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: tmphead = Analyze.trimByRMSD(matchf.replace(args.head, tmphead), 0, tmphead, 'th2', args.bbrmsd) if args.uniq == True: if args.nonat == True: if noHomoNow == 0: tmphead = Analyze.trimByUniqSeq(seqf.replace(args.head, tmphead), tmphead, 'th3', nativeSeq = nseq, h**o = exclude, homo_log = True) noHomoNow = 1 else: tmphead = Analyze.trimByUniqSeq(seqf.replace(args.head, tmphead), tmphead, 'th3', nativeSeq = nseq) else: if noHomoNow == 0: tmphead = Analyze.trimByUniqSeq(seqf.replace(args.head, tmphead), tmphead, 'th3', h**o = exclude, homo_log = True) noHomoNow = 1 else: tmphead = Analyze.trimByUniqSeq(seqf.replace(args.head, tmphead), tmphead, 'th3') if noHomoNow == 0: # no rmsd constraint and uniq, just remove h**o tmphead = Analyze.trimByRMSD(matchf.replace(args.head, tmphead), 0, tmphead, 'th4', 3.0, h**o = exclude, homo_log = True) # copy things back