Datasets:
thisisanshgupta
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Pycode

Dataset card Data Studio Files Community
text
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828
print(e)
return 0
if pccs:
pcc = pccs[elem]
self.compound_info['inchikey_id'] = pcc.inchikey
self.compound_info['pubchem_id'] = pcc.cid
self.compound_info['molecular_formula'] = pcc.molecular_formula
self.compound_info['molecular_weight'] = pcc.molecular_weight
self.compound_info['exact_mass'] = pcc.exact_mass
self.compound_info['smiles'] = pcc.canonical_smiles
if len(pccs) > 1:
print('WARNING, multiple compounds for ', self.compound_info)"
165,"def _get_other_names(self, line):
""""""Parse and extract any other names that might be recorded for the compound
Args:
line (str): line of the msp file
""""""
m = re.search(self.compound_regex['other_names'][0], line, re.IGNORECASE)
if m:
self.other_names.append(m.group(1).strip())"
166,"def _parse_meta_info(self, line):
""""""Parse and extract all meta data by looping through the dictionary of meta_info regexs
updates self.meta_info
Args:
line (str): line of the msp file
""""""
if self.mslevel:
self.meta_info['ms_level'] = self.mslevel
if self.polarity:
self.meta_info['polarity'] = self.polarity
for k, regexes in six.iteritems(self.meta_regex):
for reg in regexes:
m = re.search(reg, line, re.IGNORECASE)
if m:
self.meta_info[k] = m.group(1).strip()"
167,"def _parse_compound_info(self, line):
""""""Parse and extract all compound data by looping through the dictionary of compound_info regexs
updates self.compound_info
Args:
line (str): line of the msp file
""""""
for k, regexes in six.iteritems(self.compound_regex):
for reg in regexes:
if self.compound_info[k]:
continue
m = re.search(reg, line, re.IGNORECASE)
if m:
self.compound_info[k] = m.group(1).strip()
self._get_other_names(line)"
168,"def insert_data(self, remove_data=False, db_type='sqlite'):
""""""Insert data stored in the current chunk of parsing into the selected database
Args:
remove_data (boolean): Remove the data stored within the LibraryData object for the current chunk of
processing
db_type (str): The type of database to submit to
either 'sqlite', 'mysql' or 'django_mysql' [default sqlite]
""""""
if self.update_source:
# print ""insert ref id""
import msp2db
self.c.execute(
""INSERT INTO library_spectra_source (id, name, parsing_software) VALUES""
"" ({a}, '{b}', 'msp2db-v{c}')"".format(a=self.current_id_origin, b=self.source, c=msp2db.__version__))
self.conn.commit()
if self.compound_info_all:
self.compound_info_all = _make_sql_compatible(self.compound_info_all)
cn = ', '.join(self.compound_info.keys()) + ',created_at,updated_at'
insert_query_m(self.compound_info_all, columns=cn, conn=self.conn, table='metab_compound',
db_type=db_type)
self.meta_info_all = _make_sql_compatible(self.meta_info_all)
cn = 'id,' + ', '.join(self.meta_info.keys()) + ',library_spectra_source_id, inchikey_id'
insert_query_m(self.meta_info_all, columns=cn, conn=self.conn, table='library_spectra_meta',
db_type=db_type)
cn = ""id, mz, i, other, library_spectra_meta_id""
insert_query_m(self.spectra_all, columns=cn, conn=self.conn, table='library_spectra', db_type=db_type)
if self.spectra_annotation_all:
cn = ""id, mz, tentative_formula, mass_error, library_spectra_meta_id""