def test_write_gromacs():
water = Molecule(
[
Atom("O", [0.0, 0.0, 0.0], export={"grotype": "OW"}),
Atom("H", [0.1, 0.0, 0.0], export={"grotype": "HW1"}),
Atom("H", [-0.03333, 0.09428, 0.0], export={"grotype": "HW2"}),
],
export={"groname": "SOL"},
)
sys = System.empty(200, 3 * 200, box_vectors=np.eye(3) * 2.0)
for i in range(200):
sys.add(water.copy())
df = datafile("/tmp/dummy.gro", mode="w")
df.write("system", sys)
with assert_raises(Exception):
df = datafile("/tmp/dummy.gro")
df.write("system", sys)
df = datafile("/tmp/dummy.gro")
sread = df.read("system")
assert all(sread.type_array == sys.type_array)
def test_bond_renderer():
v = QtViewer()
v.widget.background_color = colors.black
mol = Molecule([
Atom("O", [-0.499, 0.249, 0.0]),
Atom("H", [-0.402, 0.249, 0.0]),
Atom("H", [-0.532, 0.198, 0.10])
])
mol.bonds = np.array([[0, 1], [0, 2]])
#mol = CirDB().get("molecule", "moronic acid")
#radii_map = {"O": 0.03, "H": 0.03}
radii_map = defaultdict(lambda: 0.03)
br = v.add_renderer(BondRenderer,
mol.bonds,
mol.r_array,
mol.type_array,
style='impostors')
ar = v.add_renderer(AtomRenderer,
mol.r_array,
mol.type_array,
"impostors",
radii_map=radii_map)
v.run()
def read(self, feature, *args, **kwargs):
if feature == 'molecular orbitals':
n = args[0]
basis_functions = self.data.gbasis
if feature == 'molecule':
# Angstrom to nanometers
# CJS added option to get molecule from steps of optimisation
# or optimisations for PES scans
# TODO error checking
if kwargs.has_key('step'):
return Molecule.from_arrays(
r_array=self.data.atomcoords[kwargs['step']] / 10,
type_array=np.array(
[symbols[a] for a in self.data.atomnos]))
elif kwargs.has_key('scan'):
return Molecule.from_arrays(
r_array=self.data.scancoords[kwargs['scan']] / 10,
type_array=np.array(
[symbols[a] for a in self.data.atomnos]))
else:
return Molecule.from_arrays(
r_array=self.data.atomcoords[-1] / 10,
type_array=np.array(
[symbols[a] for a in self.data.atomnos]))
else:
return getattr(self.data, feature)
def test_random_lattice():
'''Testing random made box'''
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
wat = Molecule.from_arrays(type_array=['O', 'H', 'H'])
s = random_lattice_box([na, cl, wat], [160, 160, 160], [4, 4, 4])
eq_(s.dimensions['molecule'], 160 * 3)
eq_(s.dimensions['atom'], 160 * 5)
def test_crystal():
'''Building a crystal by using spacegroup module'''
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl],
225,
repetitions=[13, 13, 13])
def test_random():
'''Testing random made box'''
from chemlab.db import ChemlabDB
cdb = ChemlabDB()
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
wat = cdb.get("molecule", 'gromacs.spce')
s = random_lattice_box([na, cl, wat], [160, 160, 160], [4, 4, 4])
def test_sort():
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl],
225,
repetitions=[3, 3, 3])
tsys.sort()
assert np.all(tsys.type_array[:tsys.n_mol / 2] == 'Cl')
def test_write_pdb():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'grotype': 'OW'}),
Atom('H', [0.1, 0.0, 0.0], export={'grotype': 'HW1'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'grotype': 'HW2'})],
export={'groname': 'SOL'})
sys = System.empty(200, 3*200, box_vectors = np.eye(3) * 2.0)
for i in range(200):
sys.add(water.copy())
df = datafile('/tmp/dummy.gro', mode="w")
df.write("system", sys)
def test_write_pdb():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'pdb.type': 'O'}),
Atom('H', [0.1, 0.0, 0.0], export={'pdb.type': 'H'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'pdb.type': 'H'})],
export={'groname': 'SOL'})
sys = System.empty(200, 3*200, box_vectors = np.eye(3) * 2.0)
for i in range(200):
water.r_array += 0.1
sys.add(water.copy())
df = datafile('/tmp/dummy.pdb', mode="w")
df.write("system", sys)
def test_serialization():
cl = Molecule([Atom.from_fields(type='Cl', r=[0.0, 0.0, 0.0])])
jsonstr = cl.tojson()
assert Molecule.from_json(jsonstr).tojson() == jsonstr
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0],[0.5, 0.5, 0.5]], [na, cl], 225, repetitions=[3,3,3])
jsonstr = tsys.tojson()
assert System.from_json(jsonstr).tojson() == jsonstr
def test_write_pdb():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'pdb.type': 'O'}),
Atom('H', [0.1, 0.0, 0.0], export={'pdb.type': 'H'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'pdb.type': 'H'})],
export={'groname': 'SOL'})
sys = System.empty()
with sys.batch() as b:
for i in range(200):
water.r_array += 0.1
b.append(water.copy())
df = datafile('/tmp/dummy.pdb', mode="w")
df.write("system", sys)
def test_write_pdb():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'pdb.type': 'O'}),
Atom('H', [0.1, 0.0, 0.0], export={'pdb.type': 'H'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'pdb.type': 'H'})],
export={'groname': 'SOL'})
sys = System.empty()
with sys.batch() as b:
for i in range(200):
water.r_array += 0.1
b.append(water.copy())
df = datafile('/tmp/dummy.pdb', mode="w")
df.write("system", sys)
def test_wireframe_renderer():
v = QtViewer()
#v.widget.background_color = black
mol = Molecule([Atom("O", [-0.499, 0.249, 0.0]),
Atom("H", [-0.402, 0.249, 0.0]),
Atom("H", [-0.532, 0.198, 0.10])])
mol.bonds = np.array([[0, 1],[0, 2]])
mol = CirDB().get("molecule", "moronic acid")
ar = v.add_renderer(WireframeRenderer, mol.r_array, mol.type_array, mol.bonds)
# Try without bonds
#ar2 = v.add_renderer(WireframeRenderer, mol.r_array + 0.5, mol.type_array, np.array([]))
v.run()
def test_wireframe_renderer():
v = QtViewer()
#v.widget.background_color = black
mol = Molecule([Atom("O", [-0.499, 0.249, 0.0]),
Atom("H", [-0.402, 0.249, 0.0]),
Atom("H", [-0.532, 0.198, 0.10])])
mol.bonds = np.array([[0, 1],[0, 2]])
mol = CirDB().get("molecule", "moronic acid")
ar = v.add_renderer(WireframeRenderer, mol.r_array, mol.type_array, mol.bonds)
# Try without bonds
#ar2 = v.add_renderer(WireframeRenderer, mol.r_array + 0.5, mol.type_array, np.array([]))
v.run()
def test_bonds():
# TODO: deprecate this shit
from chemlab.io import datafile
bz = datafile("tests/data/benzene.mol").read('molecule')
na = Molecule([
Atom('O', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]),
Atom('H', [0.0, 0.0, 0.0]),
])
# Adding bonds
s = System()
with s.batch() as b:
b.append(bz)
assert_npequal(s.bonds, bz.bonds)
assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2])
assert_npequal(s.bond_orders, bz.bond_orders)
s.add(bz)
assert_npequal(
s.type_array,
['C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C'])
eq_(s.dimensions['atom'], 12)
assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 7)))
# Reordering
s.bonds = np.array([[0, 1], [6, 8]])
s.reorder_molecules([1, 0])
assert_eqbonds(s.bonds, np.array([[6, 7], [0, 2]]))
# Selection
ss = subsystem_from_molecules(s, [1])
assert_npequal(ss.bonds, np.array([[0, 1]]))
def test_write_pdb():
water = Molecule(
[
Atom("O", [0.0, 0.0, 0.0], export={"pdb.type": "O"}),
Atom("H", [0.1, 0.0, 0.0], export={"pdb.type": "H"}),
Atom("H", [-0.03333, 0.09428, 0.0], export={"pdb.type": "H"}),
],
export={"groname": "SOL"},
)
sys = System.empty(200, 3 * 200, box_vectors=np.eye(3) * 2.0)
for i in range(200):
water.r_array += 0.1
sys.add(water.copy())
df = datafile("/tmp/dummy.pdb", mode="w")
df.write("system", sys)
def test_serialization():
cl = Molecule([Atom.from_fields(type='Cl', r=[0.0, 0.0, 0.0])])
jsonstr = cl.to_json()
m = Molecule.from_json(jsonstr)
eq_(Molecule.from_json(jsonstr).to_json(), jsonstr)
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
[na, cl],
225,
repetitions=[3, 3, 3])
jsonstr = tsys.to_json()
npeq_(System.from_json(jsonstr).r_array, tsys.r_array)
def test_write_gromacs():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'grotype': 'OW'}),
Atom('H', [0.1, 0.0, 0.0], export={'grotype': 'HW1'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'grotype': 'HW2'})],
export={'groname': 'SOL'})
sys = System.empty(200, 3*200, box_vectors = np.eye(3)*2.0)
for i in range(200):
sys.add(water.copy())
df = datafile('/tmp/dummy.gro', mode="w")
df.write('system', sys)
df = datafile('/tmp/dummy.gro')
sread = df.read('system')
assert all(sread.type_array == sys.type_array)
def test_residue():
m = Molecule.from_arrays(type_array=['H', 'H', 'H', 'O', 'O'],
residue_name=['VAL', 'ALA'],
maps={('atom', 'residue'): [0, 0, 0, 1, 1]})
assert_npequal(m.sub(residue_index=0).type_array, ['H', 'H', 'H'])
s = System([m, m])
assert_npequal(s.maps['atom', 'residue'].value, [0, 0, 0, 1, 1, 2, 2, 2, 3, 3])
def _make_water():
mol = Molecule([
Atom("O", [-4.99, 2.49, 0.0]),
Atom("H", [-4.02, 2.49, 0.0]),
Atom("H", [-5.32, 1.98, 1.0])
],
bonds=[[0, 1], [0, 2]],
export={'hello': 1.0})
return mol
def test_random_lattice():
'''Testing random made box'''
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
wat = Molecule.from_arrays(type_array=['O', 'H', 'H'])
s = random_lattice_box([na, cl, wat], [160, 160, 160], [4, 4, 4])
eq_(s.dimensions['molecule'], 160 * 3)
eq_(s.dimensions['atom'], 160 * 5)
def test_init(self):
mol = _make_water()
eq_(mol.export, {'hello': 1.0})
assert_npequal(mol.get_attribute('type_array').value, ['O', 'H', 'H'])
assert_npequal(mol.type_array, ['O', 'H', 'H'])
assert_npequal(mol.bonds, [[0, 1], [0, 2]])
mol = Molecule.empty()
eq_(mol.dimensions['atom'], 0)
eq_(mol.dimensions['bond'], 0)
def test_residue():
m = Molecule.from_arrays(type_array=['H', 'H', 'H', 'O', 'O'],
residue_name=['VAL', 'ALA'],
maps={('atom', 'residue'): [0, 0, 0, 1, 1]})
assert_npequal(m.sub(residue_index=0).type_array, ['H', 'H', 'H'])
s = System([m, m])
assert_npequal(s.maps['atom', 'residue'].value,
[0, 0, 0, 1, 1, 2, 2, 2, 3, 3])
def test_write_gromacs():
water = Molecule([
Atom('O', [0.0, 0.0, 0.0], export={'grotype': 'OW'}),
Atom('H', [0.1, 0.0, 0.0], export={'grotype': 'HW1'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'grotype': 'HW2'})
],
export={'groname': 'SOL'})
sys = System.empty(200, 3 * 200, box_vectors=np.eye(3) * 2.0)
for i in range(200):
sys.add(water.copy())
df = datafile('/tmp/dummy.gro', mode="w")
df.write('system', sys)
df = datafile('/tmp/dummy.gro')
sread = df.read('system')
assert all(sread.type_array == sys.type_array)
def test_init(self):
mol = _make_water()
eq_(mol.export, {'hello': 1.0})
assert_npequal(mol.get_attribute('type_array').value, ['O', 'H', 'H'])
assert_npequal(mol.type_array, ['O', 'H', 'H'])
assert_npequal(mol.bonds, [[0, 1], [0, 2]])
mol = Molecule.empty()
eq_(mol.dimensions['atom'], 0)
eq_(mol.dimensions['bond'], 0)
def test_atom_renderer():
'''Simple rendering of atoms as spheres'''
mol = Molecule([Atom("O", [-0.499, 0.249, 0.0]),
Atom("H", [-0.402, 0.249, 0.0]),
Atom("H", [-0.532, 0.198, 0.10])])
v = QtViewer()
ar = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array)
v.run()
def test_bond_renderer():
v = QtViewer()
v.widget.background_color = colors.black
mol = Molecule([Atom("O", [-0.499, 0.249, 0.0]),
Atom("H", [-0.402, 0.249, 0.0]),
Atom("H", [-0.532, 0.198, 0.10])])
mol.bonds = np.array([[0, 1],[0, 2]])
#mol = CirDB().get("molecule", "moronic acid")
#radii_map = {"O": 0.03, "H": 0.03}
radii_map = defaultdict(lambda: 0.03)
br = v.add_renderer(BondRenderer, mol.bonds, mol.r_array,
mol.type_array, style='impostors')
ar = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array,
"impostors", radii_map = radii_map)
v.run()
def test_text_ui():
v = QtViewer()
mol = Molecule([Atom("O", [-0.499, 0.249, 0.0]),
Atom("H", [-0.402, 0.249, 0.0]),
Atom("H", [-0.532, 0.198, 0.10])])
# To add some interaction to it
ar = v.add_renderer(AtomRenderer, mol.r_array, mol.type_array, "impostors")
tr = v.add_ui(TextUI, 100, 100, 'Hello, Crap')
v.run()
def test_write_gromacs():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], name="OW"),
Atom('H', [0.1, 0.0, 0.0], name='HW1'),
Atom('H', [-0.03333, 0.09428, 0.0], name='HW2')],
name='SOL')
sys = System.empty()
with sys.batch() as b:
for i in range(200):
b.append(water.copy())
sys.box_vectors = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
df = datafile('/tmp/dummy.gro', mode="w")
df.write('system', sys)
with assert_raises(Exception):
df = datafile('/tmp/dummy.gro')
df.write('system', sys)
df = datafile('/tmp/dummy.gro')
sread = df.read('system')
assert all(sread.type_array == sys.type_array)
def test_camera_autozoom():
v = QtViewer()
mol = Molecule([Atom("O", [-0.499, 0.249, 0.0]),
Atom("H", [-0.402, 0.249, 0.0]),
Atom("H", [-0.532, 0.198, 0.10])])
s = datafile('tests/data/3ZJE.pdb').read('system')
# To add some interaction to it
ar = v.add_renderer(AtomRenderer, s.r_array, s.type_array, "impostors")
v.widget.camera.autozoom(s.r_array)
v.run()
def test_write_gromacs():
water = Molecule([Atom('O', [0.0, 0.0, 0.0], name="OW"),
Atom('H', [0.1, 0.0, 0.0], name='HW1'),
Atom('H', [-0.03333, 0.09428, 0.0], name='HW2')],
name='SOL')
sys = System.empty()
with sys.batch() as b:
for i in range(200):
b.append(water.copy())
sys.box_vectors = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
df = datafile('/tmp/dummy.gro', mode="w")
df.write('system', sys)
with assert_raises(Exception):
df = datafile('/tmp/dummy.gro')
df.write('system', sys)
df = datafile('/tmp/dummy.gro')
sread = df.read('system')
assert all(sread.type_array == sys.type_array)
def test_serialization():
cl = Molecule([Atom.from_fields(type='Cl', r=[0.0, 0.0, 0.0])])
jsonstr = cl.to_json()
m = Molecule.from_json(jsonstr)
eq_(Molecule.from_json(jsonstr).to_json(), jsonstr)
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl],
225,
repetitions=[3, 3, 3])
jsonstr = tsys.to_json()
npeq_(System.from_json(jsonstr).r_array, tsys.r_array)
def get_system(self):
self.coordinates = self.interaction_manager.get_coordinates()
atoms = []
for index in range(len(self.interaction_manager.atoms)):
atom = self.interaction_manager.atoms[index]
type = atom.atom_type
if type.upper() == "C":
if atom.get_free_valency()!=0:
type = "Ne"
pos = 3.5 * self.coordinates[index]
atoms.append(Atom(type,pos))
mol = Molecule(atoms, self.interaction_manager.get_bonds_array())
system = System([mol])
system.bonds = np.array(self.interaction_manager.get_bonds_array())
return system
def test_serialization():
cl = Molecule([Atom.from_fields(type='Cl', r=[0.0, 0.0, 0.0])])
jsonstr = cl.tojson()
assert Molecule.from_json(jsonstr).tojson() == jsonstr
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
# Fract position of Na and Cl, space group 255
tsys = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], [na, cl],
225,
repetitions=[3, 3, 3])
jsonstr = tsys.tojson()
assert System.from_json(jsonstr).tojson() == jsonstr
def test_bonds():
from chemlab.io import datafile
bz = datafile("tests/data/benzene.mol").read('molecule')
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
# Adding bonds
s = System.empty(2, 2 * bz.n_atoms)
s.add(bz)
assert_npequal(s.bonds, bz.bonds)
assert_npequal(bz.bond_orders, [1, 2, 2, 1, 1, 2])
assert_npequal(s.bond_orders, bz.bond_orders)
s.add(bz)
assert_npequal(s.bonds, np.concatenate((bz.bonds, bz.bonds + 6)))
#assert_npequal(s.bond_orders)
# Reordering
orig = np.array([[0, 1], [6, 8]])
s.bonds = orig
s.reorder_molecules([1, 0])
assert_npequal(s.bonds, np.array([[6, 7], [0, 2]]))
# This doesn't change the bond_ordering
# Selection
ss = subsystem_from_molecules(s, [1])
assert_npequal(ss.bonds, np.array([[0, 1]]))
import inspect
ss2 = System.from_arrays(**dict(inspect.getmembers(ss)))
ss2.r_array += 10.0
ms = merge_systems(ss, ss2)
assert_npequal(ms.bonds, np.array([[0, 1], [6, 7]]))
assert_npequal(ms.bond_orders, np.array([1, 1]))
# From_arrays
s = System.from_arrays(mol_indices=[0], bonds=bz.bonds, **bz.__dict__)
assert_npequal(s.bonds, bz.bonds)
assert_npequal(s.bond_orders, bz.bond_orders)
# Get molecule entry
# Test the bonds when they're 0
s.bonds = np.array([])
assert_equals(s.get_derived_molecule_array('formula'), 'C6')
def split_groups(mol):
groups = []
unselected = [x for x in range(mol.n_atoms)]
while len(unselected) > 0:
new_atoms = set()
new_atoms.add(unselected[0])
atoms = []
new_bonds = []
new_bond_orders = []
while len(new_atoms) > 0:
a = list(new_atoms)[0]
atoms.append(a)
new_atoms.remove(a)
for bond_index, bond in enumerate(mol.bonds):
if atoms[-1] == bond[0] and bond[1] not in atoms:
new_atoms.add(bond[1])
if atoms[-1] == bond[1] and bond[0] not in atoms:
new_atoms.add(bond[0])
if a in bond and bond.tolist() not in new_bonds:
new_bonds.append(bond.tolist())
new_bond_orders.append(mol.bond_orders[bond_index])
atoms.sort()
groups.append([atoms, new_bonds, new_bond_orders])
unselected = [x for x in range(mol.n_atoms) if x not in sum([y[0] for y in groups],[])]
molecules = []
for group in groups:
new_bonds_reduced = np.array([[group[0].index(x[0]), group[0].index(x[1])] for x in group[1]])
numpy_vectors = [system.r_array[x] for x in group[0]]
new_molecule = Molecule.from_arrays(r_array=np.array(numpy_vectors),
type_array=system.type_array[a],
bonds=new_bonds_reduced,
bond_orders=group[2]
)
new_molecule.export['vectors'] = numpy_vectors
molecules.append(new_molecule)
return molecules
from chemlab.core import Atom, Molecule, crystal
from chemlab.graphics.qt import display_system
# Molecule templates
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
s = crystal(
[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], # Fractional Positions
[na, cl], # Molecules
225, # Space Group
cellpar=[.54, .54, .54, 90, 90, 90], # unit cell parameters
repetitions=[5, 5, 5]) # unit cell repetitions in each direction
display_system(s)
from chemlab.graphics import display_system
# Spacing between two grid points
spacing = 0.3
# an 8x8x8 grid, for a total of 512 points
grid_size = (8, 8, 8)
# Preallocate the system
# 512 molecules, and 512*3 atoms
s = System.empty(512, 512*3)
# Water template, it contains export informations for gromacs
# more about export later...
water_tmp = Molecule([Atom('O', [0.0, 0.0, 0.0], export={'grotype': 'OW'}),
Atom('H', [0.1, 0.0, 0.0], export={'grotype': 'HW1'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'grotype':'HW2'})],
export={'groname': 'SOL'})
for a in range(grid_size[0]):
for b in range(grid_size[1]):
for c in range(grid_size[2]):
grid_point = np.array([a,b,c]) * spacing # array operation
water_tmp.move_to(grid_point)
s.add(water_tmp)
# Adjust boxsize for periodic conditions
s.box_vectors = np.eye(3) * 8 * spacing
# Visualize to verify that the system was setup correctly
# display_system(s)
thr_b = rval + threshold
#thr_a2 = thr_a * thr_a
thr_b2 = thr_b * thr_b
dr2 = ((r_array[i] - r_array[j])**2).sum()
# print(dr2)
if dr2 < thr_b2:
bonds.append((i, j))
return np.array(bonds)
# END_PATCH ---
Si = Molecule([Atom('Si', [0.0, 0.0, 0.0])])
la = 0.5431
s = crystal(
[[0.0, 0.0, 0.0], [0.25, 0.25, 0.25]], # Fractional Positions
[Si, Si], # Molecules
225, # Space Group
cellpar=[la, la, la, 90, 90, 90], # unit cell parameters
repetitions=[2, 2, 2]) # unit cell repetitions in each direction
bonds = guess_bonds(s.r_array, s.type_array, threshold=0.02)
#s.bonds = [[0,1], [1, 2]]
v = QtViewer()
v.add_renderer(BallAndStickRenderer,
s.r_array,
# Spacing between two grid points
spacing = 0.3
# an 8x8x8 grid, for a total of 512 points
grid_size = (8, 8, 8)
# Preallocate the system
# 512 molecules, and 512*3 atoms
s = System.empty(512, 512 * 3)
# Water template, it contains export informations for gromacs
# more about export later...
water_tmp = Molecule([
Atom('O', [0.0, 0.0, 0.0], export={'grotype': 'OW'}),
Atom('H', [0.1, 0.0, 0.0], export={'grotype': 'HW1'}),
Atom('H', [-0.03333, 0.09428, 0.0], export={'grotype': 'HW2'})
],
export={'groname': 'SOL'})
for a in range(grid_size[0]):
for b in range(grid_size[1]):
for c in range(grid_size[2]):
grid_point = np.array([a, b, c]) * spacing # array operation
water_tmp.move_to(grid_point)
s.add(water_tmp)
# Adjust boxsize for periodic conditions
s.box_vectors = np.eye(3) * 8 * spacing
# Visualize to verify that the system was setup correctly
# display_system(s)
from chemlab.core import System, Atom, Molecule
import numpy as np
class MyBallAndStickRepresentation(BallAndStickRepresentation):
def on_atom_selection_changed(self):
sel = self.selection_state['atoms'].indices
cols = np.array(self.atom_colors.array)
cols[sel, -1] = 50
self.atom_renderer.update_colors(cols)
self.viewer.update()
a1 = Atom('Ar', [0.0, 0.0, 0.0])
a2 = Atom('N', [0.0, 0.5, 1.0])
mol = Molecule([a1, a2])
system = System([mol])
viewer = QtMolecularViewer()
viewer.add_representation(MyBallAndStickRepresentation, system)
def print_indices():
indices = viewer.representation.selection_state['atoms'].indices
if len(indices) > 0:
print(indices)
viewer.schedule(print_indices)
viewer.run()