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
