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thisisanshgupta
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Pycode

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if not self.compound_info['inchikey_id'] in self.compound_ids:
self.compound_info_all.append(tuple(self.compound_info.values()) + (
str(datetime.datetime.now()),
str(datetime.datetime.now()),
))
self.compound_ids.append(self.compound_info['inchikey_id'])"
161,"def _store_meta_info(self):
""""""Update the meta dictionary with the current chunk of meta data details
""""""
# In the mass bank msp files, sometimes the precursor_mz is missing but we have the neutral mass and
# the precursor_type (e.g. adduct) so we can calculate the precursor_mz
if not self.meta_info['precursor_mz'] and self.meta_info['precursor_type'] and \
self.compound_info['exact_mass']:
self.meta_info['precursor_mz'] = get_precursor_mz(float(self.compound_info['exact_mass']),
self.meta_info['precursor_type'])
if not self.meta_info['polarity']:
# have to do special check for polarity (as sometimes gets missed)
m = re.search('^\[.*\](\-|\+)', self.meta_info['precursor_type'], re.IGNORECASE)
if m:
polarity = m.group(1).strip()
if polarity == '+':
self.meta_info['polarity'] = 'positive'
elif polarity == '-':
self.meta_info['polarity'] = 'negative'
if not self.meta_info['accession']:
self.meta_info['accession'] = 'unknown accession'
self.meta_info_all.append(
(str(self.current_id_meta),) +
tuple(self.meta_info.values()) +
(str(self.current_id_origin), self.compound_info['inchikey_id'],)
)"
162,"def _parse_spectra_annotation(self, line):
""""""Parse and store the spectral annotation details
""""""
if re.match('^PK\$NUM_PEAK(.*)', line, re.IGNORECASE):
self.start_spectra_annotation = False
return
saplist = line.split()
sarow = (
self.current_id_spectra_annotation,
float(saplist[self.spectra_annotation_indexes['m/z']]) if 'm/z' in self.spectra_annotation_indexes else None,
saplist[self.spectra_annotation_indexes[
'tentative_formula']] if 'tentative_formula' in self.spectra_annotation_indexes else None,
float(saplist[self.spectra_annotation_indexes[
'mass_error(ppm)']]) if 'mass_error(ppm)' in self.spectra_annotation_indexes else None,
self.current_id_meta)
self.spectra_annotation_all.append(sarow)
self.current_id_spectra_annotation += 1"
163,"def _parse_spectra(self, line):
""""""Parse and store the spectral details
""""""
if line in ['\n', '\r\n', '//\n', '//\r\n', '', '//']:
self.start_spectra = False
self.current_id_meta += 1
self.collect_meta = True
return
splist = line.split()
if len(splist) > 2 and not self.ignore_additional_spectra_info:
additional_info = ''.join(map(str, splist[2:len(splist)]))
else:
additional_info = ''
srow = (
self.current_id_spectra, float(splist[0]), float(splist[1]), additional_info,
self.current_id_meta)
self.spectra_all.append(srow)
self.current_id_spectra += 1"
164,"def _set_inchi_pcc(self, in_str, pcp_type, elem):
""""""Check pubchem compounds via API for both an inchikey and any available compound details
""""""
if not in_str:
return 0
try:
pccs = pcp.get_compounds(in_str, pcp_type)
except pcp.BadRequestError as e:
print(e)
return 0
except pcp.TimeoutError as e:
print(e)
return 0
except pcp.ServerError as e:
print(e)
return 0
except URLError as e:
print(e)
return 0
except BadStatusLine as e: