#Add atoms, bonds, and angles
len_bond = 2.0 #0.97*sigma #Equilibrium bond length
theta = (25.0/180.0)*math.pi
sep = 2.0 # Must be <= len_bond
#Loop over all molecules (here only a single molecule type)
imol = 1; iatm = 1; ibnd = 1; iang = 1 #Index of one past the last atom, bond, etc. added
for imol in range(1, num_mols+1):
iatm_beg = iatm
ibnd_beg = ibnd
iang_beg = iang
config.append_atom_unbonded( atm_t_bb, 0.0 )
iatm += 1
config.append_atom_bonded(1, 0.0, len_bond, 'efjc', iatm-1, sep=sep)
iatm += 1
for i in range(3,natm+1):
config.append_atom_bonded(atm_t_bb, 0.0, len_bond, 'efjc',
iatm-1, im2=iatm-2, theta=theta, sep=sep)
iatm += 1
for i in range(1, nbnd+1):
j = iatm_beg + i - 1
config.add_bond(bnd_t_bb, j, j+1)
ibnd += 1
for i in range(1, nang+1):
j = iatm_beg + i - 1
config.add_angle(ang_t_bb, j, j+1, j+2)
iang += 1
#Add atoms, bonds, etc
#Loop over all molecules (here only a single molecule type)
imol = 1
iatm = 1
ibnd = 1 #Index of atom, bond, etc. of the next entity to be added
for imol in range(1, num_mols + 1):
iatm_beg = iatm
ibnd_beg = ibnd
#Backbone
#Put first atom at the origin
config.add_atom(atm_t_bb, 0.0, np.zeros((3, )))
iatm += 1
#Put second atom along x-axis
config.append_atom_bonded(atm_t_bb, 0.0, len_bond, 'alignx', iatm - 1)
iatm += 1
#Put the rest of the backbone atoms
for i in range(3, na_bbone + 1):
config.append_atom_bonded(atm_t_bb,
0.0,
len_bond,
'alignx',
iatm - 1,
im2=iatm - 2,
theta=theta_bb,
sep=sep)
iatm += 1
#Backbone bonds
nbnd = na_bbone - 1
for i in range(1, nbnd + 1):
theta = (45.0 / 180.0) * math.pi #Avg. initial bond angle
#Loop over all chains
iatm = 0
ibnd = 0
iang = 0 #Index of the last atom, bond, etc. added
for imol in range(1, num_mols + 1):
iatm_beg = iatm + 1
ibnd_beg = ibnd + 1
iang_beg = iang + 1
#First atom can be at any location
iatm = config.append_atom_unbonded(atm_t_m, 0.0, sep=sep)
#Add second atom bonded to the first as a freely jointed link
iatm = config.append_atom_bonded(atm_t_m,
0.0,
len_bond,
'efjc',
iatm,
sep=sep)
#Add rest of the atoms as freely rotating links
for i in range(3, natm + 1):
iatm = config.append_atom_bonded(atm_t_m,
0.0,
len_bond,
'efrc',
iatm,
im2=iatm - 1,
theta=theta,
sep=sep)
#Add bonds
for i in range(1, nbnd + 1):
j = iatm_beg + i - 1