def test_bond_guessing():
from chemlab.db import ChemlabDB, CirDB
from chemlab.graphics import display_molecule
from chemlab.io import datafile
mol = datafile('tests/data/3ZJE.pdb').read('molecule')
print(mol.r_array)
mol.guess_bonds()
assert mol.bonds.size > 0
# We should find the bond guessing also for systems
# System Made of two benzenes
bz = datafile("tests/data/benzene.mol").read('molecule')
bzbonds = bz.bonds
bz.bonds = np.array([])
# Separating the benzenes by large amount
bz2 = bz.copy()
bz2.r_array += 2.0
s = System([bz, bz2])
s.guess_bonds()
assert_eqbonds(s.bonds, np.concatenate((bzbonds, bzbonds + 6)))
# Separating benzenes by small amount
bz2 = bz.copy()
bz2.r_array += 0.15
s = System([bz, bz2])
s.guess_bonds()
assert_eqbonds(s.bonds, np.concatenate((bzbonds, bzbonds + 6)))
def test_reorder_molecules(self):
mols = self._make_molecules()
system = System(mols)
system.bonds = np.array([[0, 1], [3, 5]])
# Reordering
system.reorder_molecules([1, 0, 2, 3])
assert_eqbonds(system.bonds, [[0, 2], [3, 4]])
def test_bond_orders():
# Get a molecule with some bonds
wat = _make_water()
wat_o = wat.copy()
# 0,1 0,2
assert_npequal(wat.bond_orders, np.array([0, 0]))
# Remove a bond
wat.bonds = np.array([[0, 1]])
assert_npequal(wat.bond_orders, np.array([0]))
wat.bond_orders = np.array([2])
# Try with a system
s = System()
s.add(wat_o)
s.add(wat)
assert_npequal(s.bond_orders, np.array([0, 0, 2]))
s.reorder_molecules([1, 0])
# Bonds get sorted accordingly
assert_npequal(s.bond_orders, np.array([2, 0, 0]))
s.bonds = np.array([[0, 1], [0, 2], [3, 4], [3, 5]])
assert_npequal(s.bond_orders, np.array([2, 0, 0, 0]))
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_from_batch(self):
mols = self._make_molecules()
system = System()
with system.batch() as batch:
[batch.append(mol) for mol in mols]
self._assert_init(system)
def test_subsystem_from_atoms(self):
mols = self._make_molecules()
system = System(mols)
sub = subsystem_from_atoms(
system,
np.array(
[True, True, False, False, False, False, False, False, False]))
assert_equals(sub.n_mol, 1)
def load_molecule(name, format=None):
'''Read a `~chemlab.core.Molecule` from a file.
.. seealso:: `chemlab.io.datafile`
'''
mol = datafile(name, format=format).read('molecule')
display_system(System([mol]))
def display_molecule(mol, autozoom=True):
'''Display a `~chemlab.core.Molecule` instance in the viewer.
This function wraps the molecule in a system before displaying
it.
'''
s = System([mol])
display_system(s, autozoom=True)
def test_remove_atoms(self):
# This will remove the first and last molecules
mols = self._make_molecules()
system = System(mols)
system.remove_atoms([0, 1, 11])
assert_eqbonds(system.bonds, [[0, 1], [0, 2], [3, 4], [3, 5]])
assert_npequal(
system.type_array,
np.array(['O', 'H', 'H', 'O', 'H', 'H'], dtype='object'))
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 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_local():
db = ChemlabDB()
bz = db.get("molecule", "example.norbornene")
pre_string = bz.tojson()
db = LocalDB("/tmp/testdb/")
db.store("molecule", 'norbornene', bz, nowarn=True)
post_string = db.get('molecule', 'norbornene').tojson()
assert pre_string == post_string
# Do the same thing for a system of 3 norbornenes
s = System([bz.copy() for i in range(3)])
pre_string = s.tojson()
db.store("system", 'norbornene-3', s, nowarn=True)
post_string = db.get('system', 'norbornene-3').tojson()
assert pre_string == post_string
def test_local():
db = ChemlabDB()
bz = db.get("molecule", "example.norbornene")
pre_dict = bz.to_dict()
db = LocalDB("/tmp/testdb/")
db.store("molecule", 'norbornene', bz, nowarn=True)
post_dict = db.get('molecule', 'norbornene').to_dict()
npeq_(pre_dict['r_array'], post_dict['r_array'])
# Do the same thing for a system of 3 norbornenes
s = System([bz.copy() for i in range(3)])
pre_dict = s.to_dict()
db.store("system", 'norbornene-3', s, nowarn=True)
post_dict = db.get('system', 'norbornene-3').to_dict()
npeq_(pre_dict['r_array'], post_dict['r_array'])
def test_init(self):
mols = self._make_molecules()
system = System(mols)
self._assert_init(system)
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()
def test_from_actual_empty(self):
mols = self._make_molecules()
system = System([])
[system.add(mol) for mol in mols]
def test_subsystem_from_molecules(self):
mols = self._make_molecules()
system = System(mols)
subsystem = subsystem_from_molecules(system, np.array([0, 2]))
assert_equals(subsystem.n_mol, 2)