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find_atom_fate.py
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Wed, Aug 14, 18:25

find_atom_fate.py
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from enviPath_python.enviPath import *
from enviPath_python.enviPath import *
from util import *
import getpass
from rdkit import Chem
from rdkit.Chem import Descriptors
#---------------------------#
# enviPath SETTINGS #
#---------------------------#
# enviPath instance - Define the instance to use
INSTANCE_HOST = 'https://envipath.org'
USERNAME = 'anonymous' # TODO USER: enter your username
# MODEL - Define model for relative reasoning and output package
# New enviPath - default relative reasoning model on envipath: BBD - ML - ECC - 2022
EP_MODEL_ID = 'https://envipath.org/package/de0cdca1-c3ff-44ed-8ffd-f29c269bfa55/relative-reasoning/646afb6c-6cfc-4d4b-8d22-e196d849ec73'
# PACKAGE - prepare a new package (manually) and add it's URI here - make sure it is empty / new when running script!
EP_PACKAGE_ID = '' # TODO USER: enter the URI of your results package here to save results to enviPath
#---------------------------#
# PATHWAY SEARCH SETTINGS #
#---------------------------#
# Maximum number of TPs to predict
MAX_TP = 50
# Lower probability threshold
PROBABILITY_THRESHOLD = -1 # any value equal to or lower than the threshold will be excluded
# Set probabilities of 0 to 0.01 to continue having a weighting scheme downstream of the pathway
INCLUDE_0_PROBABILITIES = False
# Follow moiety - only compounds containing moiety in SMILES will be expanded
MOIETY = "" # e.g., "C(F)(F)F"
# To prioritize small compounds in the
SORT_TPS_BY_SIZE = True
SIZE_METRIC = 'carbon_count' # other options: 'size', 'mw'
# Follow labeled atoms
FOLLOW_LABELED_ATOM = True
ATOM_LABEL = '14'
EXPLORE_NON_ZERO_PATHWAYS = False
#---------------------------#
# FILE PATH SETTINGS #
#---------------------------#
# Input/output files
INPUT_FILE_PATH = '../input/input_structures.tsv'
OUTPUT_DIRECTORY = '../output/'
OUTPUT_FILE_TAG = 'TEST'
#---------------------------#
# CONNECT TO ENVIPATH #
#---------------------------#
eP = enviPath(INSTANCE_HOST)
password = getpass.getpass()
eP.login(USERNAME, password)
#---------------------------#
# FUNCTIONS #
#---------------------------#
def __main__(rr_id, pkg_id, tag):
rr = RelativeReasoning(eP.requester, id=rr_id)
pkg = Package(eP.requester, id=pkg_id)
input_list_raw = load_input(INPUT_FILE_PATH)
input_list = label_input_list(input_list_raw)
output_file_path = '{}TP_prediction_{}_top_{}.tsv'.format(OUTPUT_DIRECTORY, tag, MAX_TP)
outfile = open(output_file_path, 'w')
for compound_input in input_list:
result = find_path_to_stable_moiety(compound_input['smiles'], compound_input['name'], rr)
result_list = clean_result(result) # sort and name TPs
pathway_info = upload_envipath_pathway(eP, result_list, pkg)
print_result(outfile, result_list, pathway_info) # continuous writing of result file
def label_input_list(input_list):
isotopomer_list = []
for index, entry in enumerate(input_list):
mol = Chem.MolFromSmiles(entry['smiles'])
# Iterate over the atoms
c_count = 1
for atom in mol.GetAtoms():
if atom.GetSymbol() != 'C':
continue
# For each atom, set the property "atomLabel" to a custom value, let's say a1, a2, a3,...
atom.SetIsotope(14)
smiles = Chem.MolToSmiles(mol, kekuleSmiles=True)
name = entry['name']+'_C{}'.format(c_count)
isotopomer_list.append({'smiles': smiles, 'name': name})
# reset structure
atom.SetIsotope(False)
# mol = Chem.Cleanup(mol)
c_count +=1
return isotopomer_list
def remove_isomer_information(smiles):
mol = Chem.MolFromSmiles(smiles)
for atom in mol.GetAtoms():
atom.SetIsotope(False)
# mol = Chem.Cleanup(mol)
new_smiles = Chem.MolToSmiles(mol, kekuleSmiles=True)
return new_smiles
def get_molecular_weight(smiles):
mol = Chem.MolFromSmiles(smiles)
mw = Descriptors.MolWt(mol)
return mw
def get_carbon_count(smiles):
mol = Chem.MolFromSmiles(smiles)
# Iterate over the atoms to count carbons
c_count = 0
for atom in mol.GetAtoms():
if atom.GetSymbol() == 'C':
c_count += 1
return c_count
def get_size_value(smiles):
if SIZE_METRIC == 'size':
val = len(smiles)
elif SIZE_METRIC == 'mw':
val = get_molecular_weight()
elif SIZE_METRIC == 'carbon_count':
val = get_carbon_count(smiles)
else:
raise ValueError("SIZE_METRIC needs to be set to size, mw, or carbon_count")
return val
def print_result(open_file, result, pathway = None):
header = ('Name\tSMILES\tID\tPersistent_moiety\tPersistent_moiety_unlabeled\tcombined_probability\tgeneration\n')
open_file.write(header)
smallest_TP = result[0]
for TP in result:
if TP[SIZE_METRIC] < smallest_TP[SIZE_METRIC]:
smallest_TP = TP
smallest_TP_unlabeled = remove_isomer_information(smallest_TP['smiles'])
open_file.write('{}\t{}\t{}\t{}\t{}\t{}\t{}\n'.format(pathway['name'],
result[0]['smiles'],
pathway['id'],
smallest_TP['smiles'],
smallest_TP_unlabeled,
smallest_TP['combined_probability'],
smallest_TP['generation'])
)
def find_path_to_stable_moiety(input_smiles, input_name, rr):
print('\n### FIND PATH FOR COMPOUND {} ###\n'.format(input_name))
num_TP = -1 # counter starts at -1, because source compound is also in the TP list
validated_TPs = {} # container for resulting predictions
queued_items = [{'probability': 1, 'combined_probability': 1, 'smiles': input_smiles, 'generation': 0, 'parent': '',
'rules': '', 'name': input_name, SIZE_METRIC: get_size_value(input_smiles)}]
queue = [input_smiles] # queue is updated after each cycle to have top TP first, list of smiles
current_size = 10000
current_stable_moiety = ''
secondary_exploration = False
while num_TP < MAX_TP:
if len(queue) == 0:
print('\nEmpty queue - The exploration of has converged at {} predicted TPs'.format(num_TP))
return validated_TPs # stop TP prediction
smiles = queue.pop(0) # get top item in queue
data = queued_items.pop(0) # get data from queued items for new TP to explore
# if new smiles to expand is bigger than previous smiles -> return
if data[SIZE_METRIC] > current_size and data['combined_probability'] == 0:
# if any compounds in the queue still have combined p > 0, then explore those:
if EXPLORE_NON_ZERO_PATHWAYS:
queue, queued_items = remove_zero_probabilities(queue, queued_items)
secondary_exploration = True
smiles = queue.pop(0) # get top item in queue
data = queued_items.pop(0) # get data from queued items for new TP to explore
# if new smiles to expand is bigger than previous smiles -> return
if data[SIZE_METRIC] > current_size and data['combined_probability'] == 0:
print('\nNo more smaller molecules in queue '
'- The exploration of has converged at {} predicted TPs'.format(num_TP))
print('\nSMILES: {}, Stable moiety: {}, Number of TPs: {}'.format(smiles,
current_stable_moiety,
num_TP))
return validated_TPs # stop TP prediction
result_list = expand_smiles(smiles, rr) # create children
TP_dict = result_to_compound_dict(result_list)
queue, queued_items, validated_TPs = update_queue(queue, queued_items, validated_TPs,
TP_dict, data, secondary_exploration)
validated_TPs[smiles] = data
current_size = data[SIZE_METRIC]
current_stable_moiety = smiles
num_TP += 1
return validated_TPs
def remove_zero_probabilities(_queue, _queued_items):
print("clean queue...")
queue = []
queued_items = []
for entry in _queued_items:
if entry['combined_probability'] > 0:
queue.append(entry['smiles'])
queued_items.append(entry)
return queue, queued_items
def update_queue(_queue,_queued_items, _validated_TPs, _TPs, _parent_data, _secondary_exploration):
parent_probability = _parent_data['combined_probability']
parent_generation = _parent_data['generation']
parent_smiles = _parent_data['smiles']
queue_before = len(_queue)
for smiles in _TPs:
data = _TPs[smiles]
# If the probability is 0 , we don't consider the TP further
this_probability = data['probability']
if this_probability <= PROBABILITY_THRESHOLD:
continue
if _secondary_exploration and this_probability == 0:
continue
# If a moiety is given and it is not in SMILES, we don't follow the TP further
if MOIETY not in smiles:
continue
if FOLLOW_LABELED_ATOM and ATOM_LABEL not in smiles:
continue
if INCLUDE_0_PROBABILITIES and this_probability == 0:
this_probability = 0.01
# add combined probability
this_combined_probability = parent_probability * this_probability
this_generation = parent_generation + 1
rules = data['rules']
# first, check if compound already in validated. if yes, update
if smiles in _validated_TPs.keys():
_validated_TPs[smiles] = update_compound_entry(_validated_TPs[smiles],
this_combined_probability, rules,
this_generation, parent_smiles, size_metric=SIZE_METRIC,
size_value=get_size_value(smiles))
# next, check if compound is already in queue. if yes, update
elif smiles in _queue:
index = _queue.index(smiles)
assert smiles == _queued_items[index]['smiles'], \
'smiles {} does not match smiles in {}'.format(smiles, _queued_items[index])
_queued_items[index] = update_compound_entry(_queued_items[index],
this_combined_probability, rules,
this_generation, parent_smiles, size_metric=SIZE_METRIC,
size_value=get_size_value(smiles))
# else, add new item to queue
else:
data['combined_probability'] = this_combined_probability
data['generation'] = this_generation
data['parent'] = parent_smiles
data[SIZE_METRIC] = get_size_value(smiles)
_queued_items.append(data)
_queue.append(smiles)
assert len(_queued_items) == len(_queue)
# first order dict by combined probability
_queued_items.sort(reverse=True, key=lambda x: x['combined_probability'])
# then sort by size
if SORT_TPS_BY_SIZE:
_queued_items.sort(reverse=False, key=lambda x: x[SIZE_METRIC])
queue_after = len(_queue)
print('Added {} smiles to queue'.format(queue_after - queue_before))
new_queue = [] # resetting queue
[new_queue.append(x['smiles']) for x in _queued_items]
print ('New queue for compound', parent_smiles)
for q in new_queue:
print(q, _queued_items[new_queue.index(q)]['combined_probability'],
_queued_items[new_queue.index(q)][SIZE_METRIC])
return new_queue, _queued_items, _validated_TPs
#---------------------------#
# MAIN #
#---------------------------#
__main__(rr_id = EP_MODEL_ID, pkg_id = EP_PACKAGE_ID, tag = OUTPUT_FILE_TAG)

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