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dual_topology.py
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"""Using visual Python provides an illustratative animation of a dual
topology alchemical perturbation."""
from numpy import linspace
import vpython as v
from base import atom_colours, atom_sizes, draw_bond_between_atoms, System
ce8_morph = ['o34', 'h38']
ce1_morph = ['c34', 'h38', 'h39', 'h40']
def morph(sys, show_waters=True):
atoms = {'ce1': [],
'ce1_morph': [],
'ce8': [],
'ce8_morph': []}
bonds = {'ce1': [],
'ce1_morph': [],
'ce8': [],
'ce8_morph': []}
for mol in sys.mols:
if mol.display:
if mol.name == 't4p':
if not show_waters:
continue
for at in mol.atoms:
if at.type != 'm':
a = v.sphere(pos=at.xyz, radius=0.1,
color=atom_colours[at.type], opacity=0.3)
else:
for at in mol.atoms:
if mol.name == 'ce8' and at.name not in ce8_morph:
continue
a = v.sphere(pos=at.xyz, radius=atom_sizes[at.type],
color=atom_colours[at.type])
if at.name in ce8_morph + ce1_morph:
atoms['%s_morph' % mol.name].append(a)
else:
atoms[mol.name].append(a)
if mol.name == 't4p':
o = mol.atoms[0].xyz
h1 = mol.atoms[1].xyz
h2 = mol.atoms[2].xyz
v.cylinder(pos=o, axis=h1 - o, radius=0.02,
color=v.color.white, opacity=0.3)
v.cylinder(pos=o, axis=h2 - o, radius=0.02,
color=v.color.white, opacity=0.3)
if mol.name in ['ce1']:
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'n3 ', 'hn1'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'n3 ', 'hn2'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'n3 ', 's1 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 's1 ', 'o1 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 's1 ', 'o2 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 's1 ', 'c8 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c8 ', 'c9 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c9 ', 'c10'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c8 ', 'c7 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c7 ', 'c6 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c6 ', 'c5 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c10', 'c5 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c9 ', 'h9 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c10', 'h10'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c7 ', 'h7 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c6 ', 'h6 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c8 ', 'c9 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c5 ', 'n1 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'n1 ', 'n2 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'n2 ', 'c3 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c3 ', 'c1 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c1 ', 'c2 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c2 ', 'n1 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c1 ', 'h1 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c3 ', 'c4 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c1 ', 'c2 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c4 ', 'f1 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c4 ', 'f2 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c4 ', 'f3 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c1 ', 'c2 '))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c2 ', 'c11'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c11', 'c12'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c12', 'c13'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c13', 'c14'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c14', 'c15'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c15', 'c16'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c16', 'c11'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c12', 'h12'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c13', 'h13'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c15', 'h15'))
bonds[mol.name].append(
draw_bond_between_atoms(mol, 'c16', 'h16'))
if mol.name == 'ce8':
bonds['ce8_morph'].append(
draw_bond_between_atoms(mol, 'c14', 'o34'))
bonds['ce8_morph'].append(
draw_bond_between_atoms(mol, 'o34', 'h38'))
if mol.name == 'ce1':
bonds['ce1_morph'].append(
draw_bond_between_atoms(mol, 'c14', 'c34'))
bonds['ce1_morph'].append(
draw_bond_between_atoms(mol, 'c34', 'h38'))
bonds['ce1_morph'].append(
draw_bond_between_atoms(mol, 'c34', 'h39'))
bonds['ce1_morph'].append(
draw_bond_between_atoms(mol, 'c34', 'h40'))
return atoms, bonds
v.scene.background = v.vector(1.0, 1.0, 1.0)
v.scene.width = 800
v.scene.height = 800
limit = 10.0
sys1 = System('dual_topology.pdb', limit)
atoms, bonds = morph(sys1, show_waters=False)
label = v.label(pos=v.vector(4.0, 2.5, 1.0),
xoffset=0.0,
yoffset=300.0,
text="lambda = 0.00",
line=False,
height=50,
color=v.color.red)
v.scene.autoscale = False
v.scene.center = v.vector(4.0, 2.5, 1.0)
v.scene.range = 3
while True:
for lam in linspace(0.0, 1.0, 100):
v.rate(10)
# doing lambda**2 looks better for the opacity
for at in atoms['ce8_morph']:
at.opacity = lam**2 * 0.7 + 0.3
for b in bonds['ce8_morph']:
b.opacity = lam**2 * 0.7 + 0.3
for at in atoms['ce1_morph']:
at.opacity = (1 - lam)**2 * 0.7 + 0.3
for b in bonds['ce1_morph']:
b.opacity = (1 - lam)**2 * 0.7 + 0.3
label.text = "lambda = %.2f" % lam