def test_resolve_model(self, propane_ua):
constrain_mol = ConstrainedMolecule(propane_ua)
constrain_mol.solve()
assert constrain_mol.model_solved is True
propane_solved = parmed.structure.copy(constrain_mol.structure)
constrain_mol.update_xyz(propane_ua.coordinates)
assert constrain_mol.model_solved is False
constrain_mol.solve()
assert constrain_mol.model_solved is True
assert np.allclose(propane_solved.coordinates, constrain_mol.structure.coordinates)
def test_box_diethylether(self, diethylether_box):
(dee_ff, box) = diethylether_box
constrain_mol = ConstrainedMolecule(dee_ff)
for mol in box.children:
constrain_mol.update_xyz(mol.xyz * 10) # nm to angstrom
constrain_mol.solve()
optimized = constrain_mol.structure
xyz = optimized.coordinates
for bond in optimized.bonds:
idx1 = bond.atom1.idx
idx2 = bond.atom2.idx
dist = np.sqrt(np.sum((xyz[idx2] - xyz[idx1])**2))
assert np.allclose(dist, bond.type.req)
def test_update_xyz(self, ethane_ua):
constrain_mol = ConstrainedMolecule(ethane_ua)
ethane_ua.coordinates[0, 0] = -1.0
ethane_ua.coordinates[0, 1] = -0.3
ethane_ua.coordinates[0, 2] = 0.2
constrain_mol.update_xyz(ethane_ua.coordinates)
assert np.allclose(constrain_mol.structure.coordinates, ethane_ua.coordinates)
assert np.allclose(constrain_mol.model.x_start[0].value, ethane_ua.coordinates[0, 0])
assert np.allclose(constrain_mol.model.x_start[1].value, ethane_ua.coordinates[1, 0])
assert np.allclose(constrain_mol.model.y_start[0].value, ethane_ua.coordinates[0, 1])
assert np.allclose(constrain_mol.model.y_start[1].value, ethane_ua.coordinates[1, 1])
assert np.allclose(constrain_mol.model.z_start[0].value, ethane_ua.coordinates[0, 2])
assert np.allclose(constrain_mol.model.z_start[1].value, ethane_ua.coordinates[1, 2])
assert np.allclose(constrain_mol.model.x[0].value, ethane_ua.coordinates[0, 0])
assert np.allclose(constrain_mol.model.x[1].value, ethane_ua.coordinates[1, 0])
assert np.allclose(constrain_mol.model.y[0].value, ethane_ua.coordinates[0, 1])
assert np.allclose(constrain_mol.model.y[1].value, ethane_ua.coordinates[1, 1])
assert np.allclose(constrain_mol.model.z[0].value, ethane_ua.coordinates[0, 2])
assert np.allclose(constrain_mol.model.z[1].value, ethane_ua.coordinates[1, 2])
import mbuild
import foyer
from constrainmol import ConstrainedMolecule
ff = foyer.forcefields.load_OPLSAA()
dee = mbuild.load("CCOCC", smiles=True)
dee_ff = ff.apply(dee)
box = mbuild.fill_box(dee, 500, density=600)
box.save("unconstrained.pdb", overwrite=True)
constrain_mol = ConstrainedMolecule(dee_ff)
for mol in box.children:
constrain_mol.update_xyz(mol.xyz * 10) # nm to angstrom
constrain_mol.solve()
mol.xyz = constrain_mol.xyz / 10.0 # angstrom to nm
box.save("constrained.pdb", overwrite=True)
import parmed
import numpy as np
from constrainmol import ConstrainedMolecule
# Load from gro/topology
system = parmed.load_file("system.top", xyz="system.gro")
system.save("unconstrained.pdb", overwrite=True)
constrained_coordinates = np.zeros(system.coordinates.shape)
unique_res = system.split()
for (res, resids) in unique_res:
constrain_mol = ConstrainedMolecule(res)
for resid in resids:
constrain_mol.update_xyz(system[resid, :].coordinates)
constrain_mol.solve()
atom_ids = [atom.idx for atom in system.residues[resid].atoms]
constrained_coordinates[atom_ids] = constrain_mol.structure.coordinates
system.coordinates = constrained_coordinates
system.save("constrained.pdb", overwrite=True)
def test_invalid_update(self, ethane_ua):
constrain_mol = ConstrainedMolecule(ethane_ua)
with pytest.raises(TypeError):
constrain_mol.update_xyz("string")
with pytest.raises(ValueError):
constrain_mol.update_xyz([[1.0, 1.0, 1.0]])