# check if NMR file
#pdblines = open(files[0]).readlines()
#if len(filter(lambda x: x.find("MODEL")==0, pdblines)) != 0:
# nmrfile = 1
#else:
# nmrfile = 0
#
#models = go_lib.split_NMR_pdb(pdblines)
#print models
if average:
meta_list = []
xyz_list = []
for file in files:
meta_crd, xyz = go_lib.make_coords(open(file).readlines(), charmmpdb)
meta_list.append(meta_crd)
xyz_list.append(xyz)
#meta_crd, xyz = go_lib.average_coords(meta_list,xyz_list)
else:
meta_crd, xyz = go_lib.make_coords(open(files[0]).readlines(), charmmpdb)
chains = meta_crd.keys()
chains.sort()
nchain = len(chains)
sys.stdout.write("Chains found in PDB file:\n")
for c in chains:
sys.stdout.write("\t%s\n" % (c))
info_out = open(outp_base + "_info.dat", "w")
for i in info:
sys.stdout.write("%s" % (i))
info_out.write("%s" % (i))
info_out.close()
# ======================================================================
# PARSE PDB AND WRITE OUT CA-ONLY COORDS -- IF THERE IS A PDB FILE
# ======================================================================
if len(sequence) == 0: # we are building from pdb
if average:
meta_list = []
xyz_list = []
for file in files:
meta_crd, xyz = go_lib.make_coords(
open(file).readlines(), charmmpdb)
meta_list.append(meta_crd)
xyz_list.append(xyz)
else:
meta_crd, xyz = go_lib.make_coords(
open(files[0]).readlines(), charmmpdb)
else:
# if building from sequence ... make 'linear' coords
# this allows us to continue as we normally would for PDB data
meta_crd, xyz = go_lib.make_sequ_coords(sequence)
chains = meta_crd.keys()
chains.sort()
nchain = len(chains)
protein_chains = copy.deepcopy(chains)
#!/usr/bin/env python
import sys, os, go_lib
metac, xyz = go_lib.make_coords(sys.stdin.readlines())
chains = metac.keys()
#print metac
#c = chains[0]
#for i in range(1,10):
# print i, metac[c][i]["name"]
#sys.exit(0)
go_lib.write_CA_SC_pdb("stdout", xyz, metac, chains, 1)
info_out.write("Building go model from PDB file %s\n" % (files[0]))
info_out.write("Target folding temperature = %8.3f K \n" % (Tf))
info_out.write("Key for naming output files = %s\n" % (key))
if symm:
info_out.write("Will symmetrize interactions in dimer\n")
else:
info_out.write("Will not symmetrize interactions in dimer\n")
info_out.write("Non-go weighting ('gamma') = %8.3f\n" % (gamma))
info_out.write("Base for output file names = %s\n" % (outp_base))
info_out.write("Default non-go contact distance = %8.3f\n" % (ngdist))
info_out.close()
# write out CA-only coords
# ======================================================================
meta_crd, xyz = go_lib.make_coords(open(files[0]).readlines())
chains = meta_crd.keys()
chains.sort()
nchain = len(chains)
sys.stdout.write("%i chains found in PDB file:\n" % (len(chains)))
for c in chains:
sys.stdout.write("\t%s\n" % (c))
#if len(chains) >2:
# sys.stderr.write("\n******************************************************\n")
# sys.stderr.write("This version can only handle dimers\n")
# sys.stderr.write("******************************************************\n")
# sys.stderr.write("%s\n" % (Usage))
go_lib.write_CA_pdb(outp_base + ".pdb", xyz, chains)