2022-08-02T12:18:57Z 500 Atomic and Molecular Species Names A TAP-queriable database of common names of molecules and their InChIs. This is an experimental copy of http://species.vamdc.org created in the context of the LineTAP effort, augmented with names found in the CASA line list. You will probably want to query this using SQL wildcards (% and _) and the ILIKE operator. astrochemistry virtual-observatories The VAMDC consortium; Brogan, C.; Remijan, A. J. ; Markwick-Kemper, A. http://species.vamdc.org Research Catalog ivo://ivoa.net/std/linetap#species-1.0 lower(name) gin_trgm_ops lower(formula) book = xlrd.open_workbook(self.sourceToken) sheet = book.sheet_by_index(0) assert sheet.name=="speciesList" # row 0 is the column names keys = [cell.value.lower().replace(" ", "_") for cell in sheet.row(0)] # we want 'stoichiometricformula' for formula # and drop formula. keys[keys.index("formula")] = "odd-formula" keys[keys.index("stoichiometricformula")] = "formula" inchiIndex = keys.index("inchikey") for rowInd in range(1, sheet.nrows): row = sheet.row(rowInd) if row[inchiIndex].value: yield dict((key, cell.value) for key, cell in zip(keys, row)) if @inchi.startswith("1S"): @inchi = "InChI="+@inchi source_id: node_identifier species web A form to search the VAMDC species list published on the TAP service at http://dc.g-vo.org/tap. Enter parts of species names or chemical formulae here and get back matching names, inchis and inchikeys. pat = '%'+inPars[inputKeys[0].name].replace( "%", r"\\%").replace("_", r"\\_" )+'%' yield "name like %({})s or formula like %({})s".format( base.getSQLKey("name", pat, outPars), base.getSQLKey("formula", pat, outPars)) /tap/sync rows = self.getVOTableRows() self.assertEqual(len(rows), 2) self.assertEqual(rows[0]["inchikey"], "IAYPIBMASNFSPL-YZRHJBSPSA-N") self.assertEqual(rows[0]["inchikey"], rows[1]["inchikey"]) web/form self.assertHasStrings( "Oxacyclopentadiene", "C2H4O", "AHHWIHXENZJRFG-UHFFFAOYSA-N")