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
### 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]
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')
if len(pdbs) <= 1:
continue
pdbid = d.split('_')[0].lower()
opdbf = args.sdir + '/' + pdbid + '.clean.pdb'
cen = d.split('_')[1]
cenres = PDB.getResByInd(opdbf, cen[0], cen[2:])
if cenres.getResname() == 'GLY':
carbon = 'CA'
else:
carbon = 'CB'
cencoords = cenres.getAtom(carbon).getCoords()
out = d + '.' + args.o
outfh = open(out, 'w')
cons = []
for pdb in pdbs:
con = General.getBase(pdb).split('_')[-1]
cons.append([con[0], con[1:]])
for i in range(len(cons)):
conres = PDB.getResByInd(opdbf, cons[i][0], cons[i][1])
carbon = 'CB'
