def test_ring_count():
# Two rings
fused = pmd.load_file(get_fn('fused.mol2'), structure=True)
top, _ = generate_topology(fused)
rule = SMARTSGraph(name='test', parser=PARSER,
smarts_string='[#6;R2]')
match_indices = list(rule.find_matches(top))
for atom_idx in (3, 4):
assert atom_idx in match_indices
assert len(match_indices) == 2
rule = SMARTSGraph(name='test', parser=PARSER,
smarts_string='[#6;R1]')
match_indices = list(rule.find_matches(top))
for atom_idx in (0, 1, 2, 5, 6, 7, 8, 9):
assert atom_idx in match_indices
assert len(match_indices) == 8
# One ring
ring = pmd.load_file(get_fn('ring.mol2'), structure=True)
top, _ = generate_topology(ring)
rule = SMARTSGraph(name='test', parser=PARSER,
smarts_string='[#6;R1]')
match_indices = list(rule.find_matches(top))
for atom_idx in range(6):
assert atom_idx in match_indices
assert len(match_indices) == 6
def test_ringness():
ring = pmd.load_file(get_fn('ring.mol2'), structure=True)
top, _ = generate_topology(ring)
typemap = {
atom.index: {
'whitelist': set(),
'blacklist': set(),
'atomtype': None
}
for atom in top.atoms()
}
_rule_match(top, typemap, '[#6]1[#6][#6][#6][#6][#6]1', True)
not_ring = pmd.load_file(get_fn('not_ring.mol2'), structure=True)
top, _ = generate_topology(not_ring)
typemap = {
atom.index: {
'whitelist': set(),
'blacklist': set(),
'atomtype': None
}
for atom in top.atoms()
}
_rule_match(top, typemap, '[#6]1[#6][#6][#6][#6][#6]1', False)
def test_ring_count():
# Two rings
fused = pmd.load_file(get_fn('fused.mol2'), structure=True)
top, _ = generate_topology(fused)
rule = SMARTSGraph(name='test', parser=PARSER, smarts_string='[#6;R2]')
match_indices = list(rule.find_matches(top))
for atom_idx in (3, 4):
assert atom_idx in match_indices
assert len(match_indices) == 2
rule = SMARTSGraph(name='test', parser=PARSER, smarts_string='[#6;R1]')
match_indices = list(rule.find_matches(top))
for atom_idx in (0, 1, 2, 5, 6, 7, 8, 9):
assert atom_idx in match_indices
assert len(match_indices) == 8
# One ring
ring = pmd.load_file(get_fn('ring.mol2'), structure=True)
top, _ = generate_topology(ring)
rule = SMARTSGraph(name='test', parser=PARSER, smarts_string='[#6;R1]')
match_indices = list(rule.find_matches(top))
for atom_idx in range(6):
assert atom_idx in match_indices
assert len(match_indices) == 6
def test_ringness():
ring = pmd.load_file(get_fn('ring.mol2'), structure=True)
top, _ = generate_topology(ring)
_rule_match(top, '[#6]1[#6][#6][#6][#6][#6]1', True)
not_ring = pmd.load_file(get_fn('not_ring.mol2'), structure=True)
top, _ = generate_topology(not_ring)
_rule_match(top, '[#6]1[#6][#6][#6][#6][#6]1', False)
def test_ringness():
ring = pmd.load_file(get_fn('ring.mol2'), structure=True)
top, _ = generate_topology(ring)
_rule_match(top, '[#6]1[#6][#6][#6][#6][#6]1', True)
not_ring = pmd.load_file(get_fn('not_ring.mol2'), structure=True)
top, _ = generate_topology(not_ring)
_rule_match(top, '[#6]1[#6][#6][#6][#6][#6]1', False)
def test_independent_residues_molecules():
"""Test to see that _check_independent_residues works for molecules."""
butane = Alkane(4)
structure = butane.to_parmed()
topo, NULL = generate_topology(structure)
assert _check_independent_residues(topo)
structure = butane.to_parmed(residues=['RES', 'CH3'])
topo, NULL = generate_topology(structure)
assert not _check_independent_residues(topo)
def test_independent_residues_molecules():
"""Test to see that _check_independent_residues works for molecules."""
butane = Alkane(4)
structure = butane.to_parmed()
topo, NULL = generate_topology(structure)
assert _check_independent_residues(topo)
structure = butane.to_parmed(residues=['RES', 'CH3'])
topo, NULL = generate_topology(structure)
assert not _check_independent_residues(topo)
def test_ring_count():
# Two rings
fused = pmd.load_file(get_fn('fused.mol2'), structure=True)
top, _ = generate_topology(fused)
typemap = {
atom.index: {
'whitelist': set(),
'blacklist': set(),
'atomtype': None
}
for atom in top.atoms()
}
rule = SMARTSGraph(name='test',
parser=PARSER,
smarts_string='[#6;R2]',
typemap=typemap)
match_indices = list(rule.find_matches(top, typemap))
for atom_idx in (3, 4):
assert atom_idx in match_indices
assert len(match_indices) == 2
rule = SMARTSGraph(name='test',
parser=PARSER,
smarts_string='[#6;R1]',
typemap=typemap)
match_indices = list(rule.find_matches(top, typemap))
for atom_idx in (0, 1, 2, 5, 6, 7, 8, 9):
assert atom_idx in match_indices
assert len(match_indices) == 8
# One ring
ring = pmd.load_file(get_fn('ring.mol2'), structure=True)
top, _ = generate_topology(ring)
typemap = {
atom.index: {
'whitelist': set(),
'blacklist': set(),
'atomtype': None
}
for atom in top.atoms()
}
rule = SMARTSGraph(name='test',
parser=PARSER,
smarts_string='[#6;R1]',
typemap=typemap)
match_indices = list(rule.find_matches(top, typemap))
for atom_idx in range(6):
assert atom_idx in match_indices
assert len(match_indices) == 6
def test_independent_residues_atoms():
"""Test to see that _check_independent_residues works for single aotms."""
argon = mb.Compound()
argon.name = 'Ar'
structure = argon.to_parmed()
topo, NULL = generate_topology(structure)
assert _check_independent_residues(topo)
def test_independent_residues_atoms():
"""Test to see that _check_independent_residues works for single aotms."""
argon = mb.Compound()
argon.name = 'Ar'
structure = argon.to_parmed()
topo, NULL = generate_topology(structure)
assert _check_independent_residues(topo)
def test_uniqueness():
mol2 = pmd.load_file(get_fn('uniqueness_test.mol2'), structure=True)
top, _ = generate_topology(mol2)
_rule_match(top, '[#6]1[#6][#6][#6][#6][#6]1', False)
_rule_match(top, '[#6]1[#6][#6][#6][#6]1', False)
_rule_match(top, '[#6]1[#6][#6][#6]1', True)
def test_uniqueness():
mol2 = pmd.load_file(get_fn('uniqueness_test.mol2'), structure=True)
top, _ = generate_topology(mol2)
_rule_match(top, '[#6]1[#6][#6][#6][#6][#6]1', False)
_rule_match(top, '[#6]1[#6][#6][#6][#6]1', False)
_rule_match(top, '[#6]1[#6][#6][#6]1', True)
def test_cycle_finding_multiple():
fullerene = pmd.load_file(get_fn('fullerene.pdb'), structure=True)
top, _ = generate_topology(fullerene)
_prepare_atoms(top, compute_cycles=True)
cycle_lengths = [list(map(len, atom.cycles)) for atom in top.atoms()]
expected = [5, 6, 6]
assert all(sorted(lengths) == expected for lengths in cycle_lengths)
def test_cycle_finding_multiple():
fullerene = pmd.load_file(get_fn('fullerene.pdb'), structure=True)
top, _ = generate_topology(fullerene)
_prepare_atoms(top, compute_cycles=True)
cycle_lengths = [list(map(len, atom.cycles)) for atom in top.atoms()]
expected = [5, 6, 6]
assert all(sorted(lengths) == expected for lengths in cycle_lengths)
def test_uniqueness():
mol2 = pmd.load_file(get_fn('uniqueness_test.mol2'), structure=True)
top = generate_topology(mol2)
atom1 = next(top.atoms())
_rule_match(atom1, '[#6]1[#6][#6][#6][#6][#6]1', False)
_rule_match(atom1, '[#6]1[#6][#6][#6][#6]1', False)
_rule_match(atom1, '[#6]1[#6][#6][#6]1', True)
def test_uniqueness():
mol2 = pmd.load_file(get_fn('uniqueness_test.mol2'), structure=True)
top = generate_topology(mol2)
atom1 = next(top.atoms())
_rule_match(atom1, '[#6]1[#6][#6][#6][#6][#6]1', False)
_rule_match(atom1, '[#6]1[#6][#6][#6][#6]1', False)
_rule_match(atom1, '[#6]1[#6][#6][#6]1', True)
def test_fused_ring():
fused = pmd.load_file(get_fn('fused.mol2'), structure=True)
top, _ = generate_topology(fused)
rule = SMARTSGraph(name='test', parser=PARSER,
smarts_string='[#6]12[#6][#6][#6][#6][#6]1[#6][#6][#6][#6]2')
match_indices = list(rule.find_matches(top))
assert 3 in match_indices
assert 4 in match_indices
assert len(match_indices) == 2
def test_fused_ring():
fused = pmd.load_file(get_fn('fused.mol2'), structure=True)
top = generate_topology(fused)
atoms = list(top.atoms())
rule = Rule('test', parser=PARSER,
smarts_string='[#6]12[#6][#6][#6][#6][#6]1[#6][#6][#6][#6]2')
assert rule.matches(atoms[2]) is False
for _ in range(10): # Traversal order during matching is stochastic.
assert rule.matches(atoms[3]) is True
assert rule.matches(atoms[4]) is True
assert rule.matches(atoms[5]) is False
def test_not():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top = generate_topology(mol2)
atom1 = next(top.atoms())
checks = {'[!O]': True,
'[!#5]': True,
'[!C]': False,
'[!#6]': False,
}
for smart, result in checks.items():
_rule_match(atom1, smart, result)
def test_fused_ring():
fused = pmd.load_file(get_fn('fused.mol2'), structure=True)
top, _ = generate_topology(fused)
rule = SMARTSGraph(
name='test',
parser=PARSER,
smarts_string='[#6]12[#6][#6][#6][#6][#6]1[#6][#6][#6][#6]2')
match_indices = list(rule.find_matches(top))
assert 3 in match_indices
assert 4 in match_indices
assert len(match_indices) == 2
def test_precedence():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top, _ = generate_topology(mol2)
checks = {'[C,O;C]': 2,
'[C&O;C]': 0,
'[!C;O,C]': 0,
'[!C&O,C]': 2,
}
for smart, result in checks.items():
_rule_match_count(top, smart, result)
def test_not():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top, _ = generate_topology(mol2)
checks = {'[!O]': 8,
'[!#5]': 8,
'[!C]': 6,
'[!#6]': 6,
'[!C&!H]': 0,
'[!C;!H]': 0,
}
for smart, result in checks.items():
_rule_match_count(top, smart, result)
def test_lazy_cycle_finding():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top, _ = generate_topology(mol2)
rule = SMARTSGraph(smarts_string='[C]')
list(rule.find_matches(top))
assert not any([hasattr(a, 'cycles') for a in top.atoms()])
ring_tokens = ['R1', 'r6']
for token in ring_tokens:
rule = SMARTSGraph(smarts_string='[C;{}]'.format(token))
list(rule.find_matches(top))
assert all([hasattr(a, 'cycles') for a in top.atoms()])
def test_lazy_cycle_finding():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top, _ = generate_topology(mol2)
rule = SMARTSGraph(smarts_string='[C]')
list(rule.find_matches(top))
assert not any([hasattr(a, 'cycles') for a in top.atoms()])
ring_tokens = ['R1', 'r6']
for token in ring_tokens:
rule = SMARTSGraph(smarts_string='[C;{}]'.format(token))
list(rule.find_matches(top))
assert all([hasattr(a, 'cycles') for a in top.atoms()])
def test_fused_ring():
fused = pmd.load_file(get_fn('fused.mol2'), structure=True)
top, _ = generate_topology(fused)
atoms = list(top.atoms())
rule = Rule('test',
parser=PARSER,
smarts_string='[#6]12[#6][#6][#6][#6][#6]1[#6][#6][#6][#6]2')
assert rule.matches(atoms[2]) is False
for _ in range(10): # Traversal order during matching is stochastic.
assert rule.matches(atoms[3]) is True
assert rule.matches(atoms[4]) is True
assert rule.matches(atoms[5]) is False
def test_not():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top, _ = generate_topology(mol2)
atom1 = next(top.atoms())
checks = {
'[!O]': True,
'[!#5]': True,
'[!C]': False,
'[!#6]': False,
}
for smart, result in checks.items():
_rule_match(atom1, smart, result)
def test_precedence():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top = generate_topology(mol2)
atom1 = next(top.atoms())
checks = {'[C,H;C]': True,
'[C&H;C]': False,
'[!C;H,C]': False,
'[!C&H,C]': True,
}
for smart, result in checks.items():
_rule_match(atom1, smart, result)
def test_precedence():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top, _ = generate_topology(mol2)
checks = {
'[C,O;C]': 2,
'[C&O;C]': 0,
'[!C;O,C]': 0,
'[!C&O,C]': 2,
}
for smart, result in checks.items():
_rule_match_count(top, smart, result)
def test_precedence():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top = generate_topology(mol2)
atom1 = next(top.atoms())
checks = {
'[C,H;C]': True,
'[C&H;C]': False,
'[!C;H,C]': False,
'[!C&H,C]': True,
}
for smart, result in checks.items():
_rule_match(atom1, smart, result)
def test_not():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top, _ = generate_topology(mol2)
checks = {
'[!O]': 8,
'[!#5]': 8,
'[!C]': 6,
'[!#6]': 6,
'[!C&!H]': 0,
'[!C;!H]': 0,
}
for smart, result in checks.items():
_rule_match_count(top, smart, result)
def test_uniqueness():
mol2 = pmd.load_file(get_fn('uniqueness_test.mol2'), structure=True)
top, _ = generate_topology(mol2)
typemap = {
atom.index: {
'whitelist': set(),
'blacklist': set(),
'atomtype': None
}
for atom in top.atoms()
}
_rule_match(top, typemap, '[#6]1[#6][#6][#6][#6][#6]1', False)
_rule_match(top, typemap, '[#6]1[#6][#6][#6][#6]1', False)
_rule_match(top, typemap, '[#6]1[#6][#6][#6]1', True)
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_cycle_finding_multiple():
fullerene = pmd.load_file(get_fn('fullerene.pdb'), structure=True)
top, _ = generate_topology(fullerene)
typemap = {
atom.index: {
'whitelist': set(),
'blacklist': set(),
'atomtype': None
}
for atom in top.atoms()
}
_prepare_atoms(top, typemap, compute_cycles=True)
#cycle_lengths = [list(map(len, atom.cycles)) for atom in top.atoms()]
cycle_lengths = [
list(map(len, typemap[atom.index]['cycles'])) for atom in top.atoms()
]
expected = [5, 6, 6]
assert all(sorted(lengths) == expected for lengths in cycle_lengths)
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_precedence():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top, _ = generate_topology(mol2)
typemap = {
atom.index: {
'whitelist': set(),
'blacklist': set(),
'atomtype': None
}
for atom in top.atoms()
}
checks = {
'[C,O;C]': 2,
'[C&O;C]': 0,
'[!C;O,C]': 0,
'[!C&O,C]': 2,
}
for smart, result in checks.items():
_rule_match_count(top, typemap, smart, result)
def test_not():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top, _ = generate_topology(mol2)
typemap = {
atom.index: {
'whitelist': set(),
'blacklist': set(),
'atomtype': None
}
for atom in top.atoms()
}
checks = {
'[!O]': 8,
'[!#5]': 8,
'[!C]': 6,
'[!#6]': 6,
'[!C&!H]': 0,
'[!C;!H]': 0,
}
for smart, result in checks.items():
_rule_match_count(top, typemap, smart, result)
def test_fused_ring():
fused = pmd.load_file(get_fn('fused.mol2'), structure=True)
top, _ = generate_topology(fused)
typemap = {
atom.index: {
'whitelist': set(),
'blacklist': set(),
'atomtype': None
}
for atom in top.atoms()
}
rule = SMARTSGraph(
name='test',
parser=PARSER,
smarts_string='[#6]12[#6][#6][#6][#6][#6]1[#6][#6][#6][#6]2',
typemap=typemap)
match_indices = list(rule.find_matches(top, typemap))
assert 3 in match_indices
assert 4 in match_indices
assert len(match_indices) == 2
def test_lazy_cycle_finding():
mol2 = pmd.load_file(get_fn('ethane.mol2'), structure=True)
top, _ = generate_topology(mol2)
typemap = {
atom.index: {
'whitelist': set(),
'blacklist': set(),
'atomtype': None
}
for atom in top.atoms()
}
rule = SMARTSGraph(smarts_string='[C]', typemap=typemap)
list(rule.find_matches(top, typemap))
#assert not any([hasattr(a, 'cycles') for a in top.atoms()])
assert not any(['cycles' in typemap[a.index] for a in top.atoms()])
ring_tokens = ['R1', 'r6']
for token in ring_tokens:
rule = SMARTSGraph(smarts_string='[C;{}]'.format(token),
typemap=typemap)
list(rule.find_matches(top, typemap))
#assert all([hasattr(a, 'cycles') for a in top.atoms()])
assert all(['cycles' in typemap[a.index] for a in top.atoms()])
ethane = oplsaa.apply(untyped_ethane)
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 = generate_topology(untyped_ethane)
omm_system = oplsaa.createSystem(topology=omm_topology)
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 = generate_topology(untyped_ethane)
omm_system = oplsaa.createSystem(topology=omm_topology)
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)
