def get_outcomes(self,
smiles,
mincount,
template_prioritization,
start_at=-1,
end_at=-1,
singleonly=True,
stop_if=False,
template_count=10000,
max_cum_prob=1.0):
"""Performs a one-step synthesis reaction for a given SMILES string.
Each candidate in self.result.products is of type ForwardProduct
Args:
smiles (str): SMILES string of ??
mincount (int): Minimum popularity of used templates.
template_prioritization (??): Specifies method to use for ordering
templates.
start_at (int, optional): Index of first prioritized template to
use. (default: {-1})
end_at (int, optional): Index of prioritized template to stop
before. (default: {-1})
singleonly (bool, optional): Whether to reduce each product to the
largest (longest) one. (default: {True})
stop_if (bool or string, optional): SMILES string of molecule to
stop at if found, or False for no target. (default: {False})
template_count (int, optional): Maximum number of templates to use.
(default: {10000})
max_cum_prob (float, optional): Maximum cumulative probability of
all templates used. (default: {1.0})
"""
self.get_template_prioritizers(template_prioritization)
# Get sorted by popularity during loading.
if template_prioritization == gc.popularity:
prioritized_templates = self.templates
else:
self.template_prioritizer.set_max_templates(template_count)
self.template_prioritizer.set_max_cum_prob(max_cum_prob)
prioritized_templates = self.template_prioritizer.get_priority(
(self.templates, smiles))
self.mincount = mincount
self.start_at = start_at
self.singleonly = singleonly
self.stop_if = stop_if
if end_at == -1 or end_at >= len(self.templates):
self.end_at = len(self.templates)
else:
self.end_at = end_at
# Define mol to operate on
mol = Chem.MolFromSmiles(smiles)
clean_reactant_mapping(mol)
[a.SetIsotope(i + 1) for (i, a) in enumerate(mol.GetAtoms())]
reactants_smiles = Chem.MolToSmiles(mol)
smiles = Chem.MolToSmiles(
mol, isomericSmiles=USE_STEREOCHEMISTRY) # to canonicalize
# Initialize results object
if self.celery:
result = []
else:
result = ForwardResult(smiles)
for i in range(self.start_at, self.end_at):
# only use templates between the specified boundaries.
template = prioritized_templates[i]
if template['count'] > mincount:
products = self.apply_one_template(mol,
smiles,
template,
singleonly=singleonly,
stop_if=stop_if)
if self.celery:
for product in products:
result.append({
'smiles_list': product.smiles_list,
'smiles': product.smiles,
'edits': product.edits,
'template_ids': product.template_ids,
'num_examples': product.num_examples
})
else:
result.add_products(products)
return (smiles, result)
def get_outcomes(self,
smiles,
mincount,
template_prioritization,
start_at=-1,
end_at=-1,
singleonly=True,
stop_if=False,
template_count=10000,
max_cum_prob=1.0):
'''
Each candidate in self.result.products is of type ForwardProduct
'''
self.get_template_prioritizers(template_prioritization)
# Get sorted by popularity during loading.
if template_prioritization == gc.popularity:
prioritized_templates = self.templates
else:
self.template_prioritizer.set_max_templates(template_count)
self.template_prioritizer.set_max_cum_prob(max_cum_prob)
prioritized_templates = self.template_prioritizer.get_priority(
(self.templates, smiles))
self.mincount = mincount
self.start_at = start_at
self.singleonly = singleonly
self.stop_if = stop_if
if end_at == -1 or end_at >= len(self.templates):
self.end_at = len(self.templates)
else:
self.end_at = end_at
# Define mol to operate on
mol = Chem.MolFromSmiles(smiles)
clean_reactant_mapping(mol)
reactants_smiles = Chem.MolToSmiles(mol)
smiles = Chem.MolToSmiles(
mol, isomericSmiles=USE_STEREOCHEMISTRY) # to canonicalize
# Initialize results object
if self.celery:
result = []
else:
result = ForwardResult(smiles)
for i in range(self.start_at, self.end_at):
# only use templates between the specified boundaries.
template = prioritized_templates[i]
if template['count'] > mincount:
products = self.apply_one_template(mol,
smiles,
template,
singleonly=singleonly,
stop_if=stop_if)
if self.celery:
for product in products:
result.append({
'smiles_list': product.smiles_list,
'smiles': product.smiles,
'edits': product.edits,
'template_ids': product.template_ids,
'num_examples': product.num_examples
})
else:
result.add_products(products)
return (smiles, result)