def standardise_vendor_compounds(output_file, file_name, limit):
"""Process the given file and standardise the vendor
information, writing it as tab-separated fields to the output.
As we load the Vendor compounds we 'standardise' the SMILES and
determine whether they represent an isomer or not.
:param output_file: The tab-separated standardised output file
:param file_name: The (compressed) file to process
:param limit: Limit processing to this number of values (or all if 0)
:returns: The number of items processed
"""
global vendor_compounds
global num_vendor_mols
global num_vendor_molecule_failures
logger.info('Standardising %s...', file_name)
line_num = 0
num_processed = 0
with open(file_name, 'rt') as input_file:
# Check first line (a space-delimited header).
# This is a basic sanity-check to make sure the important column
# names are what we expect.
hdr = input_file.readline()
field_names = hdr.split()
# Expected minimum number of columns...
if len(field_names) < expected_min_num_cols:
error('expected at least {} columns found {}'.format(
expected_input_cols, len(field_names)))
# Check salient columns (ignoring case)...
for col_num in expected_input_cols:
actual_name = field_names[col_num].strip().lower()
if actual_name != expected_input_cols[col_num]:
error('expected "{}" in column {} found "{}"'.format(
expected_input_cols[col_num], col_num, actual_name))
# Columns look right...
for line in input_file:
line_num += 1
fields = line.split()
if len(fields) <= 1:
continue
if line_num % report_rate == 0:
logger.info(' ...at compound {:,}'.format(line_num))
osmiles = fields[smiles_col]
compound_id = real_prefix + fields[compound_col]
# Add the compound (expected to be unique)
# to our set of 'all compounds'.
if compound_id in vendor_compounds:
error('Duplicate compound ID ({})'.format(compound_id))
vendor_compounds.add(compound_id)
# Standardise and update global maps...
# And try and handle and report any catastrophic errors
# from dependent modules/functions.
std_info = standardise_utils.standardise(osmiles)
if not std_info.std:
num_vendor_molecule_failures += 1
continue
num_vendor_mols += 1
# Write the standardised data
output = [
osmiles, std_info.iso, std_info.noniso, std_info.hac,
compound_id
]
output_file.write('\t'.join(output) + '\n')
# Enough?
num_processed += 1
if limit and num_processed >= limit:
break
return num_processed
def standardise_vendor_compounds(output_file, file_name, limit):
"""Process the given file and standardise the vendor
information, writing it as tab-separated fields to the output.
As we load the Vendor compounds we 'standardise' the SMILES and
determine whether they represent an isomer or not.
:param output_file: The tab-separated standardised output file
:param file_name: The (compressed) file to process
:param limit: Limit processing to this number of values (or all if 0)
:returns: The number of items processed
"""
global vendor_compounds
global num_vendor_mols
global num_vendor_molecule_failures
logger.info('Standardising %s...', file_name)
count = 0
num_processed = 0
with gzip.open(file_name, 'rb') as input:
suppl = Chem.ForwardSDMolSupplier(input)
for mol in suppl:
count += 1
if mol is None:
logger.warning("Failed to handle record %s", count)
continue
chembl_id = mol.GetProp('chembl_id')
if count % report_rate == 0:
logger.info(' ...at compound {:,}'.format(count))
osmiles = Chem.MolToSmiles(mol)
# generate the ID. The data in the chembl_id field looks like CHEMBL153534
# so we need to string off the CHEMBL bit as our generated ID looks like CHEMBL:153534
compound_id = vendor_prefix + chembl_id[6:]
# Add the compound (expected to be unique)
# to our set of 'all compounds'.
if compound_id in vendor_compounds:
error('Duplicate compound ID ({})'.format(compound_id))
vendor_compounds.add(compound_id)
# Standardise and update global maps...
# And try and handle and report any catastrophic errors
# from dependent modules/functions.
std_info = standardise_utils.standardise(osmiles)
if not std_info.std:
num_vendor_molecule_failures += 1
continue
num_vendor_mols += 1
# Write the standardised data
output = [
osmiles, std_info.iso, std_info.noniso, std_info.hac,
compound_id
]
output_file.write('\t'.join(output) + '\n')
# Enough?
num_processed += 1
if limit and num_processed >= limit:
break
return num_processed
