def test_partial_bondorder(verbose=False):
"""Test setup of a molecule which activates partial bond order code."""
from openeye import oechem
mol = oechem.OEMol()
from openeye import oeiupac
oeiupac.OEParseIUPACName(mol, 'benzene')
positions = positions_from_oemol(mol)
oechem.OETriposAtomNames(mol)
topology = generateTopologyFromOEMol(mol)
# Load forcefield from above
ffxml = StringIO(ffxml_contents_noconstraints)
ff = ForceField(ffxml)
# Set up once using AM1BCC charges
system = ff.createSystem(topology, [mol],
chargeMethod='OECharges_AM1BCCSym',
verbose=verbose)
# Check that energy is what it ought to be -- the partial bond order
# for benzene makes the energy a bit higher than it would be without it
energy = get_energy(system, positions)
if energy < 7.50 or energy > 7.60:
raise Exception(
"Partial bond order code seems to have issues, as energy for benzene is outside of tolerance in tests."
)
# Set up once also without asking for charges
system = ff.createSystem(topology, [mol], verbose=verbose)
energy = get_energy(system, positions)
# Energy is lower with user supplied charges (which in this case are zero)
if energy < 4.00 or energy > 6.0:
raise Exception(
"Partial bond order code seems to have issues when run with user-provided charges, as energy for benzene is out of tolerance in tests."
)
def check_system_creation_from_molecule(forcefield,
mol,
chargeMethod=None,
verbose=False):
"""
Generate a System from the given OEMol and SMIRNOFF forcefield and check that its energy is finite.
Parameters
----------
forcefield : ForceField
SMIRNOFF forcefield
mol : oechem.OEMol
Molecule to test (need not have coordinates)
chargeMethod : str, optional, default=None
Charge method to use in creating system
"""
topology = generateTopologyFromOEMol(mol)
system = forcefield.createSystem(topology, [mol],
chargeMethod=chargeMethod,
verbose=verbose)
# Test energy computation.
positions = positions_from_oemol(mol)
check_energy_is_finite(system, positions)
def create_system_from_molecule(forcefield, mol, verbose=False):
"""
Generate a System from the given OEMol and SMIRNOFF forcefield, return the resulting System.
Parameters
----------
forcefield : ForceField
SMIRNOFF forcefield
mol : oechem.OEMol
Molecule to test (must have coordinates)
Returns
----------
topology : OpenMM Topology
system : OpenMM System
positions : initial atomic positions (OpenMM)
"""
# Create system
from openforcefield.utils import generateTopologyFromOEMol
topology = generateTopologyFromOEMol(mol)
system = forcefield.createSystem(topology, [mol], verbose=verbose)
# Get positions
coordinates = mol.GetCoords()
natoms = len(coordinates)
positions = np.zeros([natoms, 3], np.float32)
for index in range(natoms):
(x, y, z) = coordinates[index]
positions[index, 0] = x
positions[index, 1] = y
positions[index, 2] = z
positions = unit.Quantity(positions, unit.angstroms)
return topology, system, positions
def initialize_system(dt=0.001,
temperature=100,
forcefield_file='forcefield/smirnoff99Frosst.offxml',
smiles="C1CCCCC1"):
mol = OEMol()
# OEParseSmiles(mol, 'CCOCCSCC')
# OEParseSmiles(mol, 'c1ccccc1')
OEParseSmiles(mol, smiles)
# OEParseSmiles(mol, 'C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O')
OEAddExplicitHydrogens(mol)
masses = get_masses(mol)
num_atoms = mol.NumAtoms()
topology = generateTopologyFromOEMol(mol)
ff = ForceField(get_data_filename(forcefield_file))
nrgs, total_params, offsets = system_builder.construct_energies(
ff, mol, False)
# dt = 0.0025
# friction = 10.0
# temperature = 300
# gradient descent
dt = dt
friction = 10.0
temperature = temperature
a, b, c = get_abc_coefficents(masses, dt, friction, temperature)
buf_size = estimate_buffer_size(1e-10, a)
print("BUFFER SIZE", buf_size)
omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.SetMaxConfs(1)
omega = oeomega.OEOmega(omegaOpts)
omega.SetStrictStereo(False)
if not omega(mol):
assert 0
x0 = mol_coords_to_numpy_array(mol) / 10
intg = custom_ops.Integrator_double(dt, buf_size, num_atoms, total_params,
a, b, c)
context = custom_ops.Context_double(nrgs, intg)
x0 = minimizer.minimize_newton_cg(nrgs, x0, total_params)
return nrgs, offsets, intg, context, x0, total_params
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_AlkEthOH.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_AlkEthOH.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_AlkEthOH.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_AlkEthOH.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_AlkEthOH.ffxml'))
def initialize(input_smiles, gp):
train_reference_args = []
train_args = []
train_offset_idxs = []
train_charge_idxs = []
for smi_idx, smiles in enumerate(input_smiles):
print("processing", smiles, smi_idx, "/", len(input_smiles))
mol = OEMol()
OEParseSmiles(mol, smiles)
OEAddExplicitHydrogens(mol)
masses = get_masses(mol)
num_atoms = mol.NumAtoms()
omegaOpts = oeomega.OEOmegaOptions()
omegaOpts.SetMaxConfs(1)
omega = oeomega.OEOmega(omegaOpts)
omega.SetStrictStereo(False)
if not omega(mol):
assert 0
topology = generateTopologyFromOEMol(mol)
reference_forcefield_file = 'forcefield/smirnoff99Frosst_perturbed.offxml'
ff = ForceField(get_data_filename(reference_forcefield_file))
params = system_builder.construct_energies(ff, mol, True)
train_reference_args.append((params[0], params[1], masses, mol))
params = system_builder.construct_energies(ff, mol, False)
# global_params = args[0]
# nrg_params = args[1]
# total_params = args[2]
# masses = args[3]
# mol = args[4]
# charge_idxs = args[5]
train_args.append((gp, params[0], params[1], masses, mol, params[3]))
train_offset_idxs.append(params[2])
train_charge_idxs.append(params[3])
label_confs = [generate_conformations(a) for a in train_reference_args]
return train_args, train_offset_idxs, train_charge_idxs, label_confs
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_AlkEthOH.ffxml')
ff = ForceField(ffxml)
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 new_param_energy_vac(coords, params, T=293.15):
"""
Return potential energies associated with specified parameter perturbations.
Parameters
----------
coords: coordinates from the simulation(s) ran on the given molecule
params: arbitrary length dictionary of changes in parameter across arbitrary number of states. Highest level key is the molecule AlkEthOH_ID,
second level of keys are the new state, the values of each of these subkeys are a arbitrary length list of length 3 lists where the
length 3 lists contain information on a parameter to change in the form: [SMIRKS, parameter type, parameter value]. I.e. :
params = {'AlkEthOH_c1143':{'State 1':[['[6X4:1]-[#1:2]','k','620'],['[6X4:1]-[#6X4:2]','length','1.53'],...],'State 2':[...],...}}
T: Temperature of the system. By default set to 300 K.
Returns
-------
E_kn: a kxN matrix of the dimensional energies associated with the forcfield parameters used as input
u_kn: a kxN matrix of the dimensionless energies associated with the forcfield parameters used as input
"""
#-------------------
# CONSTANTS
#-------------------
kB = 0.0083145 #Boltzmann constant (Gas constant) in kJ/(mol*K)
beta = 1/(kB*T)
#-------------------
# PARAMETERS
#-------------------
params = params
# Determine number of states we wish to estimate potential energies for
mols = []
for i in params:
mols.append(i)
mol = 'monomers/'+mols[0]+'.mol2'
K = len(params[mols[0]].keys())
#-------------
# SYSTEM SETUP
#-------------
verbose = False # suppress echos from OEtoolkit functions
ifs = oechem.oemolistream(mol)
mol = oechem.OEMol()
# This uses parm@frosst atom types, so make sure to use the forcefield-flavor reader
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
ifs.SetFlavor( oechem.OEFormat_MOL2, flavor)
oechem.OEReadMolecule(ifs, mol )
# Perceive tripos types
oechem.OETriposAtomNames(mol)
# Load forcefield file
#ffxml = 'smirnoff99Frosst_with_AllConstraints.ffxml'#
#print('The forcefield being used is smirnoff99Frosst_with_AllConstraints.ffxml')
ffxml = get_data_filename('forcefield/smirnoff99Frosst.ffxml')
print('The forcefield being used is smirnoff99Frosst.ffxml')
ff = ForceField(ffxml)
# Generate a topology
topology = generateTopologyFromOEMol(mol)
#-----------------
# MAIN
#-----------------
# Calculate energies
E_kn = np.zeros([K,len(coords)],np.float64)
u_kn = np.zeros([K,len(coords)],np.float64)
for i,j in enumerate(params):
AlkEthOH_id = j
for k,l in enumerate(params[AlkEthOH_id]):
print("Anotha one")
for m,n in enumerate(params[AlkEthOH_id][l]):
newparams = ff.getParameter(smirks=n[0])
newparams[n[1]]=n[2]
ff.setParameter(newparams,smirks=n[0])
system = ff.createSystem(topology, [mol])
#print(newparams)
for o,p in enumerate(coords):
e = get_energy_vac(system,p)
E_kn[k,o] = e._value
u_kn[k,o] = e._value*beta
return E_kn,u_kn
coordinates = mol.GetCoords()
natoms = len(coordinates)
positions = np.zeros([natoms, 3], np.float64)
for index in range(natoms):
(x, y, z) = coordinates[index]
positions[index, 0] = x
positions[index, 1] = y
positions[index, 2] = z
positions = Quantity(positions, angstroms)
# Load forcefield
forcefield = ForceField(
get_data_filename('forcefield/smirnoff99Frosst.ffxml'))
# Define system
topology = generateTopologyFromOEMol(mol)
params = forcefield.getParameter(smirks='[#1:1]-[#8]')
params['rmin_half'] = '0.01'
params['epsilon'] = '0.01'
forcefield.setParameter(params, smirks='[#1:1]-[#8]')
system = forcefield.createSystem(topology, [mol])
"""
paramlist1 = np.array([100.,140.,60.,140.,60.])#np.arange(float(sys.argv[2]),float(sys.argv[3]),float(sys.argv[4]))
paramlist2 = np.array([109.5,76.5,76.5,142.5,142.5])
#j = sys.argv[5]
smirkseries = '[*:1]~[#6X4:2]-[*:3]'#sys.argv[6]#'[#6X4:1]-[#1:2]'
paramtype1 = 'k'#sys.argv[7]#'length'
paramtype2 = 'angle'#sys.argv[8]
