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from pymol import cmd
from chempy.models import Indexed
from chempy import Atom,Bond
# here's how you build a chemical python model from scratch...
# you can run this script as follows:
# "pymol chempy_model01.py" from unix
# "run chempy_model01.py" from within PyMOL
# first we need some raw material -- this stuff could come from
# anywhere, but I'll just start with some Python lists...
atoms = [
['C', 'CH3' ,'1','ACE'],
['C', 'C' ,'1','ACE'],
['O', 'O' ,'1','ACE'],
['H', '1HH3','1','ACE'],
['H', '2HH3','1','ACE'],
['H', '3HH3','1','ACE'],
['N', 'N' ,'2','ALA'],
['C', 'CA' ,'2','ALA'],
['C', 'CB' ,'2','ALA'],
['C', 'C' ,'2','ALA'],
['O', 'O' ,'2','ALA'],
['H', '1HB' ,'2','ALA'],
['H', '2HB' ,'2','ALA'],
['H', '3HB' ,'2','ALA'],
['H', 'H' ,'2','ALA'],
['H', 'HA' ,'2','ALA'],
['N', 'N' ,'3','NME'],
['C', 'CH3' ,'3','NME'],
['H', '1HH3','3','NME'],
['H', '2HH3','3','NME'],
['H', '3HH3','3','NME'],
['H', 'H' ,'3','NME'],
]
coords = [
[ -1.862, -11.290, 18.059],
[ -0.948, -10.106, 18.286],
[ -1.142, -9.030, 17.704],
[ -1.851, -11.572, 17.015],
[ -1.532, -12.131, 18.651],
[ -2.873, -11.038, 18.343],
[ 0.186, -10.234, 19.211],
[ 0.862, -8.940, 19.211],
[ 0.354, -8.148, 20.428],
[ 2.362, -9.114, 19.211],
[ 2.929, -9.926, 19.953],
[ -0.742, -7.998, 20.392],
[ 0.578, -8.662, 21.383],
[ 0.810, -7.143, 20.485],
[ 0.696, -11.147, 18.941],
[ 0.594, -8.401, 18.283],
[ 3.174, -8.292, 18.302],
[ 4.560, -8.671, 18.519],
[ 4.679, -9.084, 19.509],
[ 4.859, -9.412, 17.791],
[ 5.199, -7.806, 18.421],
[ 2.880, -7.315, 18.440],
]
bonds = [
[0,1,1],
[0,3,1],
[0,4,1],
[0,5,1],
[1,2,2],
[6,1,1],
[6,7,1],
[6,14,1],
[7,8,1],
[7,9,1],
[7,15,1],
[9,10,2],
[9,16,1],
[11,8,1],
[12,8,1],
[13,8,1],
[16,17,1],
[16,21,1],
[17,18,1],
[17,19,1],
[17,20,1],
]
# okay, now we'll build the object from scratch...
# create a model instance
model = Indexed()
# append the atoms onto it
for a in atoms:
new_atom = Atom()
new_atom.symbol = a[0] # elemental symbol
new_atom.name = a[1] # atom name
new_atom.resi = a[2] # residue identifier
new_atom.resn = a[3] # residue name
model.atom.append(new_atom)
# (note that there are a bunch of other fields we're not using -- and none are required)
# add coordinates onto the atoms
for a in model.atom: # now assign coordinates
a.coord = coords.pop(0)
# now specify the bonds
for a in bonds:
new_bond = Bond()
new_bond.index = [a[0],a[1]] # atom indices (zero-based)
new_bond.order = a[2] # bond order
model.bond.append(new_bond)
# finally, load the model into PyMOL
cmd.load_model(model,"example")
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