cid, resnum = args.resid
for seqf in seqfs:
pdbf = General.changeExt( seqf.replace(args.head + '_', ''), 'pdb')
if not os.path.isfile(pdbf):
print(pdbf + ' doesn\'t exist!')
continue
outf = General.changeExt(pdbf, args.o)
if args.wgap != None: # specific to gap
assert args.conR == False, 'wgap and conR cannot be specified simultaneously'
dirname = General.getBase(pdbf)
pdbf = args.wgap + '/' + dirname + '/'+ pdbf
index = PDB.findPositionInPDB(pdbf, resnum, cid)
aacol = Analyze.readColumn(seqf, index, top = args.uplimit)
if args.conR: # should contacting residue be constrained?
conid = General.getBase(seqf).split('_')[-1]
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
base = General.getBase(pdb)
matchf = args.head + '_' + base + '.match'
if not os.path.isfile(matchf):
continue
outname = General.getBase(matchf) + '.' + args.o
if os.path.isfile(outname):
continue
if outname in seen:
continue
seen[outname] = 1
# for the gap test only
if args.wgap != None:
pdb = args.wgap + '/' + mut.dir + '/' + pdb
##
pos = PDB.findPositionInPDB(pdb, str(mut.n), mut.c)
if pos == -1:
print('cannot found the residue in fragment pdb: '+ pdb)
continue
pdb = General.removePath(pdb)
cmd = ['python', selfbin +'/envForMatches.py','--m', matchf, '--n', str(pos-1), '--o', outname]
if args.uplimit != None:
cmd.extend(['--uplimit', args.uplimit])
if args.wgap != None:
cmd.append('--wgap')
cmd = ' '.join(cmd)
job = General.jobOnCluster([cmd], mut.dir, os.path.realpath(outname))
job.submit(3)
jobs.append(job)
sleep(0.5)
dirs = [x for x in os.listdir('.') if os.path.isdir(x)]
dirs.sort()
odir = os.getcwd()
for d in dirs:
os.chdir(odir)
os.chdir(d)
pdbs = glob.glob('*.pdb')
cmds = []
resn = int(d.split('_')[1][2:])
for pdb in pdbs:
matchf = args.head + '_' + General.changeExt(pdb, 'match')
if not os.path.isfile(matchf):
continue
pos = PDB.findPositionInPDB(pdb, resn)
# if output file is already there, skip the job
if os.path.isfile('nr'+args.id +'_'+matchf):
continue
cmd = ['python', selfbin + '/removeLocalRedundancy.py', '--m', matchf, '--cres', str(pos), '--id', args.id, '--outh', 'nr'+args.id]
if not args.db == None:
cmd.extend(['--db', args.db])
if args.conR:
conresn = General.getBase(pdb).split('_')[2][1:]
conpos = PDB.findPositionInPDB(pdb, conresn)
cmd.extend(['--conres', str(conpos)])
if args.env != None:
cmd.extend(['--env', args.env])
cmd = ' '.join(cmd)
cmds.append(cmd)
pdbs = glob.glob('*.pdb')
pdbs.sort()
for pdb in pdbs:
base = General.getBase(pdb)
matchf = args.head + '_' + base + '.match'
if not os.path.isfile(matchf):
continue
outname = General.getBase(matchf) + '.' + args.o
if os.path.isfile(outname):
continue
if outname in seen:
continue
seen[outname] = 1
pos = PDB.findPositionInPDB(pdb, str(mut.n), mut.c)
if pos == -1:
print('cannot found the residue in fragment pdb: '+ pdb)
continue
con = base.split('_')[-1]
conc, conn = con[0], con[1:]
conpos = PDB.findPositionInPDB(pdb, str(conn), conc)
cmd = ['python', selfbin +'/envForMatches_pair.py','--m', matchf, '--n', str(pos-1), str(conpos-1), '--o', outname]
if args.uplimit != None:
cmd.extend(['--uplimit', args.uplimit])
cmd = ' '.join(cmd)
job = General.jobOnCluster([cmd], mut.dir, os.path.realpath(outname))
job.submit(3)