def clean_reaction(self):
"""This function takes reaction smiles of the form:
a.b.c>d.e.f>g.h
and changes them to the form:
a.b.c.d.e.f>>g.h
Unmapped reactants are moved to the agents to create the form:
mapped_reactants>unmapped_reactants>product
Returns:
rsmi (str): Reaction SMILES in the form a.b.c.d.e.f>>g.h
clean_rsmi (str): Reaction SMILES in the form mapped_reactants>unmapped_reactants>product
"""
#Split into Reactants and Products
split_reaction = self.rsmi.split(">")
#Get reactant and product smiles string with . separators
reactants = split_reaction[0]
self.agents = split_reaction[1]
self.products = split_reaction[2]
if len(self.agents) == 0:
self.reactants = reactants
else:
self.reactants = '.'.join([reactants, self.agents])
self.rsmi = '>>'.join([self.reactants, self.products])
reaction = rdChemReactions.ReactionFromSmarts(self.rsmi)
reaction.RemoveUnmappedReactantTemplates()
self.clean_rsmi = rdChemReactions.ReactionToSmiles(reaction)
return self.rsmi, self.clean_rsmi
def getReactionFromSmilesFile(smartsfile, rxnfile):
with open(smartsfile) as handler:
smarts = handler.readline()
rxn = rdChemReactions.ReactionFromSmarts(smarts)
smi = rdChemReactions.ReactionToSmiles(rxn)
mdl = rdChemReactions.ReactionToRxnBlock(rxn)
with open(rxnfile, 'w') as handler:
handler.write(mdl)
return storeReaction(smi, rxnfile), smi
def hash_template(self, template):
""" Hashes the reaction template.
Parameters:
template (str): template SMIRKS pattern
Returns:
hashed_template (str): sha224 hash of the template SMIRKS pattern
"""
template = rdChemReactions.ReactionFromSmarts(template)
rdChemReactions.RemoveMappingNumbersFromReactions(template)
template = rdChemReactions.ReactionToSmiles(template)
self.hashed_template = hashlib.sha224(template.encode('utf8')).hexdigest()
return self.hashed_template
def validate_reaction_smiles(reaction_smiles):
"""Validates reaction SMILES.
Args:
reaction_smiles: Text reaction SMILES.
Returns:
Updated reaction SMILES.
Raises:
ValueError: If the reaction contains errors.
"""
try:
reaction = rdChemReactions.ReactionFromSmarts(reaction_smiles,
useSmiles=True)
rdChemReactions.SanitizeRxn(reaction)
except ValueError as error:
raise ValueError(
f'reaction contains errors: {reaction_smiles}') from error
_, num_errors = reaction.Validate()
if num_errors:
raise ValueError(f'reaction contains errors: {reaction_smiles}')
return rdChemReactions.ReactionToSmiles(reaction)
def getReaction(rfile):
rxn = rdChemReactions.ReactionFromRxnFile(rfile)
smi = rdChemReactions.ReactionToSmiles(rxn)
return storeReaction(smi, rfile), smi