def species_topologies(self, species_topologies):
self._constrained_species = []
if self._species_topologies is None:
if not isinstance(species_topologies, list):
raise TypeError(
'"species_topologies" should be a list. '
"See help(mosdef_Cassandra.System) for details.")
for topology in species_topologies:
if not isinstance(topology, parmed.Structure):
raise TypeError("Each species should be a "
"parmed.Structure")
# If no bonds in topology don't try to apply constraints
# Store "None" in _constrained_species instead
if len(topology.bonds) > 0:
constrain = ConstrainedMolecule(topology)
constrain.solve()
topology.coordinates = constrain.xyz
self._constrained_species.append(constrain)
else:
self._constrained_species.append(None)
self._species_topologies = [
parmed.structure.copy(s) for s in species_topologies
]
else:
raise AttributeError("species_topologies cannot be "
"modified after System object is created. "
"Create a new System object if you wish to "
"edit the species_topolgies")
def test_benzene(self, benzene_oplsaa):
constrain_mol = ConstrainedMolecule(benzene_oplsaa)
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_solved_model(self, ethane_ua):
constrain_mol = ConstrainedMolecule(ethane_ua)
constrain_mol.solve()
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])
assert constrain_mol.model_solved is True
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_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])
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_copy_coordinates(self, ethane_ua):
constrain_mol = ConstrainedMolecule(ethane_ua)
assert np.allclose(constrain_mol.structure.coordinates, ethane_ua.coordinates)
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]])
def test_invalid_init(self):
with pytest.raises(TypeError):
ConstrainedMolecule("structure")
def test_model_constraints(self, ethane_ua):
constrain_mol = ConstrainedMolecule(ethane_ua)
assert np.allclose(constrain_mol.model.bond_lengths[(0, 1)], ethane_ua.bonds[0].type.req)
def test_model_solved(self, ethane_ua):
constrain_mol = ConstrainedMolecule(ethane_ua)
assert constrain_mol.model_solved is False
def test_create_model(self, ethane_ua):
constrain_mol = ConstrainedMolecule(ethane_ua)
assert isinstance(constrain_mol.model, pyo.ConcreteModel)
import mbuild
import foyer
from constrainmol import ConstrainedMolecule
ff = foyer.forcefields.load_OPLSAA()
mol = mbuild.load("c1ccccc1O", smiles=True)
mol_ff = ff.apply(mol)
mol_ff.save("unconstrained.pdb", overwrite=True)
constrain_mol = ConstrainedMolecule(mol_ff)
constrain_mol.solve()
# Before we update the coordinates let's see
# how much they changed
diff = mol_ff.coordinates - constrain_mol.xyz
print("Final (x,y,z) - initial (x,y,z)")
print(diff)
mol_ff.coordinates = constrain_mol.xyz
mol_ff.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_xyz_setter(self, benzene_oplsaa):
mol = ConstrainedMolecule(benzene_oplsaa)
new_xyz = np.zeros(benzene_oplsaa.coordinates.shape)
with pytest.raises(ValueError):
mol.xyz = new_xyz
def test_xyz_getter(self, benzene_oplsaa):
mol = ConstrainedMolecule(benzene_oplsaa)
assert np.allclose(mol.xyz, benzene_oplsaa.coordinates)
def test_no_bonds(self):
with pytest.raises(ValueError):
ConstrainedMolecule(parmed.Structure())
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)
def test_copy_bonds(self, ethane_ua):
constrain_mol = ConstrainedMolecule(ethane_ua)
assert len(constrain_mol.structure.bonds) == len(ethane_ua.bonds)