else:
lcrowd = len(xyz_crowd[crowd_chain])
ncrowd_res = lcrowd * ncrowd
crowd_map = go_lib.make_crowd_map_protein(nonbonded['sig'], \
ncrowd_res, ncrowd, rcrowd)
nres_crowd = nres_tot + ncrowd_res
if nchain > 1:
go_map_intra,qlist_intra = go_lib.make_go_map(nonbonded['ncintra'], nonbonded['hbintra'], \
nres_tot, scscale, bbscale)
nongo_map = go_lib.make_nongo_map(nonbonded['nnc'], \
nres_tot)
go_and_nongo = go_lib.mergemap(go_map, nongo_map)
GOMODEL_nbfix = go_lib.gotozero(go_map, nongo_map, nres_tot)
if ncrowd > 0 and charmm:
crowd_nbfix = go_lib.gotozero(crowd_map, go_map, nres_crowd)
time_f = time.time()
print time_f - time_a
print "got here 00"
if (kh == 1) and charmm:
print "got here 01"
GOMODEL_nbfix_kh = go_lib.gotozero(go_map, globalkh, nres_tot)
print "got here 1"
if ncrowd > 0:
crowd_nbfix_kh = go_lib.gotozero(crowd_map, globalkh, nres_crowd)
if nchain > 1:
print "got here 2"
if threebodyexcl > 0:
threebody =go_lib.merge_threebody_matrix(threebody,xyz)
if len(sequence) > 0:
nonbonded = go_lib.calc_ncon_intra_helical(meta_crd[chains[0]],gamma)
if use_list:
nonbonded['nc'] = go_lib.make_nc_from_list(meta_crd[chains[0]],go_list_file)
nonbonded['hb'] = {}
if use_siglist:
nonbonded['sig'] = go_lib.make_sig_from_list(meta_crd[chains[0]],sig_list_file)
go_map,nongo_map, qlist = go_lib.make_go_nongo_map(nonbonded, \
nres_tot,scscale,bbscale)
go_and_nongo = go_lib.mergemap(go_map,nongo_map)
GOMODEL_nbfix = go_lib.gotozero(go_map,nongo_map,nres)
if water > 0:
winte = go_lib.calc_nbond_w(residues)
else:
winte = {}
# write linear pdb for each chain.
# these will probably overlap, so will need to be translated/rotated
# before energy/force evaluation
# ======================================================================
if len(sequence) == 0:
for chain in chains:
go_angles = go_lib.calc_angles(meta_crd[chain],link,0,0)
bb_bonds = go_lib.calc_bonds(meta_crd[chain],link)