def test_smirff_energies_vs_parmatfrosst(verbose=False):
"""Test evaluation of energies from parm@frosst ffxml files versus energies of equivalent systems."""
from openeye import oechem
prefix = 'AlkEthOH_'
molecules = [ 'r118', 'r12', 'c1161', 'r0', 'c100', 'c38', 'c1266' ]
# Loop over molecules, load OEMols and prep for comparison/do comparison
for molnm in molecules:
f_prefix = os.path.join('molecules', prefix+molnm )
mol2file = get_data_filename( f_prefix+'.mol2')
prmtop = get_data_filename( f_prefix+'.top')
crd = get_data_filename( f_prefix+'.crd')
# Load special parm@frosst with parm99/parm@frosst bugs re-added for testing
forcefield = ForceField( get_data_filename('forcefield/Frosst_AlkEtOH_parmAtFrosst.ffxml') )
# Load OEMol
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream(mol2file)
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
ifs.SetFlavor( oechem.OEFormat_MOL2, flavor)
oechem.OEReadMolecule(ifs, mol )
oechem.OETriposAtomNames(mol)
# Do comparison
results = compare_molecule_energies( prmtop, crd, forcefield, mol, verbose = verbose )
def test_merge_system():
"""Test merging of a system created from AMBER and another created from SMIRFF."""
#Create System from AMBER
prefix = os.path.join('systems', 'amber', 'cyclohexane_ethanol_0.4_0.6')
prmtop = get_data_filename(prefix + '.prmtop')
incrd = get_data_filename(prefix + '.inpcrd')
topology0, system0, positions0 = create_system_from_amber(prmtop, incrd)
from openeye import oechem
# Load simple OEMol
ifs = oechem.oemolistream(
get_data_filename('molecules/AlkEthOH_c100.mol2'))
mol = oechem.OEMol()
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
ifs.SetFlavor(oechem.OEFormat_MOL2, flavor)
oechem.OEReadMolecule(ifs, mol)
oechem.OETriposAtomNames(mol)
# Load forcefield file
forcefield = ForceField(
get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
topology1, system1, positions1 = create_system_from_molecule(
forcefield, mol)
merge_system(topology0,
topology1,
system0,
system1,
positions0,
positions1,
verbose=True)
def check_boxes(forcefield, description="", chargeMethod=None, verbose=False):
"""Test creation of System from boxes of mixed solvents.
"""
# Read monomers
mols = list()
monomers = ['cyclohexane', 'ethanol', 'propane', 'methane', 'butanol']
from openeye import oechem
mol = oechem.OEGraphMol()
for monomer in monomers:
filename = get_data_filename(os.path.join('systems', 'monomers', monomer + '.sdf'))
ifs = oechem.oemolistream(filename)
while oechem.OEReadMolecule(ifs, mol):
oechem.OETriposAtomNames(mol)
mols.append( oechem.OEGraphMol(mol) )
if verbose: print('%d reference molecules loaded' % len(mols))
# Read systems.
boxes = ['cyclohexane_ethanol_0.4_0.6.pdb', 'propane_methane_butanol_0.2_0.3_0.5.pdb']
from simtk.openmm.app import PDBFile
for box in boxes:
filename = get_data_filename(os.path.join('systems', 'packmol_boxes', box))
pdbfile = PDBFile(filename)
f = partial(check_system_creation_from_topology, forcefield, pdbfile.topology, mols, pdbfile.positions, chargeMethod=chargeMethod, verbose=verbose)
f.description = 'Test creation of System object from %s %s' % (box, description)
yield f
def test_read_typelist(self):
atomtypes = AtomTyper.read_typelist(
get_data_filename('atomtypes/basetypes.smarts'))
decorators = AtomTyper.read_typelist(
get_data_filename('atomtypes/decorators.smarts'))
replacements = AtomTyper.read_typelist(
get_data_filename('atomtypes/replacements.smarts'))
def test_smirff_energies_vs_parmatfrosst(verbose=False):
"""Test evaluation of energies from parm@frosst ffxml files versus energies of equivalent systems."""
from openeye import oechem
prefix = 'AlkEthOH_'
molecules = ['r118', 'r12', 'c1161', 'r0', 'c100', 'c38', 'c1266']
# Loop over molecules, load OEMols and prep for comparison/do comparison
for molnm in molecules:
f_prefix = os.path.join('molecules', prefix + molnm)
mol2file = get_data_filename(f_prefix + '.mol2')
prmtop = get_data_filename(f_prefix + '.top')
crd = get_data_filename(f_prefix + '.crd')
# Load special parm@frosst with parm99/parm@frosst bugs re-added for testing
forcefield = ForceField(
get_data_filename('forcefield/Frosst_AlkEtOH_parmAtFrosst.ffxml'))
# Load OEMol
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream(mol2file)
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
ifs.SetFlavor(oechem.OEFormat_MOL2, flavor)
oechem.OEReadMolecule(ifs, mol)
oechem.OETriposAtomNames(mol)
# Do comparison
results = compare_molecule_energies(prmtop,
crd,
forcefield,
mol,
verbose=verbose)
def test_improper(verbose=False):
"""Test implement of impropers on benzene."""
from openeye import oechem
# Load benzene
ifs = oechem.oemolistream(get_data_filename('molecules/benzene.mol2'))
mol = oechem.OEMol()
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
ifs.SetFlavor(oechem.OEFormat_MOL2, flavor)
oechem.OEReadMolecule(ifs, mol)
ifs.close()
# Load forcefield
ffxml = get_data_filename('forcefield/benzene_minimal.ffxml')
ff = ForceField(ffxml)
# Load AMBER files and compare
crd = get_data_filename('molecules/benzene.crd')
top = get_data_filename('molecules/benzene.top')
g0, g1, e0, e1 = compare_molecule_energies(top,
crd,
ff,
mol,
skip_assert=True)
# Check that torsional energies the same to 1 in 10^6
rel_error = np.abs((g0['torsion'] - g1['torsion']) / g0['torsion'])
if rel_error > 2e-5: #Note that this will not be tiny because we use six-fold impropers and they use a single improper
raise Exception(
"Improper torsion energy for benzene differs too much (relative error %.4g) between AMBER and SMIRFF."
% rel_error)
def test_atomtyper(self):
typetag = 'atomtype'
atomtypes = AtomTyper.read_typelist(get_data_filename('atomtypes/basetypes.smarts'))
replacements = AtomTyper.read_typelist(get_data_filename('atomtypes/replacements.smarts'))
molecules = read_molecules('zinc-subset-tripos.mol2.gz', verbose=False)
atomtyper = AtomTyper(atomtypes, typetag, replacements=replacements)
for molecule in molecules:
atomtyper.assignTypes(molecule)
def __init__(self, *args, **kwargs):
"""
Initialize TestCase including files used in all smarty tests
"""
unittest.TestCase.__init__(self, *args, **kwargs)
self.basetypes = get_data_filename('atomtypes/basetypes.smarts')
self.alkethoh_answers = get_data_filename(
'atomtypes/initial_AlkEthOH.smarts')
self.simple_decs = get_data_filename('atomtypes/decorators.smarts')
self.combine_decs = get_data_filename(
'atomtypes/new-decorators.smarts')
self.replacements = get_data_filename('atomtypes/replacements.smarts')
# import molecules
self.mols_zinc = smarty.utils.read_molecules(
get_data_filename('molecules/zinc-subset-tripos.mol2.gz'),
verbose=False)
self.mols_zinc_ref = smarty.utils.read_molecules(
get_data_filename('molecules/[email protected]'),
verbose=False)
self.mols_alkethoh = smarty.utils.read_molecules(
get_data_filename('molecules/AlkEthOH_test_filt1_tripos.mol2'),
verbose=False)
self.mols_alkethoh_ref = smarty.utils.read_molecules(
get_data_filename('molecules/AlkEthOH_test_filt1_ff.mol2'),
verbose=False)
def test_atomtyper(self):
typetag = 'atomtype'
atomtypes = AtomTyper.read_typelist(
get_data_filename('atomtypes/basetypes.smarts'))
replacements = AtomTyper.read_typelist(
get_data_filename('atomtypes/replacements.smarts'))
molecules = read_molecules('zinc-subset-tripos.mol2.gz', verbose=False)
atomtyper = AtomTyper(atomtypes, typetag, replacements=replacements)
for molecule in molecules:
atomtyper.assignTypes(molecule)
def test_gromacs_roundtrip():
"""Save a System (a mixture) to GROMACS, read back in, verify yields same energy and force terms."""
forcefield = ForceField(
get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
filename = get_data_filename(
os.path.join('systems', 'packmol_boxes',
'cyclohexane_ethanol_0.4_0.6.pdb'))
from simtk.openmm.app import PDBFile
pdbfile = PDBFile(filename)
mol2files = [
get_data_filename(os.path.join('systems', 'monomers', 'ethanol.mol2')),
get_data_filename(
os.path.join('systems', 'monomers', 'cyclohexane.mol2'))
]
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
mols = []
mol = oechem.OEMol()
for mol2file in mol2files:
ifs = oechem.oemolistream(mol2file)
ifs.SetFlavor(oechem.OEFormat_MOL2, flavor)
mol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
oechem.OETriposAtomNames(mol)
mols.append(oechem.OEGraphMol(mol))
# setup system
system = forcefield.createSystem(pdbfile.topology, mols)
# Create ParmEd structure, save to AMBER
a, topfile = tempfile.mkstemp(suffix='.top')
a, grofile = tempfile.mkstemp(suffix='.gro')
save_system_to_gromacs(pdbfile.topology, system, pdbfile.positions,
topfile, grofile)
# Read back in and cross-check energies
top = parmed.load_file(topfile)
gro = parmed.load_file(grofile)
gromacssys = top.createSystem(nonbondedMethod=app.NoCutoff,
constraints=None,
implicitSolvent=None)
groups0, groups1, energy0, energy1 = compare_system_energies(
pdbfile.topology,
pdbfile.topology,
gromacssys,
system,
pdbfile.positions,
verbose=False)
# Remove temp files
os.remove(topfile)
os.remove(grofile)
def test_create_system_molecules_parmatfrosst_gbsa(verbose=False):
"""Test creation of a System object from small molecules to test parm@frosst forcefield with GBSA support.
"""
forcefield = ForceField(
get_data_filename('forcefield/Frosst_AlkEtOH_GBSA.ffxml'))
for f in check_AlkEtOH(forcefield,
"to test Parm@Frosst parameters",
verbose=verbose):
yield f
def test_create_system_boxes_parmatfrosst(verbose=False):
"""Test creation of a System object from some boxes of mixed solvents to test parm@frosst forcefield.
"""
forcefield = ForceField(
get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
for f in check_boxes(forcefield,
description="to test Parm@frosst parameters",
verbose=verbose):
yield f
def test_parameter_completeness_check(self):
"""Test that proper exceptions are raised if a force field fails to assign parameters to valence terms in a molecule."""
from openeye import oechem
mol = oechem.OEMol()
oechem.OEParseSmiles(mol, 'CCC')
oechem.OEAddExplicitHydrogens(mol)
oechem.OETriposAtomNames(mol)
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
topology = generateTopologyFromOEMol(mol)
# Test nonbonded error checking by wiping out required LJ parameter
params = ff.getParameter(paramID='n0001')
params['smirks'] = '[#136:1]'
ff.setParameter(paramID='n0001', params=params)
ff.setParameter(paramID='n0002', params=params)
with self.assertRaises(Exception):
system = ff.createSystem(topology, [mol])
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
# Test bond error checking by wiping out a required bond parameter
params = ff.getParameter(paramID='b0001')
params['smirks'] = '[#136:1]~[*:2]'
ff.setParameter(paramID='b0001', params=params)
with self.assertRaises(Exception):
system = ff.createSystem(topology, [mol])
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
# Test angle error checking by wiping out a required angle parameter
params = ff.getParameter(paramID='a0001')
params['smirks'] = '[#136:1]~[*:2]~[*:3]'
ff.setParameter(paramID='a0001', params=params)
with self.assertRaises(Exception):
system = ff.createSystem(topology, [mol])
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
# Test torsion error checking by wiping out a required torsion parameter
params = ff.getParameter(paramID='t0001')
params['smirks'] = '[#136:1]~[*:2]~[*:3]~[*:4]'
ff.setParameter(paramID='t0001', params=params)
ff.setParameter(paramID='t0004', params=params)
with self.assertRaises(Exception):
system = ff.createSystem(topology, [mol])
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
def check_AlkEtOH(forcefield, description="", chargeMethod=None, verbose=False):
"""Test creation of System from AlkEtOH small molecules.
"""
from openeye import oechem
ifs = oechem.oemolistream(get_data_filename('molecules/AlkEtOH-tripos.mol2.gz'))
mol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
args = { 'verbose' : verbose, 'chargeMethod' : chargeMethod }
f = partial(check_system_creation_from_molecule, forcefield, mol, **args)
f.description ='Testing creation of system object from small molecules (%s) %s' % (mol.GetTitle(), description)
yield f
def test_atomtyper_AlkEthOH(self):
# Test to make sure that AlkEthOH gets 100% at T=0 starting from correct
# types
basetypes_filename = get_data_filename('atomtypes/basetypes.smarts')
initialtypes_filename = get_data_filename(
'atomtypes/initial_AlkEthOH.smarts')
decorators_filename = get_data_filename(
'atomtypes/new-decorators.smarts')
replacements_filename = get_data_filename(
'atomtypes/replacements.smarts')
molecules = smarty.utils.read_molecules(
get_data_filename('molecules/AlkEthOH_test_filt1_tripos.mol2'),
verbose=False)
reference_typed_molecules = smarty.utils.read_molecules(
get_data_filename('molecules/AlkEthOH_test_filt1_ff.mol2'),
verbose=False)
# Construct atom type sampler.
atomtype_sampler = smarty.AtomTypeSampler(
molecules,
basetypes_filename,
initialtypes_filename,
decorators_filename,
replacements_filename=replacements_filename,
reference_typed_molecules=reference_typed_molecules,
verbose=False,
temperature=0)
# Start sampling atom types.
fracfound = atomtype_sampler.run(2)
# Ensure fraction found is 1.0
if fracfound < 1.0:
raise Exception("Not finding 100% of AlkEthOH when starting from"
" correct SMARTS.")
def test_atomtyper(self):
basetypes_filename = get_data_filename('atomtypes/basetypes.smarts')
initialtypes_filename = get_data_filename('atomtypes/basetypes.smarts')
decorators_filename = get_data_filename('atomtypes/decorators.smarts')
replacements_filename = get_data_filename(
'atomtypes/replacements.smarts')
molecules = smarty.utils.read_molecules(
get_data_filename('molecules/zinc-subset-tripos.mol2.gz'),
verbose=False)
reference_typed_molecules = smarty.utils.read_molecules(
get_data_filename('molecules/[email protected]'),
verbose=False)
# Construct atom type sampler.
atomtype_sampler = smarty.AtomTypeSampler(
molecules,
basetypes_filename,
initialtypes_filename,
decorators_filename,
replacements_filename=replacements_filename,
reference_typed_molecules=reference_typed_molecules,
verbose=False,
decorator_behavior='simple-decorators')
# Start sampling atom types.
atomtype_sampler.run(2)
def test_change_parameters(verbose=False):
"""Test modification of forcefield parameters."""
from openeye import oechem
# Load simple OEMol
ifs = oechem.oemolistream(
get_data_filename('molecules/AlkEthOH_c100.mol2'))
mol = oechem.OEMol()
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
ifs.SetFlavor(oechem.OEFormat_MOL2, flavor)
oechem.OEReadMolecule(ifs, mol)
oechem.OETriposAtomNames(mol)
# Load forcefield file
ffxml = get_data_filename('forcefield/Frosst_AlkEtOH.ffxml')
ff = ForceField(ffxml)
from smarty.forcefield import generateTopologyFromOEMol
topology = generateTopologyFromOEMol(mol)
# Create initial system
system = ff.createSystem(topology, [mol], verbose=verbose)
# Get initial energy before parameter modification
positions = positions_from_oemol(mol)
old_energy = get_energy(system, positions)
# Get params for an angle
params = ff.getParameter(smirks='[a,A:1]-[#6X4:2]-[a,A:3]')
# Modify params
params['k'] = '0.0'
ff.setParameter(params, smirks='[a,A:1]-[#6X4:2]-[a,A:3]')
# Write params
ff.writeFile(tempfile.TemporaryFile(suffix='.ffxml'))
# Make sure params changed energy! (Test whether they get rebuilt on system creation)
system = ff.createSystem(topology, [mol], verbose=verbose)
energy = get_energy(system, positions)
if verbose:
print("New energy/old energy:", energy, old_energy)
if np.abs(energy - old_energy) < 0.1:
raise Exception("Error: Parameter modification did not change energy.")
def test_change_parameters(verbose=False):
"""Test modification of forcefield parameters."""
from openeye import oechem
# Load simple OEMol
ifs = oechem.oemolistream(get_data_filename('molecules/AlkEthOH_c100.mol2'))
mol = oechem.OEMol()
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
ifs.SetFlavor( oechem.OEFormat_MOL2, flavor)
oechem.OEReadMolecule(ifs, mol )
oechem.OETriposAtomNames(mol)
# Load forcefield file
ffxml = get_data_filename('forcefield/Frosst_AlkEtOH.ffxml')
ff = ForceField(ffxml)
from smarty.forcefield import generateTopologyFromOEMol
topology = generateTopologyFromOEMol(mol)
# Create initial system
system = ff.createSystem(topology, [mol], verbose=verbose)
# Get initial energy before parameter modification
positions = positions_from_oemol(mol)
old_energy=get_energy(system, positions)
# Get params for an angle
params = ff.getParameter(smirks='[a,A:1]-[#6X4:2]-[a,A:3]')
# Modify params
params['k']='0.0'
ff.setParameter(params, smirks='[a,A:1]-[#6X4:2]-[a,A:3]')
# Write params
ff.writeFile( tempfile.TemporaryFile(suffix='.ffxml') )
# Make sure params changed energy! (Test whether they get rebuilt on system creation)
system=ff.createSystem(topology, [mol], verbose=verbose)
energy=get_energy(system, positions)
if verbose:
print("New energy/old energy:", energy, old_energy)
if np.abs(energy-old_energy)<0.1:
raise Exception("Error: Parameter modification did not change energy.")
def check_boxes(forcefield, description="", chargeMethod=None, verbose=False):
"""Test creation of System from boxes of mixed solvents.
"""
# Read monomers
mols = list()
monomers = ['cyclohexane', 'ethanol', 'propane', 'methane', 'butanol']
from openeye import oechem
mol = oechem.OEGraphMol()
for monomer in monomers:
filename = get_data_filename(
os.path.join('systems', 'monomers', monomer + '.sdf'))
ifs = oechem.oemolistream(filename)
while oechem.OEReadMolecule(ifs, mol):
oechem.OETriposAtomNames(mol)
mols.append(oechem.OEGraphMol(mol))
if verbose: print('%d reference molecules loaded' % len(mols))
# Read systems.
boxes = [
'cyclohexane_ethanol_0.4_0.6.pdb',
'propane_methane_butanol_0.2_0.3_0.5.pdb'
]
from simtk.openmm.app import PDBFile
for box in boxes:
filename = get_data_filename(
os.path.join('systems', 'packmol_boxes', box))
pdbfile = PDBFile(filename)
f = partial(check_system_creation_from_topology,
forcefield,
pdbfile.topology,
mols,
pdbfile.positions,
chargeMethod=chargeMethod,
verbose=verbose)
f.description = 'Test creation of System object from %s %s' % (
box, description)
yield f
def read_typelist(cls, filename):
"""
Read an atomtype or decorator list from a file.
Parameters
----------
filename : str
The name of the file to be read
Returns
-------
typelist : list of tuples
Typelist[i] is element i of the typelist in format [smarts, typename]
"""
if filename is None:
return None
if not os.path.exists(filename):
built_in = utils.get_data_filename(filename)
if not os.path.exists(built_in):
raise Exception("File '%s' not found." % filename)
filename = built_in
typelist = list()
ifs = open(filename)
lines = ifs.readlines()
used_typenames = list()
for line in lines:
# Strip trailing comments
index = line.find('%')
if index != -1:
line = line[0:index]
# Split into tokens.
tokens = line.split()
# Process if we have enough tokens
if len(tokens) >= 2:
smarts = tokens[0]
typename = ' '.join(tokens[1:])
if typename not in used_typenames:
typelist.append([smarts,typename])
used_typenames.append(typename)
else:
raise Exception("Error in file '%s' -- each entry must "
"have a unique name." % filename )
ifs.close()
return typelist
def check_AlkEtOH(forcefield,
description="",
chargeMethod=None,
verbose=False):
"""Test creation of System from AlkEtOH small molecules.
"""
from openeye import oechem
ifs = oechem.oemolistream(
get_data_filename('molecules/AlkEtOH-tripos.mol2.gz'))
mol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
args = {'verbose': verbose, 'chargeMethod': chargeMethod}
f = partial(check_system_creation_from_molecule, forcefield, mol,
**args)
f.description = 'Testing creation of system object from small molecules (%s) %s' % (
mol.GetTitle(), description)
yield f
def test_atomtyper(self):
basetypes_filename = get_data_filename('atomtypes/basetypes.smarts')
initialtypes_filename = get_data_filename('atomtypes/basetypes.smarts')
decorators_filename = get_data_filename('atomtypes/decorators.smarts')
replacements_filename = get_data_filename('atomtypes/replacements.smarts')
molecules = smarty.utils.read_molecules(get_data_filename('molecules/zinc-subset-tripos.mol2.gz'), verbose=False)
reference_typed_molecules = smarty.utils.read_molecules(get_data_filename('molecules/[email protected]'), verbose=False)
# Construct atom type sampler.
atomtype_sampler = smarty.AtomTypeSampler(molecules, basetypes_filename, initialtypes_filename, decorators_filename, replacements_filename=replacements_filename, reference_typed_molecules=reference_typed_molecules, verbose=False, decorator_behavior='simple-decorators')
# Start sampling atom types.
atomtype_sampler.run(2)
def test_molecule_labeling(verbose=False):
"""Test using labelMolecules to see which parameters applied to an oemol."""
from openeye import oechem
mol = oechem.OEMol()
oechem.OEParseSmiles(mol, 'CCC')
oechem.OEAddExplicitHydrogens(mol)
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
labels = ff.labelMolecules([mol], verbose=verbose)
# Check that force terms aren't empty
print(labels[0].keys())
if not 'HarmonicBondGenerator' in labels[0].keys():
raise Exception("No force term assigned for harmonic bonds.")
if not 'HarmonicAngleGenerator' in labels[0].keys():
raise Exception("No force term assigned for harmonic angles.")
if not 'PeriodicTorsionGenerator' in labels[0].keys():
raise Exception("No force term assigned for periodic torsions.")
if not 'NonbondedGenerator' in labels[0].keys():
raise Exception("No nonbonded force term assigned.")
def test_molecule_labeling(verbose = False):
"""Test using labelMolecules to see which parameters applied to an oemol."""
from openeye import oechem
mol = oechem.OEMol()
oechem.OEParseSmiles(mol, 'CCC')
oechem.OEAddExplicitHydrogens(mol)
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
labels = ff.labelMolecules( [mol], verbose = verbose)
# Check that force terms aren't empty
print(labels[0].keys())
if not 'HarmonicBondGenerator' in labels[0].keys():
raise Exception("No force term assigned for harmonic bonds.")
if not 'HarmonicAngleGenerator' in labels[0].keys():
raise Exception("No force term assigned for harmonic angles.")
if not 'PeriodicTorsionGenerator' in labels[0].keys():
raise Exception("No force term assigned for periodic torsions.")
if not 'NonbondedGenerator' in labels[0].keys():
raise Exception("No nonbonded force term assigned.")
def __init__(self, *args, **kwargs):
"""
Initialize TestCase and then read in odds from files in smarty/data
"""
unittest.TestCase.__init__(self,*args, **kwargs)
self.atom_OR_bases = utils.parse_odds_file("odds_files/atom_OR_bases.smarts" , False)
self.atom_OR_decors = utils.parse_odds_file("odds_files/atom_decorators.smarts", False)
self.atom_AND_decors = utils.parse_odds_file("odds_files/atom_decorators.smarts", False)
self.bond_OR_bases = utils.parse_odds_file("odds_files/bond_OR_bases.smarts", False)
self.bond_AND_decors = utils.parse_odds_file("odds_files/bond_AND_decorators.smarts", False)
self.atom_odds = utils.parse_odds_file("odds_files/atom_index_odds.smarts", False)
self.bond_odds = utils.parse_odds_file("odds_files/bond_index_odds.smarts", False)
self.molecules = utils.read_molecules("test_filt1_tripos.mol2", False)
self.SMIRFF = "forcefield/Frosst_AlkEtOH.ffxml"
self.outputFile = 'test_smirky'
replacement_file = utils.get_data_filename("odds_files/substitutions.smarts")
self.replacements = smarty.AtomTyper.read_typelist(replacement_file)
self.replacements = [ [short, smarts] for [smarts, short] in self.replacements]
self.correctDict = {'VdW': [ ["[#1:1]-[#6]", 'HC'], [ "[#1:1]-[#6]-[#7,#8,F,#16,Cl,Br]", 'H1'], [ "[#1:1]-[#6](-[#7,#8,F,#16,Cl,Br])-[#7,#8,F,#16,Cl,Br]", 'H2'], [ "[#1:1]-[#6](-[#7,#8,F,#16,Cl,Br])(-[#7,#8,F,#16,Cl,Br])-[#7,#8,F,#16,Cl,Br]", 'H3'], [ "[#1:1]-[#8]", 'HO'], [ "[#6X4:1]", 'CT'], [ "[#8X2:1]", 'OS'], [ "[#8X2+0:1]-[#1]", 'OH'] ],
'Bond': [ ["[#6X4:1]-[#6X4:2]", 'CT-CT'], [ "[#6X4:1]-[#1:2]", 'CT-H'], [ "[#8:1]~[#1:2]", 'O~H'], [ "[#6X4:1]-[#8;X2;H1:2]", "CT-OH"], [ "[#6X4:1]-[#8;X2;H0:2]", "CT-OS"] ],
'Angle': [ [ "[a,A:1]-[#6&X4:2]-[a,A:3]", 'any-CT-any'], [ "[#1:1]-[#6&X4:2]-[#1:3]", "H-CT-H"], [ "[#6&X4:1]-[#6&X4:2]-[#6&X4:3]", 'CT-CT-CT'], [ "[#8&X2:1]-[#6&X4:2]-[#8&X2:3]", 'O-CT-O'], [ "[#6&X4:1]-[#8&X2:2]-[#1:3]", 'CT-OH-HO'], [ "[#6X4:1]-[#8X2:2]-[#6X4:3]", 'CT-OS-CT'] ],
'Torsion': [["[a,A:1]-[#6&X4:2]-[#6&X4:3]-[a,A:4]", 'any-CT-CT-any'], [ "[a,A:1]-[#6&X4:2]-[#8&X2:3]-[#1:4]", 'any-CT-OH-HO'], [ "[a,A:1]-[#6&X4:2]-[#8&X2:3]-[!#1:4]", 'any-CT-OS-!H'], [ "[#1:1]-[#6&X4:2]-[#6&X4:3]-[#1:4]", 'H-CT-CT-H'], [ "[#1:1]-[#6&X4:2]-[#6&X4:3]-[#6&X4:4]", 'H-CT-CT-CT'], [ "[#6&X4:1]-[#6&X4:2]-[#8&X2:3]-[#1:4]", 'CT-CT-OH-HO'], [ "[#6&X4:1]-[#6&X4:2]-[#6&X4:3]-[#6&X4:4]", 'CT-CT-CT-CT'], [ "[#6&X4:1]-[#6&X4:2]-[#8&X2:3]-[#6&X4:4]", 'CT-CT-OS-CT'], [ "[#6&X4:1]-[#8&X2:2]-[#6&X4:3]-[O&X2&H0:4]", 'CT-OS-CT-OS'], [ "[#8&X2:1]-[#6&X4:2]-[#6&X4:3]-[#8&X2:4]", 'O-CT-CT-O'], [ "[#8&X2:1]-[#6&X4:2]-[#6&X4:3]-[#1:4]", 'O-CT-CT-H'], [ "[#1:1]-[#6&X4:2]-[#6&X4:3]-[O&X2:4]", 'H-CT-CT-O'] ]}
def __init__(self, *args, **kwargs):
"""
Initialize TestCase and then read in odds from files in smarty/data
"""
unittest.TestCase.__init__(self,*args, **kwargs)
self.atom_OR_bases = utils.parse_odds_file("odds_files/atom_OR_bases.smarts" , False)
self.atom_OR_decors = utils.parse_odds_file("odds_files/atom_decorators.smarts", False)
self.atom_AND_decors = utils.parse_odds_file("odds_files/atom_decorators.smarts", False)
self.bond_OR_bases = utils.parse_odds_file("odds_files/bond_OR_bases.smarts", False)
self.bond_AND_decors = utils.parse_odds_file("odds_files/bond_AND_decorators.smarts", False)
self.atom_odds = utils.parse_odds_file("odds_files/atom_index_odds.smarts", False)
self.bond_odds = utils.parse_odds_file("odds_files/bond_index_odds.smarts", False)
self.molecules = read_molecules("test_filt1_tripos.mol2", False)
self.SMIRFF = "forcefield/Frosst_AlkEthOH.ffxml"
self.outputFile = 'test_smirky'
replacement_file = utils.get_data_filename("odds_files/substitutions.smarts")
self.replacements = smarty.AtomTyper.read_typelist(replacement_file)
self.replacements = [ [short, smarts] for [smarts, short] in self.replacements]
self.correctDict = {'VdW': [ ["[#1:1]-[#6]", 'HC'], [ "[#1:1]-[#6]-[#7,#8,F,#16,Cl,Br]", 'H1'], [ "[#1:1]-[#6](-[#7,#8,F,#16,Cl,Br])-[#7,#8,F,#16,Cl,Br]", 'H2'], [ "[#1:1]-[#6](-[#7,#8,F,#16,Cl,Br])(-[#7,#8,F,#16,Cl,Br])-[#7,#8,F,#16,Cl,Br]", 'H3'], [ "[#1:1]-[#8]", 'HO'], [ "[#6X4:1]", 'CT'], [ "[#8X2:1]", 'OS'], [ "[#8X2+0:1]-[#1]", 'OH'] ],
'Bond': [ ["[#6X4:1]-[#6X4:2]", 'CT-CT'], [ "[#6X4:1]-[#1:2]", 'CT-H'], [ "[#8:1]~[#1:2]", 'O~H'], [ "[#6X4:1]-[#8;X2;H1:2]", "CT-OH"], [ "[#6X4:1]-[#8;X2;H0:2]", "CT-OS"] ],
'Angle': [ [ "[a,A:1]-[#6&X4:2]-[a,A:3]", 'any-CT-any'], [ "[#1:1]-[#6&X4:2]-[#1:3]", "H-CT-H"], [ "[#6&X4:1]-[#6&X4:2]-[#6&X4:3]", 'CT-CT-CT'], [ "[#8&X2:1]-[#6&X4:2]-[#8&X2:3]", 'O-CT-O'], [ "[#6&X4:1]-[#8&X2:2]-[#1:3]", 'CT-OH-HO'], [ "[#6X4:1]-[#8X2:2]-[#6X4:3]", 'CT-OS-CT'] ],
'Torsion': [["[a,A:1]-[#6&X4:2]-[#6&X4:3]-[a,A:4]", 'any-CT-CT-any'], [ "[a,A:1]-[#6&X4:2]-[#8&X2:3]-[#1:4]", 'any-CT-OH-HO'], [ "[a,A:1]-[#6&X4:2]-[#8&X2:3]-[!#1:4]", 'any-CT-OS-!H'], [ "[#1:1]-[#6&X4:2]-[#6&X4:3]-[#1:4]", 'H-CT-CT-H'], [ "[#1:1]-[#6&X4:2]-[#6&X4:3]-[#6&X4:4]", 'H-CT-CT-CT'], [ "[#6&X4:1]-[#6&X4:2]-[#8&X2:3]-[#1:4]", 'CT-CT-OH-HO'], [ "[#6&X4:1]-[#6&X4:2]-[#6&X4:3]-[#6&X4:4]", 'CT-CT-CT-CT'], [ "[#6&X4:1]-[#6&X4:2]-[#8&X2:3]-[#6&X4:4]", 'CT-CT-OS-CT'], [ "[#6&X4:1]-[#8&X2:2]-[#6&X4:3]-[O&X2&H0:4]", 'CT-OS-CT-OS'], [ "[#8&X2:1]-[#6&X4:2]-[#6&X4:3]-[#8&X2:4]", 'O-CT-CT-O'], [ "[#8&X2:1]-[#6&X4:2]-[#6&X4:3]-[#1:4]", 'O-CT-CT-H'], [ "[#1:1]-[#6&X4:2]-[#6&X4:3]-[O&X2:4]", 'H-CT-CT-O'] ]}
def test_atomtyper_AlkEthOH(self):
# Test to make sure that AlkEthOH gets 100% at T=0 starting from correct
# types
basetypes_filename = get_data_filename('atomtypes/basetypes.smarts')
initialtypes_filename = get_data_filename('atomtypes/initial_AlkEthOH.smarts')
decorators_filename = get_data_filename('atomtypes/new-decorators.smarts')
replacements_filename = get_data_filename('atomtypes/replacements.smarts')
molecules = smarty.utils.read_molecules(get_data_filename('molecules/AlkEthOH_test_filt1_tripos.mol2'), verbose=False)
reference_typed_molecules = smarty.utils.read_molecules(get_data_filename('molecules/AlkEthOH_test_filt1_ff.mol2'), verbose=False)
# Construct atom type sampler.
atomtype_sampler = smarty.AtomTypeSampler(molecules, basetypes_filename, initialtypes_filename, decorators_filename, replacements_filename=replacements_filename, reference_typed_molecules=reference_typed_molecules, verbose=False, temperature = 0)
# Start sampling atom types.
fracfound = atomtype_sampler.run(2)
# Ensure fraction found is 1.0
if fracfound < 1.0:
raise Exception("Not finding 100% of AlkEthOH when starting from"
" correct SMARTS.")
#!/bin/env python
from openeye.oechem import *
from smarty.utils import get_data_filename
from smarty.forcefield import *
# Create an oemol
mol = OEMol()
OEParseSmiles(mol, 'CCC')
OEAddExplicitHydrogens(mol)
ff = ForceField( get_data_filename('forcefield/Frosst_AlkEtOH.ffxml') )
labels= ff.labelMolecules( [mol], verbose = True )
print labels
for mol_entry in range(len(labels)):
for force in labels[mol_entry].keys():
print("\n%s:" % force)
for (atom_indices, pid, smirks) in labels[mol_entry][force]:
atomstr=''
for idx in atom_indices:
atomstr += '%6s' % idx
print("%s : %s \t smirks %s" % (atomstr, pid, smirks) )
def test_read_ffxml_gbsa():
"""Test reading of ffxml files with GBSA support.
"""
forcefield = ForceField(
get_data_filename('forcefield/Frosst_AlkEtOH_GBSA.ffxml'))
def test_read_ffxml():
"""Test reading of ffxml files.
"""
forcefield = ForceField(
get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
def test_label_molecules(verbose=False):
"""Test labeling/getting stats on labeling molecules"""
molecules = smarty.utils.read_molecules(
get_data_filename('molecules/AlkEtOH-tripos.mol2.gz'), verbose=verbose)
ffxml = get_data_filename('forcefield/Frosst_AlkEtOH.ffxml')
get_molecule_parameterIDs(molecules, ffxml)
def test_label_molecules(verbose=False):
"""Test labeling/getting stats on labeling molecules"""
molecules = smarty.utils.read_molecules(get_data_filename('molecules/AlkEtOH-tripos.mol2.gz'), verbose=verbose)
ffxml = get_data_filename('forcefield/Frosst_AlkEtOH.ffxml')
get_molecule_parameterIDs( molecules, ffxml)
def test_component_combination():
"""Test that a system still yields the same energy after building it again out of its components."""
# We've had issues where subsequent instances of a molecule might have zero charges
# Here we'll try to catch this (and also explicitly check the charges) by re-building
# a system out of its components
forcefield = ForceField(
get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
filename = get_data_filename(
os.path.join('systems', 'packmol_boxes',
'cyclohexane_ethanol_0.4_0.6.pdb'))
from simtk.openmm.app import PDBFile
pdbfile = PDBFile(filename)
mol2files = [
get_data_filename(os.path.join('systems', 'monomers', 'ethanol.mol2')),
get_data_filename(
os.path.join('systems', 'monomers', 'cyclohexane.mol2'))
]
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
mols = []
mol = oechem.OEMol()
for mol2file in mol2files:
ifs = oechem.oemolistream(mol2file)
ifs.SetFlavor(oechem.OEFormat_MOL2, flavor)
mol = oechem.OEGraphMol()
while oechem.OEReadMolecule(ifs, mol):
oechem.OETriposAtomNames(mol)
mols.append(oechem.OEGraphMol(mol))
# setup system
system = forcefield.createSystem(pdbfile.topology,
mols,
chargeMethod='OECharges_AM1BCCSym')
# Make parmed structure
structure = parmed.openmm.topsystem.load_topology(pdbfile.topology, system,
pdbfile.positions)
# Split the system, then re-compose it out of its components
tmp = structure.split()
strs, nums = [], []
for s, n in tmp:
strs.append(s)
nums.append(n)
nums = [len(n) for n in nums]
# Re-compose system from components
new_structure = strs[0] * nums[0]
for idx in range(1, len(nums)):
new_structure += strs[idx] * nums[idx]
# Swap in coordinates again
new_structure.positions = structure.positions
# Create System
newsys = new_structure.createSystem(nonbondedMethod=app.NoCutoff,
constraints=None,
implicitSolvent=None)
# Cross check energies
groups0, groups1, energy0, energy1 = compare_system_energies(
pdbfile.topology,
pdbfile.topology,
system,
newsys,
pdbfile.positions,
verbose=False)
# Also check that that the number of components is equal to the number I expect
if not len(nums) == 2:
print("Error: Test system has incorrect number of components.")
raise Exception(
'Incorrect number of components in cyclohexane/ethanol test system.'
)
# Also check that none of residues have zero charge
for resnr in range(len(structure.residues)):
abscharges = [
abs(structure.residues[resnr].atoms[idx].charge)
for idx in range(len(structure.residues[resnr].atoms))
]
if sum(abscharges) == 0:
raise Exception(
'Error: Residue %s in cyclohexane-ethanol test system has a charge of zero, which is incorrect.'
% resnr)
def test_create_system_boxes_parmatfrosst(verbose=False):
"""Test creation of a System object from some boxes of mixed solvents to test parm@frosst forcefield.
"""
forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
for f in check_boxes(forcefield, description="to test Parm@frosst parameters", verbose=verbose):
yield f
def test_create_system_molecules_parmatfrosst(verbose=False):
"""Test creation of a System object from small molecules to test parm@frosst forcefield.
"""
forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
for f in check_AlkEtOH(forcefield, "to test Parm@Frosst parameters", verbose=verbose):
yield f
def test_read_molecules(self):
molecules = smarty.utils.read_molecules(get_data_filename('molecules/zinc-subset-tripos.mol2.gz'), verbose=False)
def test_read_ffxml():
"""Test reading of ffxml files.
"""
forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
def test_read_typelist(self):
atomtypes = AtomTyper.read_typelist(get_data_filename('atomtypes/basetypes.smarts'))
decorators = AtomTyper.read_typelist(get_data_filename('atomtypes/decorators.smarts'))
replacements = AtomTyper.read_typelist(get_data_filename('atomtypes/replacements.smarts'))
def test_read_molecules(self):
molecules = smarty.utils.read_molecules(
get_data_filename('molecules/zinc-subset-tripos.mol2.gz'),
verbose=False)
