
if test_reaction.isIsomorphic(reaction):
reaction.reactants = labeled_reactants
reaction.products = labeled_products
break
return reaction, name
def __init__(self, smiles=[], rmg_species=None):
"""
A class that holds information for Species object
"""
assert isinstance(smiles, list)
self._conformers = None
if ((len(smiles) != 0) and rmg_species):
# Provide both a list of smiles and an rmg_species
assert isinstance(
rmg_species,
(rmgpy.molecule.Molecule,
rmgpy.species.Species))
if isinstance(rmg_species, rmgpy.molecule.Molecule):
rmg_species = RMGSpecies(molecule=[rmg_species])
try:
rmg_species.generate_resonance_structures()
except:
logging.info(
"Could not generate resonance structures for this species... Using molecule provided")
else:
try:
rmg_species.generate_resonance_structures()
except:
logging.info(
"Could not generate resonance structures for this species... Using molecule provided")
smiles_list = []
for rmg_mol in rmg_species.molecule:
smiles_list.append(rmg_mol.toSMILES())
for s in smiles_list:
if s in smiles:
continue
if not(s in smiles):
smiles.append(s)
assert len(smiles) == len(
smiles_list), "The list of smiles presented does not match the possible species provided"
self.smiles = smiles
self.rmg_species = rmg_species
elif (rmg_species and (len(smiles) == 0)):
# RMG species provided, but not smiles
assert isinstance(
rmg_species,
(rmgpy.molecule.Molecule,
rmgpy.species.Species))
if isinstance(rmg_species, rmgpy.molecule.Molecule):
rmg_species = RMGSpecies(molecule=[rmg_species])
try:
rmg_species.generate_resonance_structures()
except:
logging.info(
"Could not generate resonance structures for this species... Using molecule provided")
else:
try:
rmg_species.generate_resonance_structures()
except:
logging.info(
"Could not generate resonance structures for this species... Using molecule provided")
smiles = []
for rmg_mol in rmg_species.molecule:
smiles.append(rmg_mol.toSMILES())
self.smiles = smiles
self.rmg_species = rmg_species
elif ((not rmg_species) and (len(smiles) != 0)):
# smiles provided but not species
species_list = []
for smile in smiles:
molecule = RMGMolecule(SMILES=smile)
species_list.append(molecule.generate_resonance_structures())
if len(smiles) != 1:
got_one = False
for s1 in species_list:
for s2 in species_list:
for m1 in s1:
for m2 in s2:
if m1.isIsomorphic(m2):
got_one = True
assert got_one, "SMILESs provided describe different species"
smiles_list = []
for mol in species_list[0]:
smiles_list.append(mol.toSMILES())
self.smiles = smiles_list
self.rmg_species = species_list[0]
else:
self.smiles = []
self.rmg_species = rmg_species
def update_dictionary_entries(old_entries, need_to_add):
"""
Expects dictionary of species entries and
unique list of species (as SMILES) that need to be added
Creates new entries for the species that need to be added
Returns old and new entries
"""
list(set(need_to_add))
for j, species in enumerate(need_to_add):
molecule = RMGMolecule(SMILES=species)
adjlist = molecule.toAdjacencyList()
multiplicity = None
if re.search('(?<=multiplicity ).*', adjlist):
multiplicity = int(
re.search('(?<=multiplicity ).*', adjlist).group(0))
adjlist = re.sub(r'multiplicity .*',
'multiplicity [{}]'.format(multiplicity), adjlist)
group = rmgpy.molecule.group.Group()
group.fromAdjacencyList(adjlist)
atom_counts = {}
rel_label = ''
for atom in ['C', 'H', 'O']:
count = species.count(atom)
if count > 0:
rel_label = rel_label + atom + str(count)
assert rel_label != ''
"""
3 Scenerios:
No old -> no need for ID number: max_ID = -1
Only one old -> needs to have ID of 1: max_ID = 0
Multiple old -> needs to have a unique ID: max_ID > 0
"""
new_ID = None
max_ID = -1
duplicate = False
for old_label in old_entries:
old_entry = old_entries[old_label]
if group.isIsomorphic(old_entry.item):
duplicate = True
print '{} found to be duplicate'.format(old_entry)
continue
if rel_label not in old_label:
continue
if rel_label == old_label and max_ID == -1:
# Atleast one with same label
max_ID = 0
if old_label.find('-') > 0:
old_label, ID_str = old_label.split('-')
ID = int(ID_str)
if old_label == rel_label and ID > max_ID:
# Multiple exisitng labels
max_ID = ID
if max_ID > -1:
# Existing label
new_ID = max_ID + 1
rel_label = rel_label + '-' + str(new_ID)
if not duplicate:
entry = Entry()
entry.label = rel_label
entry.item = group
assert rel_label not in old_entries.keys()
old_entries[rel_label] = entry
entry_labels = [old_entries[key].label for key in old_entries]
assert len(entry_labels) == len(list(
set(entry_labels))), 'Non-unique labels in dictionary'
return old_entries
def calculate_conformer(self, conformer, calculator):
if isinstance(calculator, Gaussian):
calc = calculator.get_conformer_calc(conformer=conformer,
convergence='Tight')
else:
calc = calculator.get_conformer_calc(conformer=conformer)
scratch = calculator.scratch
scratch_dir = os.path.join(calculator.scratch, "species",
conformer.smiles, "conformers")
f = calc.label + ".log"
if not os.path.exists(os.path.join(scratch_dir, f)):
logging.info("Submitting conformer calculation for {}".format(
calc.label))
label = self.submit_conformer(conformer, calc, "general")
while not self.check_complete(label):
time.sleep(15)
else:
logging.info(
"It appears that we already have a complete log file for {}".
format(calc.label))
complete, converged = calculator.verify_output_file(
os.path.join(scratch_dir, f))
if not complete:
logging.info(
"It seems that the file never completed for {} completed, running it again"
.format(calc.label))
label = self.submit_conformer(conformer, calc, "general")
while not self.check_complete(label):
time.sleep(15)
complete, converged = calculator.verify_output_file(
os.path.join(scratch_dir, f))
if (complete and converged):
logging.info("{} was successful and was validated!".format(
calc.label))
atoms = self.read_log(os.path.join(scratch_dir, f))
starting_molecule = RMGMolecule(SMILES=conformer.smiles)
starting_molecule = starting_molecule.toSingleBonds()
test_molecule = RMGMolecule()
test_molecule.fromXYZ(atoms.arrays["numbers"],
atoms.arrays["positions"])
if not starting_molecule.isIsomorphic(test_molecule):
logging.info(
"Output geometry of {} is not isomorphic with input geometry"
.format(calc.label))
result = False
else:
logging.info("{} was successful and was validated!".format(
calc.label))
result = True
if not complete:
logging.info("It appears that {} was killed prematurely".format(
calc.label))
result = False
elif not converged:
logging.info("{} did not converge".format(calc.label))
result = False
if isinstance(calculator, Gaussian):
if not calc.convergence.lower() in [
"tight", "verytight", "loose"
]:
logging.info("{} failed QM optimization".format(
calc.label))
else:
logging.info(
"Resubmitting {} with default convergence criteria".
format(calc.label))
atoms = self.read_log(os.path.join(scratch_dir, f))
conformer.ase_molecule = atoms
conformer.update_coords_from("ase")
calc = calculator.get_conformer_calc(conformer,
convergence="")
logging.info(
"Removing the old log file that didn't converge, restarting from last geometry"
)
os.remove(os.path.join(scratch_dir, f))
label = self.submit_conformer(conformer, calc, "general")
while not self.check_complete(label):
time.sleep(15)
scratch_dir = os.path.join(calculator.scratch, "species",
conformer.smiles, "conformers")
f = calc.label + ".log"
if not os.path.exists(os.path.join(scratch_dir, f)):
logging.info(
"It seems that {} was never run...".format(
calc.label))
result = False
complete, converged = calculator.verify_output_file(
os.path.join(scratch_dir, f))
if not complete:
logging.info(
"It appears that {} was killed prematurely".format(
calc.label))
result = False
elif not converged:
logging.info("{} failed second QM optimization".format(
calc.label))
result = False
else:
atoms = self.read_log(os.path.join(scratch_dir, f))
starting_molecule = RMGMolecule(
SMILES=conformer.smiles)
starting_molecule = starting_molecule.toSingleBonds()
test_molecule = RMGMolecule()
test_molecule.fromXYZ(atoms.arrays["numbers"],
atoms.arrays["positions"])
if not starting_molecule.isIsomorphic(test_molecule):
logging.info(
"Output geometry of {} is not isomorphic with input geometry"
.format(calc.label))
result = False
else:
logging.info(
"{} was successful and was validated!".format(
calc.label))
result = True
if not result:
fail_dir = os.path.join(scratch_dir, "failures")
try:
os.makedirs(os.path.join(scratch_dir, "failures"))
except OSError:
logging.info("{} already exists...".format(fail_dir))
move(os.path.join(scratch_dir, f),
os.path.join(scratch_dir, "failures", f))
return False
return True
def get_labeled_reaction(self):
"""
A method that will return a labeled reaction given a reaction label or rmg_reaction
A label or an rmg_reaction needs to be provided in order for this method to work.
If both are provided, we assert that the label matches the reaction.
Variables:
- label (str): the reaction label of interest
- rmg_reaction (RMGReaction): the reaction of interest
Returns:
- reaction (RMGReaction): An RMGReaction with labeled reactants and products
- name (str): The string corresponding to the reaction family matched to the reaction of interest
"""
if not (self.rmg_database or self.ts_databases):
self.rmg_database, self.ts_databases = self.load_databases()
assert (self.label or self.rmg_reaction
), "You must provide a reaction or a reaction label"
match = False # We have not found a labeled reaction that matches the one provided.
if self.label: # A reaction label was provided
# Generating lists of lists. Main list is the reactans or products
# Secondary list is composed of the resonance structures for that species
r, p = self.label.split("_")
rmg_reactants = [
RMGMolecule(smiles=smile).generate_resonance_structures()
for smile in r.split("+")
]
rmg_products = [
RMGMolecule(smiles=smile).generate_resonance_structures()
for smile in p.split("+")
]
combos_to_try = list(
itertools.product(list(itertools.product(*rmg_reactants)),
list(itertools.product(*rmg_products))))
# looping though each reaction family and each combination of reactants and products
for name, family in list(
self.rmg_database.kinetics.families.items()):
logging.info("Trying to match reacction to {}".format(family))
for rmg_reactants, rmg_products in combos_to_try:
# Making a test reaction
test_reaction = RMGReaction(reactants=list(rmg_reactants),
products=list(rmg_products))
try: # Trying to label the reaction
labeled_r, labeled_p = family.get_labeled_reactants_and_products(
test_reaction.reactants, test_reaction.products)
except: # Failed to match a reaction to the family
logging.error(
"Couldn't match {} to {}, trying different combination..."
.format(test_reaction, name))
continue
if not (labeled_r and labeled_p):
# Catching an error where it matched the reaction but the reactants and products we not return...
# A weird bug in RMG that I can explain
continue
if ((len(labeled_r) > 0)
and (len(labeled_p) > 0)): # We found a match.
if match:
# We found a match already, but we were able to label the reaction again...
# This would happen if different combinations of resonance structures match up
logging.warning(
"This reaction has been already labeled... \
it seems that resonance structures \for reactants and products exist."
)
logging.warning("Skipping this duplicate for now")
continue
logging.info(
"Matched reaction to {} family".format(name))
# Copying labed reactions and saving them for later
labeled_reactants = deepcopy(labeled_r)
labeled_products = deepcopy(labeled_p)
match_reaction = RMGReaction(
reactants=deepcopy(labeled_r),
products=deepcopy(labeled_p))
# Setting it true that we matche the reaction and remembering the
# RMG reaction family and family name
match = True
final_family = family
final_name = name
elif self.rmg_reaction: #RMGReaction but no label
rmg_reactants = []
rmg_products = []
for react in self.rmg_reaction.reactants:
if isinstance(react, RMGSpecies):
rmg_reactants.append(react.molecule)
elif isinstance(react, RMGMolecule):
rmg_reactants.append(react.generate_resonance_structures())
for prod in self.rmg_reaction.products:
if isinstance(prod, RMGSpecies):
rmg_products.append(prod.molecule)
elif isinstance(prod, RMGMolecule):
rmg_products.append(prod.generate_resonance_structures())
combos_to_try = list(
itertools.product(list(itertools.product(*rmg_reactants)),
list(itertools.product(*rmg_products))))
for name, family in list(
self.rmg_database.kinetics.families.items()):
logging.info("Trying to match reaction to {}".format(name))
for rmg_reactants, rmg_products in combos_to_try:
# Making a test reaction
test_reaction = RMGReaction(reactants=list(rmg_reactants),
products=list(rmg_products))
try: # Trying to label the reaction
labeled_r, labeled_p = family.get_labeled_reactants_and_products(
test_reaction.reactants, test_reaction.products)
if not (labeled_r and labeled_p):
logging.error(
"Unable to determine a reaction for the forward direction. Trying the reverse direction."
)
raise ActionError
except:
try:
# Trying the reverse reaction if the forward reaction doesn't work
# This is useful for R_Addition reactions
labeled_r, labeled_p = family.get_labeled_reactants_and_products(
test_reaction.products,
test_reaction.reactants)
except:
logging.error(
"Couldn't match {} to {}, trying different combination..."
.format(test_reaction, name))
continue
if not (labeled_r and labeled_p):
# Catching an error where it matched the reaction but the reactants and products we not return...
# A weird bug in RMG that I can explain
continue
if ((len(labeled_r) > 0)
and (len(labeled_p) > 0)): # We found a match.
if match:
# We found a match already, but we were able to label the reaction again...
# This would happen if different combinations of resonance structures match up
logging.warning(
"This reaction has been already labeled... \
it seems that resonance structures \for reactants and products exist."
)
logging.warning("Skipping this duplicate for now")
continue
logging.info(
"Matched reaction to {} family".format(name))
# Copying labed reactions and saving them for later
labeled_reactants = deepcopy(labeled_r)
labeled_products = deepcopy(labeled_p)
match_reaction = RMGReaction(
reactants=deepcopy(labeled_r),
products=deepcopy(labeled_p))
# Setting it true that we matche the reaction and remembering the
# RMG reaction family and family name
match = True
final_family = family
final_name = name
assert match, "Could not idetify labeled reactants and products"
reaction_list = final_family.generate_reactions(
match_reaction.reactants, match_reaction.products)
assert reaction_list, "Could not match a reaction to a reaction family..."
for reaction in reaction_list:
if match_reaction.is_isomorphic(reaction):
reaction.reactants = labeled_reactants
reaction.products = labeled_products
break
self.rmg_reaction = reaction
self.reaction_family = final_name
return self.rmg_reaction, self.reaction_family