def test_apply_subfuncs():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
oplsaa = Forcefield(name='oplsaa')
ethane = oplsaa.apply(mol2)
typemap = oplsaa.run_atomtyping(mol2, use_residue_map=False)
oplsaa._apply_typemap(mol2, typemap)
ethane2 = oplsaa.parametrize_system(mol2)
# Note: Check ParmEd issue #1067 to see if __eq__ is implemented
# assert ethane == ethane2
assert ethane.box == ethane2.box
assert ethane.positions == ethane2.positions
for a1, a2 in zip(ethane.atoms, ethane2.atoms):
assert a1.name == a2.name
assert a1.idx == a2.idx
assert a1.atom_type == a2.atom_type
for b1, b2 in zip(ethane.bonds, ethane2.bonds):
assert b1.atom1.atom_type == b2.atom1.atom_type
assert b1.atom2.atom_type == b2.atom2.atom_type
assert b1.type == b2.type
for ang1, ang2 in zip(ethane.angles, ethane2.angles):
assert ang1.type == ang2.type
def test_residue_map():
ethane = pmd.load_file(get_fn('ethane.mol2'), structure=True)
ethane *= 2
oplsaa = Forcefield(name='oplsaa')
map_with = oplsaa.run_atomtyping(ethane, use_residue_map=True)
map_without = oplsaa.run_atomtyping(ethane, use_residue_map=False)
assert all([a['atomtype'] for a in map_with.values()])
assert all([a['atomtype'] for a in map_without.values()])
struct_with = ethane
struct_without = ethane
oplsaa._apply_typemap(struct_with, map_with)
oplsaa._apply_typemap(struct_without, map_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)
map_with = oplsaa.run_atomtyping(topo, use_residue_map=True)
map_without = oplsaa.run_atomtyping(topo, use_residue_map=False)
assert all([a['atomtype'] for a in map_with.values()][0])
assert all([a['atomtype'] for a in map_without.values()][0])
topo_with = topo
topo_without = topo
oplsaa._apply_typemap(topo_with, map_with)
oplsaa._apply_typemap(topo_without, map_without)
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]
