# calculate parameters
# ======================================================================
link = 0
eps_res = 0.0054 * Tf
bonds_a = go_lib.calc_bonds(meta_crd[chains[0]], link)
bonds_b = go_lib.calc_bonds(meta_crd[chains[1]], link)
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)
nresi)
threebody[chaini][chaini] = go_lib.calc_threebody_intra(meta_crd[chaini], \
inte3, threebodyexcl)
print len(threebody[chaini][chaini].keys())
#
# inter-subunit contacts
for j in range(i + 1, nchain):
chainj = chains[j]
if ignore_inter:
# null intermolecular contacts
nonbondedx[chaini][chainj] = { 'nc': {}, 'nnc': {}, 'hb': {}, 'siga': {}, \
'sigb': {} }
else:
if aacut < 0.0: # do K&B
nonbondedx[chaini][chainj] = go_lib.calc_ncon_inter(meta_crd[chaini], \
meta_crd[chainj], \
ngdist, gamma, geomh, fixrep)
else:
nonbondedx[chaini][chainj] = go_lib.calc_ncon_inter_simplecut(meta_crd[chaini], \
meta_crd[chainj], \
ngdist, gamma, fixrep, aacut)
if kh == 1:
khmap[chaini][chainj] = go_lib.calc_kh_inter(
meta_crd[chaini], meta_crd[chainj], E0, LAMBDA)
if len(crowdprot) > 0:
bb_bonds_crow = go_lib.calc_bonds(meta_crd_crowd[crowd_chain], link)
if (defbon == 1 or len(sequence) > 0):
bb_bonds_crow = map(lambda x: (x[0], x[1], go_lib.std_bond), bb_bonds)
bb_angles_crow = go_lib.calc_angles(meta_crd_crowd[crowd_chain], link,
stata)
bonds = {}
angles = {}
dihedrals = {}
nonbonded = {}
for i in range(nchain):
chaini = chains[i]
bonds[chaini] = go_lib.calc_bonds(meta_crd[chaini], link)
angles[chaini] = go_lib.calc_angles(meta_crd[chaini], link)
dihedrals[chaini] = go_lib.setup_dihe(meta_crd[chaini], link)
nonbonded[chaini] = {}
nonbonded[chaini][chaini] = go_lib.calc_ncon_intra(meta_crd[chaini],
ngdist, gamma)
for j in range(i + 1, nchain):
chainj = chains[j]
nonbonded[chaini][chainj] = go_lib.calc_ncon_inter(
meta_crd[chaini], meta_crd[chainj], ngdist, gamma)
#bonds = go_lib.average_bonded_list(bonds)
#print nonbonded.keys()
#print nonbonded['A'.keys()
#print nonbonded.keys()
#print "inter"
#x = nonbonded['A ']['B ']
#nbx = x['nc']
#for k in nbx.keys():
# print k[0],k[1],nbx[k][0], nbx[k][1]
#
#print "intra"
#x = nonbonded['A ']['A ']