def test_residue_map():
ethane = pmd.load_file(get_fn('ethane.mol2'), structure=True)
ethane *= 2
oplsaa = Forcefield(name='oplsaa')
topo, NULL = generate_topology(ethane)
with_map = pmd.openmm.load_topology(
topo, oplsaa.createSystem(topo, use_residue_map=True))
without_map = pmd.openmm.load_topology(
topo, oplsaa.createSystem(topo, use_residue_map=False))
for atom_with, atom_without in zip(with_map.atoms, without_map.atoms):
assert atom_with.type == atom_without.type
b_with = atom_with.bond_partners
b_without = atom_without.bond_partners
assert [a0.type for a0 in b_with] == [a1.type for a1 in b_without]
assert [a0.idx for a0 in b_with] == [a1.idx for a1 in b_without]
def test_residue_map():
ethane = pmd.load_file(get_fn('ethane.mol2'), structure=True)
ethane *= 2
oplsaa = Forcefield(name='oplsaa')
topo, NULL = generate_topology(ethane)
topo_with = oplsaa.run_atomtyping(topo, use_residue_map=True)
topo_without = oplsaa.run_atomtyping(topo, use_residue_map=False)
assert all([a.id for a in topo_with.atoms()][0])
assert all([a.id for a in topo_without.atoms()][0])
struct_with = pmd.openmm.load_topology(topo_with, oplsaa.createSystem(topo_with))
struct_without = pmd.openmm.load_topology(topo_without, oplsaa.createSystem(topo_without))
for atom_with, atom_without in zip(struct_with.atoms, struct_without.atoms):
assert atom_with.type == atom_without.type
b_with = atom_with.bond_partners
b_without = atom_without.bond_partners
assert [a0.type for a0 in b_with] == [a1.type for a1 in b_without]
assert [a0.idx for a0 in b_with] == [a1.idx for a1 in b_without]
def test_residue_map():
ethane = pmd.load_file(get_fn('ethane.mol2'), structure=True)
ethane *= 2
oplsaa = Forcefield(name='oplsaa')
topo, NULL = generate_topology(ethane)
topo_with = oplsaa.run_atomtyping(topo, use_residue_map=True)
topo_without = oplsaa.run_atomtyping(topo, use_residue_map=False)
assert all([a.id for a in topo_with.atoms()][0])
assert all([a.id for a in topo_without.atoms()][0])
struct_with = pmd.openmm.load_topology(topo_with,
oplsaa.createSystem(topo_with))
struct_without = pmd.openmm.load_topology(
topo_without, oplsaa.createSystem(topo_without))
for atom_with, atom_without in zip(struct_with.atoms,
struct_without.atoms):
assert atom_with.type == atom_without.type
b_with = atom_with.bond_partners
b_without = atom_without.bond_partners
assert [a0.type for a0 in b_with] == [a1.type for a1 in b_without]
assert [a0.idx for a0 in b_with] == [a1.idx for a1 in b_without]
ethane = oplsaa.apply(untyped_ethane, references_file='ethane.bib')
print("Atoms:")
for atom in ethane.atoms:
print('Atom {} is typed as {}'.format(atom, atom.type))
print("Bonds:")
for bond in ethane.bonds:
print('{} '.format(bond))
print("Angles:")
for angle in ethane.angles:
print('{} '.format(angle))
print("Dihedrals:")
for dihedral in ethane.dihedrals:
print('{} '.format(dihedral))
# Save to GROMACS
ethane.save('ethane.gro')
ethane.save('ethane.top')
# Within the `Forcefield.apply` method, an intermediate OpenMM system is
# created. If you wish to use OpenMM, e.g. for use of potential forms not
# yet supported by ParmEd, you can simply stop the conversion process
# after the OpenMM System creation by directly invoking the internal
# method calls:
from foyer.forcefield import generate_topology
omm_topology, positions = generate_topology(untyped_ethane)
omm_system = oplsaa.createSystem(topology=omm_topology)
