nonbondedx = {}
threebody = {}
if kh == 1:
khmap = {}
#print meta_crd[chaini]
import time
time_a = time.time()
NSFAC = 1.0
disulfides = disulf_str.split(":")
#nresprot = 0
for i in range(nchain):
chaini = chains[i]
print chaini
#print meta_crd[chaini][142]
bb_bonds = go_lib.calc_bonds(meta_crd[chaini], link)
if (defbon == 1 or len(sequence) > 0):
bb_bonds = map(lambda x: (x[0], x[1], go_lib.std_bond), bb_bonds)
bb_angles = go_lib.calc_angles(meta_crd[chaini], link, stata)
bb_dihedrals = go_lib.setup_dihe(meta_crd[chaini], link, fixalpha,
zerodihe, nativedihe)
nonbondedx[chaini] = {}
if kh == 1:
khmap[chaini] = {}
#nonbonded[chaini][chaini],tmp_nsfac = go_lib.calc_ncon_intra(meta_crd[chaini],tfmap[chaini][chaini],ngdist,gamma,geomh,fixrep)
if (aacut < 0.0): # do Karanicolas&Brooks
nonbondedx[chaini][chaini] = go_lib.calc_ncon_intra(
meta_crd[chaini], ngdist, gamma, geomh, fixrep)
else:
nonbondedx[chaini][chaini] = go_lib.calc_ncon_intra_simplecut(meta_crd[chaini], ngdist, \
nres = len(xyz[c])
for i in range(1, nres + 1):
idx += 1
name = meta_crd[c][i]["name"]
mass = go_lib.massmap[name]
residues.append(("G%i" % (idx), mass))
go_lib.write_topology(outp_base + "_top.inp", residues, key)
# 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
for j in range(i+1,nchain):
chainj = chains[j]
tfmap[chaini][chainj] = tfbb
# new ----------------------------------------------
bonds = {}
angles = {}
dihedrals = {}
nonbonded = {}
threebody ={}
NSFAC = 1.0
disulfides = disulf_str.split(":")
for i in range(nchain):
chaini = chains[i]
bb_bonds = go_lib.calc_bonds(meta_crd[chaini],link)
if (defbon==1 or len(sequence)>0):
bb_bonds = map(lambda x: (x[0],x[1],go_lib.std_bond), bb_bonds)
bb_angles = go_lib.calc_angles(meta_crd[chaini],link,stata)
bb_dihedrals = go_lib.setup_dihe(meta_crd[chaini],link)
nonbonded[chaini] = {}
#nonbonded[chaini][chaini],tmp_nsfac = go_lib.calc_ncon_intra(meta_crd[chaini],tfmap[chaini][chaini],ngdist,gamma,geomh,fixrep)
nonbonded[chaini][chaini] = go_lib.calc_ncon_intra(meta_crd[chaini],ngdist,gamma,geomh,fixrep)
#
# include disulfides if necc...
clen = len(chaini)
my_disulfides = map(lambda x: x[clen:], filter(lambda x: x.find(chaini)==0,disulfides))
#
if len(my_disulfides)>0:
ds_bonds, ds_angles, ds_dihedrals = go_lib.calc_disulf_bonded(meta_crd[chaini],tfbb,my_disulfides)
go_lib.write_topology(outp_base + "_top.inp", residues, key)
# calculate parameters
# ======================================================================
link = 0
eps_res = 0.0054 * Tf
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()