time_c = time.time()
print time_c - time_a
#print nonbonded['PROT']
orig_angles = angles
orig_bonds = bonds
if symm:
bonds = go_lib.average_bonded_list(bonds)
angles = go_lib.average_bonded_list(angles)
nonbonded = go_lib.average_nonbonded_matrix(nonbondedx)
dihedrals = dihedrals[chains[0]]
else:
unmerged_bonds = bonds
unmerged_angles = angles
unmerged_dihedrals = dihedrals
bonds = go_lib.merge_bonded(bonds)
angles = go_lib.merge_bonded(angles)
dihedrals = go_lib.merge_dihe(dihedrals)
if len(Tf) == 1:
nonbonded, NSFAC = go_lib.merge_nonbonded_matrix(nonbondedx, xyz, Tf)
else:
nonbonded, NSFAC = go_lib.merge_nonbonded_matrix(
nonbondedx, xyz, Tf[1:])
time_d = time.time()
print time_d - time_a
#print len(nonbonded['nnc'])
if threebodyexcl > 0:
threebody = go_lib.merge_threebody_matrix(threebody, xyz)
if len(sequence) > 0:
angles_a = go_lib.calc_angles(meta_crd[chains[0]], link)
angles_b = go_lib.calc_angles(meta_crd[chains[1]], link)
dihedrals_a = go_lib.setup_dihe(meta_crd[chains[0]], link)
dihedrals_b = go_lib.setup_dihe(meta_crd[chains[1]], link)
nonbonded_a = go_lib.calc_ncon_intra(meta_crd[chains[0]], ngdist, gamma)
nonbonded_b = go_lib.calc_ncon_intra(meta_crd[chains[1]], ngdist, gamma)
nonbonded_ab = go_lib.calc_ncon_inter(meta_crd[chains[0]], meta_crd[chains[1]],
ngdist, gamma)
if symm:
bonds = go_lib.average_bonded(bonds_a, bonds_b)
angles = go_lib.average_bonded(angles_a, angles_b)
nonbonded = go_lib.average_nonbonded_intra(nonbonded_a, nonbonded_b)
nonbonded_ab_sym = go_lib.symmetrize_nb(nonbonded_ab, nres_tot)
dihedrals = dihedrals_a
else:
bonds = go_lib.merge_bonded(bonds_a, bonds_b)
angles = go_lib.merge_bonded(angles_a, angles_b)
nonbonded = go_lib.merge_nonbonded(nonbonded_a, nonbonded_b, nonbonded_ab)
dihedrals = go_lib.merge_bonded(dihedrals_a, dihedrals_b)
go_map,nongo_map, qlist, nat_scale_fac = go_lib.make_go_nongo_map(nonbonded, \
eps_res, nres_tot)
go_and_nongo = go_lib.mergemap(go_map, nongo_map)
GOMODEL_nbfix = go_lib.gotozero(go_map, nongo_map, nres_tot)
# write out parameters
# ======================================================================
go_lib.write_parms(outp_base + "_parm.inp", key, bonds, angles, dihedrals,
nonbonded['sig'], go_and_nongo, nat_scale_fac, Tf)
go_lib.write_parms(outp_base + "_GOMODEL_parm.inp", key, bonds, angles,