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a_molecule = [
# a list of models
[ # a list of chains
["A",[
[1081,"","ASN",[
[[" O ",""],
[1.0,22.87," O"],
[0.287,20.822,40.742]],
[[" C ",""],
[1.0,22.17," C"],
[0.303,20.8649,39.5379]],
[[" ND2",""],
[1.0,29.17," N"],
[1.363,16.5869,37.908]],
[[" OD1",""],
[1.0,32.810001373291," O"],
[2.877,18.049,38.597]],
[[" CG ",""],
[1.0,27.4," C"],
[1.711,17.676,38.529]],
[[" CB ",""],
[1.0,24.58," C"],
[0.547,18.528,39.102]],
[[" CA ",""],
[1.0,23.18," C"],
[0.657,19.99,38.7]],
[[" N ",""],
[1.0,22.87," N"],
[0.531,20.0909,37.2929]]]
],
[1082,"","GLN",[
[[" O ",""],
[1.0,19.223," O"],
[0.419,24.068,39.868]],
[[" C ",""],
[1.0,20.54," C"],
[1.431,23.549,40.3401]],
[[" NE2",""],
[1.0,14.77," N"],
[5.637,22.1359,39.458]],
[[" OE1",""],
[1.0,25.2299," O"],
[5.2859,23.3729,41.34]],
[[" CD ",""],
[1.0,25.7," C"],
[5.08,23.136,40.01]],
[[" CG ",""],
[1.0,19.98," C"],
[4.176,24.007,39.253]],
[[" CB ",""],
[1.0,21.63," C"],
[3.038,23.178,38.604]],
[[" CA ",""],
[1.0,20.56," C"],
[2.118,22.47,39.593]],
[[" N ",""],
[1.0,21.99," N"],
[1.156,21.65,38.894]]]
]
] # end of chain A content
] # end of chain A
] # end of list of chains
] # end of list of models
# Return a python_mol
#
#
#
def jiggled_mol(reference_mol, current_mol, traj_frac):
def jiggle_random():
import random
return (random.random() - 0.5)
def jiggled_pos(ref_pos, current_pos):
if (traj_frac < 0): # magic value
# make a starting set of coords
return map(lambda x1:
jiggle_random() * 1.0 + x1,
ref_pos)
else:
q = 1 - traj_frac
return map(lambda x, x_ref:
traj_frac * x_ref + q * x +
0.4 * q * jiggle_random(),
current_pos, ref_pos)
def jiggled_atom(ref_atom, current_atom):
ref_pos = ref_atom[2]
cur_pos = current_atom[2]
ret = [ref_atom[0], ref_atom[1], jiggled_pos(ref_pos, cur_pos)]
return ret
def jiggled_residue(ref_res, cur_res):
ret = [ref_res[0], ref_res[1], ref_res[2], map(jiggled_atom, ref_res[3], cur_res[3])]
return ret
def jiggled_chain(ref_chain, cur_chain):
ret = [ref_chain[0],
map(jiggled_residue,
ref_chain[1],
cur_chain[1])]
return ret
def jiggled_model(ref_model, cur_model):
ret = map(jiggled_chain, ref_model, cur_model)
return ret
j_mod = map (jiggled_model, reference_mol, current_mol)
return j_mod
#
def disrupt(reference_mol, biggness):
ret = jiggled_mol(reference_mol, reference_mol, -1)
return ret
#
max_count = 5000.0
mol_no = add_molecule(a_molecule, "test molecule")
if (not mol_no == -1):
set_rotation_centre(*centre_of_mass(mol_no))
for count in range(int(max_count) + 1):
current_mol = disrupt(a_molecule,0.8)
new_mol = jiggled_mol(a_molecule, current_mol,
count / max_count)
#print "cycle ", count, count/max_count, max_count
clear_and_update_molecule(mol_no, new_mol)
# gtk stuff
if gtk.events_pending():
gtk.main_iteration(False)
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