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