def find_species_by_smiles(rmg_spc: list, smiles: str) -> Molecule:
"""
for list of rmg species find species by smiles
:param rmg_spc: list of rmg species list
:param smiles: (str) species as smiles
:return: rmg species
"""
sp1 = Molecule().from_smiles(smiles)
display(sp1)
mol = None
res = sp1.generate_resonance_structures()
for i, x in enumerate(rmg_spc):
for s in res:
if x.is_isomorphic(s):
print(x.molecule)
print(x.thermo.comment)
mol = x
if mol is None:
print("couldn't find the species")
else:
return mol
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