def searchPdbEntries(self): """ Set the list of matched entries and the dictionary holding the number of matches. They need to be defined as globals to this module. Return True on error. Also searches the PDB and BMRB databases itself. """ # modification_time = os.path.getmtime("/Users/jd/.cshrc") # self.match.d[ "1brv" ] = EntryInfo(time=modification_time) ## following statement is equivalent to a unix command like: nTdebug("Looking for entries from the PDB database.") self.entry_list_pdb.addList(getPdbEntries()) if not self.entry_list_pdb: nTerror("No PDB entries found") return True nTmessage("Found %s PDB entries." % len(self.entry_list_pdb))
""" Collect data needed for nrgcing from RCSB-PDB REST calls. Execute like: python $CINGROOT/python/cing/NRG/getRCSB_PDB.py """ from cing import cingDirTmp from cing.Libs.NTutils import * # @UnusedWildImport from cing.NRG.PDBEntryLists import getPdbEntries from cing.NRG.PDBEntryLists import writeEntryListToFile cing.verbosity = cing.verbosityDebug cingDirTmpTest = os.path.join(cingDirTmp, "getRCSB_PDB") mkdirs(cingDirTmpTest) os.chdir(cingDirTmpTest) testing = False if testing: # testing with smaller set pdbList = getPdbEntries(mustHaveExperimentalNmrData=True, onlySolidState=True) else: pdbList = getPdbEntries(mustHaveExperimentalNmrData=True) nTmessage("getPdbEntries exp: %d" % (len(pdbList))) writeEntryListToFile("hasExpData.csv", pdbList)
""" Collect data needed for nrgcing from RCSB-PDB REST calls. Execute like: python $CINGROOT/python/cing/NRG/getRCSB_PDB.py """ from cing import cingDirTmp from cing.Libs.NTutils import * #@UnusedWildImport from cing.NRG.PDBEntryLists import getPdbEntries from cing.NRG.PDBEntryLists import writeEntryListToFile cing.verbosity = cing.verbosityDebug cingDirTmpTest = os.path.join(cingDirTmp, 'getRCSB_PDB') mkdirs(cingDirTmpTest) os.chdir(cingDirTmpTest) testing = False if testing: # testing with smaller set pdbList = getPdbEntries(mustHaveExperimentalNmrData=True, onlySolidState=True) else: pdbList = getPdbEntries(mustHaveExperimentalNmrData=True) nTmessage("getPdbEntries exp: %d" % (len(pdbList))) writeEntryListToFile('hasExpData.csv', pdbList)