code stringlengths 3 6.57k |
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C(=O) |
MMPbasedMCSSObjectClass(MMPDataObjectClass) |
__init__(self, logger_object) |
logging.getLogger('lillymol_file_logger') |
logging.disable(logging.CRITICAL) |
MMPbasedMCSSObjectClass(mmplogger) |
MMPDataObjectClass.__init__(self, logger_object) |
len(logging.Logger.manager.loggerDict) |
clean_out_data_mcss_obj(self) |
self.clean_out_data() |
self.mcs_mmp.clear() |
enumerate_fragment_properties(self) |
fragments (iw_descr only calcs largest frag) |
tempfile.NamedTemporaryFile(delete=False, suffix='.smi') |
tempfile.NamedTemporaryFile(delete=False) |
open(frag_smi_file.name, "w") |
isinstance(item, int) |
f.write(self.refsmi_dict[item]+" "+str(item) |
len(self.refsmi_dict) |
self.logger.debug("Ran iwdescr with exit status %s" % exit_status) |
open(frag_smi_props_out.name, "r") |
csv.reader(csv_file, delimiter=' ') |
self.logger.warn("When this was written, NATOMs was in array position 1 (zero indexed) |
sys.exit("When this was written, NATOMs was in array position 1 (zero indexed) |
int(row[0]) |
int(row[1]) |
frag_smi_props_out.close() |
len(self.ref_smi_props) |
len(self.refsmi_dict) |
cutoff (hard) |
cutoff (soft) |
threshold (soft) |
my_mmp_object.get_largest_mcs_pairs('myoutput.csv', 'BOTH', 'DICER') |
my_mmp_object.get_largest_mcs_pairs('myoutput.csv', 'DOUBLE', 'RDKIT') |
if (mdc_atm_soft is not None and mdc_atm_soft_threshold is None) |
sys.exit("Error, mdc_atm_soft and mdc_atm_soft_threshold must be specified together.") |
process_mcss_list_to_string(prefix, input_list) |
len(input_list) |
range(0, num_of_entries, 4) |
str((i_/4) |
str(molid_L) |
str(molid_R) |
str(sum(input_list[0 + i_]) |
str(input_list[1 + i_]) |
str(input_list[2 + i_]) |
str(input_list[3 + i_]) |
len(input_list[1]) |
str(molid_L) |
str(molid_R) |
str(sum(input_list[0]) |
str(self.refsmi_dict[input_list[2]]) |
str(self.refsmi_dict[input_list[3]]) |
disambiguate_double_list(input_list) |
len(input_list) |
not (1,11) |
many (1,11) |
range(0, num_of_entries, 4) |
remove_atom_num_dupes(input_list) |
self.logger.info('Opening output file for write: %s' % out_file) |
cut_type.upper() |
cut_type.upper() |
cut_type.upper() |
self.logger.warn('cut_type specification is incorrect, using single cut: %s' % cut_type.upper() |
if (len(self.single_pairs_dict) |
and (len(self.double_pairs_dict) |
self.logger.debug('No data found in single_pairs_dict and/or double_pairs_dict, expect no results') |
sys.exit("Error: no data found in single_pairs_dict and/or double_pairs_dict, nothing to find and write") |
self.iterator_single_pairs_dict_numeric(inc_attachpt=False) |
if (molid_L, molid_R) |
self.iterator_double_pairs_dict_numeric(inc_attachpt=False) |
ctx1_smi.replace("[1", "[9") |
ctx1_smi.replace("[2", "[1") |
ctx1_smi.replace("[9", "[2") |
print("ERR >>>") |
print(("{} {} {} {} {} {}".format(molid_L, molid_R, ctx1_id, ctx2_id, frag_L_id, frag_R_id) |
print(("{} {} {}".format(ctx1_id, ctx1_smi, self.refsmi_dict[ctx1_smi]) |
print("") |
ctx2_smi.replace("[1", "[9") |
ctx2_smi.replace("[2", "[1") |
ctx2_smi.replace("[9", "[2") |
if (molid_L, molid_R) |
len(num_atoms_existing) |
sum(num_atoms_existing) |
sum(ctx_natoms) |
if (ctx_natoms[0] > mdc_atm_soft) |
and (ctx_natoms[1] > mdc_atm_soft) |
len(num_atoms_existing) |
min(ctx_natoms) |
min(num_atoms_existing) |
min(ctx_natoms) |
min(num_atoms_existing) |
open(out_file, "w") |
final_out.write('CUT_TYPE,MOL_ID_L,MOL_ID_R,NATOMS,MCSS,FRAG_L,FRAG_R\n') |
for (molid_L, molid_R) |
len(self.largest_mcs_mmp_result[(molid_L, molid_R) |
are (1) |
num_atoms (2) |
fragment (3&4) |
len(self.largest_mcs_mmp_result[(molid_L, molid_R) |
print("Double won (a) |
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