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)
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 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_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 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_MDL_aromaticity(verbose=False):
"""Test support for alternate aromaticity models."""
ffxml = StringIO(ffxml_MDL_contents)
ff = ForceField(ffxml)
from openeye import oechem
mol = oechem.OEMol()
oechem.OEParseSmiles(mol, 'c12c(cccc1)occ2')
oechem.OEAddExplicitHydrogens(mol)
labels = ff.labelMolecules([mol], verbose=True)
# The bond 6-7 should get the b16 parameter iff the MDL model is working, otherwise it will pick up just the generic
details = labels[0]['HarmonicBondGenerator']
found = False
for (atom_indices, pid, smirks) in details:
if pid == 'b16' and atom_indices == [6, 7]:
found = True
if not found: raise Exception("Didn't find right param.")
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_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_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 test_create_system_molecules_features(verbose=False):
"""Test creation of a System object from small molecules to test various ffxml features
"""
ffxml = StringIO(ffxml_contents)
forcefield = ForceField(ffxml)
for chargeMethod in [None, 'BCC', 'OECharges_AM1BCCSym']:
for f in check_AlkEtOH(
forcefield,
description="to test ffxml features with charge method %s" %
str(chargeMethod),
chargeMethod=chargeMethod,
verbose=verbose):
yield f
def test_create_system_boxes_features(verbose=False):
"""Test creation of a System object from some boxes of mixed solvents to test ffxml features.
"""
ffxml = StringIO(ffxml_contents)
forcefield = ForceField(ffxml)
for chargeMethod in [None, 'BCC', 'OECharges_AM1BCCSym']:
for f in check_boxes(
forcefield,
description=
"to test Parm@frosst parameters with charge method %s" %
str(chargeMethod),
chargeMethod=chargeMethod,
verbose=verbose):
yield f
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 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 get_molecule_parameterIDs( oemols, ffxml):
"""Process a list of oemols with a specified SMIRFF ffxml file and determine which parameters are used by which molecules, returning collated results.
Parameters
----------
oemols : list
List of OpenEye OEChem molecules to parse; must have explicit hydrogens.
Returns
-------
parameters_by_molecule : dict
Parameter IDs used in each molecule, keyed by isomeric SMILES
generated from provided OEMols. Each entry in the dict is a list
which does not necessarily have unique entries; i.e. parameter IDs
which are used more than once will occur multiple times.
parameters_by_ID : dict
Molecules in which each parameter ID occur, keyed by parameter ID.
Each entry in the dict is a set of isomeric SMILES for molecules
in which that parameter occurs. No frequency information is stored.
"""
# Create storage
parameters_by_molecule = {}
parameters_by_ID = {}
# Generate isomeric SMILES
isosmiles = list()
for mol in oemols:
smi = oechem.OECreateIsoSmiString(mol)
if not smi in isosmiles:
isosmiles.append(smi)
# If the molecule is already here, raise exception
else:
raise ValueError("Error: get_molecule_parameterIDs has been provided a list of oemols which contains the same molecule, having isomeric smiles %s, more than once." % smi )
# Label molecules
ff = ForceField( ffxml )
labels = ff.labelMolecules( oemols )
# Organize labels into output dictionary by looping over all molecules/smiles
for idx in range(len(isosmiles)):
# Pull smiles, initialize storage
smi = isosmiles[idx]
parameters_by_molecule[smi] = []
# Organize data for this molecule
data = labels[idx]
for force_type in data.keys():
for (atom_indices, pid, smirks) in data[force_type]:
# Store pid to molecule
parameters_by_molecule[smi].append(pid)
# Store which molecule this pid occurred in
if pid not in parameters_by_ID:
parameters_by_ID[pid] = set()
parameters_by_ID[pid].add(smi)
else:
parameters_by_ID[pid].add(smi)
return parameters_by_molecule, parameters_by_ID
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_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_read_ffxml():
"""Test reading of ffxml files.
"""
forcefield = ForceField(
get_data_filename('forcefield/Frosst_AlkEtOH.ffxml'))
def convert_frcmod_to_ffxml( infile, inxml, outxml ):
"""Convert a modified AMBER frcmod (with SMIRKS replacing atom types) to SMIRFF ffxml format by inserting parameters into a template ffxml file.
Parameters
----------
infile : str
File name of input SMIRKS-ified frcmod file containing parameters
inxml : str
File name of template SMIRFF FFXML file into which to insert these parameters.
outxml : str
File name of resulting output SMIRFF FFXML
Notes:
-------
Input XML file will normally be the template of a SMIRFF XML file without any parameters present (but with requisite force types already specified).
"""
# Obtain sections from target file
file = open(infile, 'r')
text = file.readlines()
file.close()
sections = {}
# Section names from frcmod which we will parse
secnames = ['NONBON', 'BOND', 'ANGL', 'IMPR', 'DIHE']
# Tags that will be used in the FFXML for these (same order)
tag = ['Atom', 'Bond', 'Angle', 'Improper', 'Proper']
# Force names in the FFXML (same order)
force_section = ['NonbondedForce', 'HarmonicBondForce', 'HarmonicAngleForce', 'PeriodicTorsionForce', 'PeriodicTorsionForce']
ct = 0
thissec = None
# Why is this a while loop and not a for line in text loop?
while ct < len(text):
line = text[ct]
tmp = line.split()
# Skip lines starting with comment or which are blank
if line[0]=='#' or len(tmp) < 1:
ct+=1
continue
# Check first entry to see if it's a section name, if so initialize storage
if tmp[0] in secnames:
thissec = tmp[0]
sections[thissec] = []
# Otherwise store
else:
sections[thissec].append(line)
ct+=1
# Read template forcefield file
ff = ForceField(inxml)
# Use functions to parse sections from target file and add parameters to force field
param_id_by_section={}
param_prefix_by_sec = {'NONBON':'n' , 'BOND':'b', 'ANGL':'a', 'DIHE':'t', 'IMPR':'i'}
for (idx, name) in enumerate(secnames):
param_id_by_section[name] = 1
for line in sections[name]:
# Parse line for parameters
if name=='NONBON':
params = _parse_nonbon_line(line)
elif name=='BOND':
params = _parse_bond_line(line)
elif name=='DIHE':
params = _parse_dihe_line(line)
elif name=='IMPR':
params = _parse_impr_line(line)
elif name=='ANGL':
params = _parse_angl_line(line)
# Add parameter ID
params['id'] = param_prefix_by_sec[name]+str( param_id_by_section[name] )
smirks = params['smirks']
#Check smirks is valid for chemical enviroment parsing:
env = environment.ChemicalEnvironment(smirks)
# If it's not a torsion, just store in straightforward way
if not (name=='IMPR' or name=='DIHE'):
# Check for duplicates first
if ff.getParameter( smirks, force_type = force_section[idx] ):
raise ValueError("Error: parameter for %s is already present in forcefield." % smirks )
else:
ff.addParameter( params, smirks, force_section[idx], tag[idx] )
# Increment parameter id
param_id_by_section[name] +=1
# If it's a torsion, check to see if there are already parameters and
# if so, add a new term to this torsion
else:
# If we have parameters already
oldparams = ff.getParameter(smirks, force_type=force_section[idx])
if oldparams:
# Find what number to use
idnr = 1
paramtag = 'k%s' % idnr
# This was "while paramtag in params" so it was overwriting k2 etc.
while paramtag in oldparams:
idnr+=1
paramtag = 'k%s' % idnr
# Construct new param object with updated numbers
for paramtag in ('periodicity1', 'phase1', 'idivf1', 'k1'):
if paramtag in params:
val = params.pop(paramtag)
oldparams[paramtag[:-1]+str(idnr) ] = val
# Store
ff.setParameter( oldparams, smirks=smirks, force_type=force_section[idx])
else:
# Otherwise, just store new parameters
ff.addParameter( params, smirks, force_section[idx], tag[idx])
# Increment parameter ID
param_id_by_section[name] += 1
# Write SMIRFF XML file
ff.writeFile(outxml)
# Roundtrip to fix formatting (for some reason etree won't format it properly on first write after modification)
tmp = ForceField(outxml)
tmp.writeFile(outxml)
def get_molecule_parameterIDs(oemols, ffxml):
"""Process a list of oemols with a specified SMIRFF ffxml file and determine which parameters are used by which molecules, returning collated results.
Parameters
----------
oemols : list
List of OpenEye OEChem molecules to parse; must have explicit hydrogens.
Returns
-------
parameters_by_molecule : dict
Parameter IDs used in each molecule, keyed by isomeric SMILES
generated from provided OEMols. Each entry in the dict is a list
which does not necessarily have unique entries; i.e. parameter IDs
which are used more than once will occur multiple times.
parameters_by_ID : dict
Molecules in which each parameter ID occur, keyed by parameter ID.
Each entry in the dict is a set of isomeric SMILES for molecules
in which that parameter occurs. No frequency information is stored.
"""
# Create storage
parameters_by_molecule = {}
parameters_by_ID = {}
# Generate isomeric SMILES
isosmiles = list()
for mol in oemols:
smi = oechem.OECreateIsoSmiString(mol)
if not smi in isosmiles:
isosmiles.append(smi)
# If the molecule is already here, raise exception
else:
raise ValueError(
"Error: get_molecule_parameterIDs has been provided a list of oemols which contains the same molecule, having isomeric smiles %s, more than once."
% smi)
# Label molecules
ff = ForceField(ffxml)
labels = ff.labelMolecules(oemols)
# Organize labels into output dictionary by looping over all molecules/smiles
for idx in range(len(isosmiles)):
# Pull smiles, initialize storage
smi = isosmiles[idx]
parameters_by_molecule[smi] = []
# Organize data for this molecule
data = labels[idx]
for force_type in data.keys():
for (atom_indices, pid, smirks) in data[force_type]:
# Store pid to molecule
parameters_by_molecule[smi].append(pid)
# Store which molecule this pid occurred in
if pid not in parameters_by_ID:
parameters_by_ID[pid] = set()
parameters_by_ID[pid].add(smi)
else:
parameters_by_ID[pid].add(smi)
return parameters_by_molecule, parameters_by_ID