ccid, cresnum = conid[0], conid[1:] cindex = PDB.findPositionInPDB(pdbf, cresnum, ccid) cres = PDB.getResByInd(pdbf, ccid, cresnum).getResname() cres = PDB.t2s(cres) caacol = Analyze.readColumn(seqf, cindex, top = args.uplimit) if args.env != None: # environment corrected counts envf = General.getBase(seqf.replace(args.head, args.envhead)) + '.' + args.env if not os.path.isfile(envf): print(envf + ' doesn\'t exist!') continue ### this is a dynamic part if not args.conR: envcolInd = range(2, 7) envcols = Analyze.readMultiColumn(envf, envcolInd, top = args.uplimit) if not (len(aacol) == len(envcols[0])): envcols = [x[:len(aacol)] for x in envcols] condcol, crdcol, fdcol = envcols[0:3] if args.pp: phicol, psicol = envcols[3], envcols[4] else: envcolInd = list(range(2, 7)) envcolInd.extend(list(range(9, 14))) envcols = Analyze.readMultiColumn(envf, envcolInd, top = args.uplimit) if not (len(aacol) == len(envcols[0])): envcols = [x[:len(aacol)] for x in envcols] condcol, crdcol, fdcol = envcols[0:3] condcol2, crdcol2, fdcol2 = envcols[5:8] if args.pp: phicol, psicol = envcols[3], envcols[4]
