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 setup_molecules(self):
merged_reacts = None
merged_prods = None
if len(self.autotst_reaction.rmg_reaction.reactants) == 2:
merged_reacts = Molecule.merge(
self.autotst_reaction.rmg_reaction.reactants[0],
self.autotst_reaction.rmg_reaction.reactants[1])
if len(self.autotst_reaction.rmg_reaction.products) == 2:
merged_prods = Molecule.merge(
self.autotst_reaction.rmg_reaction.products[0],
self.autotst_reaction.rmg_reaction.products[1])
return merged_reacts, merged_prods
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_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
