ldir = General.createLocalSpace() odir = os.getcwd() errorfree = True smart = False if args.rmsd == None: smart = True else: rmsdeff = args.rmsd for pdb in args.p: # set rmsd cutoff using Craig's function residues = PDB.ConRes(pdb) segments = Fragment.getSegments(residues) if smart: rmsdeff = mustpress.rmsdEff(segments, args.params[0], args.params[1]) seqout = args.head + '_' + General.changeExt(pdb, 'seq') matchout = General.changeExt(seqout, 'match') if os.path.isfile(seqout): continue # search is additonal to a previous round if args.more != None: oseqf = args.more + '_' + General.changeExt(pdb, 'seq') if not os.path.isfile(oseqf): continue olen = sum([1 for x in open(oseqf)]) if olen >= args.topn: omatchf = General.changeExt(oseqf, 'match')
ldir = General.createLocalSpace()
# copy .match and .seq
sub.call(['cp', matchf, seqf, ldir])
os.chdir(ldir)
tmphead = args.head
if args.rmsd != None:
if noHomoNow == 0:
tmphead = Analyze.trimByRMSD(matchf, -1, tmphead, 'th1', args.rmsd, sorted = False, h**o = exclude, homo_log = True)
noHomoNow = 1
else:
tmphead = Analyze.trimByRMSD(matchf, -1, tmphead, 'th1', args.rmsd, sorted = False)
if args.smart:
if len(segments) == 1:
smartcut = mustpress.rmsdEff(segments, 20, 0.9)
else:
if max(resnums) - min(resnums) < 8: # this is considered close, even there is gap between two segments
smartcut = mustpress.rmsdEff(segments, 20, 0.9) - 0.2 # this is about 0.5
else:
smartcut = mustpress.rmsdEff(segments, 15, 1.1) # this is about 0.9
if noHomoNow == 0:
tmphead = Analyze.trimByRMSD(matchf.replace(args.head, tmphead), 0, tmphead, 'ts', smartcut, h**o = exclude, homo_log = True)
noHomoNow = 1
else:
tmphead = Analyze.trimByRMSD(matchf.replace(args.head, tmphead), 0, tmphead, 'ts', smartcut)
elif args.bbrmsd != None:
if noHomoNow == 0:
tmphead = Analyze.trimByRMSD(matchf.replace(args.head, tmphead), 0, tmphead, 'th2', args.bbrmsd, h**o = exclude)
noHomoNow = 1
else:
