if len(sys.argv)< 3:

print "Usage: proc_N-mer.py tip_file cluster_file n_mer dist_cutoff >> n_mer_outfile"

return

infile = sys.argv[1]

infile2 = sys.argv[2]

n_mer = int(sys.argv[3])

cutoff = float(sys.argv[4])

p = protein(infile, center='TIP')

p.initCGResiMap()

with open(infile2) as fp:

for line in fp:

cg = cgroup(line.strip())

if cg.getSize() == n_mer:

if p.cgResiGroupFilter(cg, cutoff) == True:

print cg.getString()

elif cg.getSize() < n_mer:

continue

else:

# generate combinations

for idx in list(itertools.combinations(range(cg.getSize()),n_mer)):

sub_cg = cgroup()

sub_cg.pdb = cg.pdb

sub_cg.chain = cg.chain

for i in idx: # iterate all the tuples

sub_cg.AAgroup = sub_cg.AAgroup + cg.AAgroup[i]

sub_cg.resi.append(cg.resi[i])

if p.cgResiGroupFilter(sub_cg, cutoff) == True:

print sub_cg.getString()