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 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 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)