def generate_vacuum_hybrid_topology(mol_name="naphthalene", ref_mol_name="benzene"):
from topology_proposal import SmallMoleculeSetProposalEngine, TopologyProposal
import simtk.openmm.app as app
from openmoltools import forcefield_generators
from perses.tests.utils import createOEMolFromIUPAC, createSystemFromIUPAC, get_data_filename
m, unsolv_old_system, pos_old, top_old = createSystemFromIUPAC(mol_name)
refmol = createOEMolFromIUPAC(ref_mol_name)
initial_smiles = oechem.OEMolToSmiles(m)
final_smiles = oechem.OEMolToSmiles(refmol)
gaff_xml_filename = get_data_filename("data/gaff.xml")
forcefield = app.ForceField(gaff_xml_filename, 'tip3p.xml')
forcefield.registerTemplateGenerator(forcefield_generators.gaffTemplateGenerator)
solvated_system = forcefield.createSystem(top_old)
gaff_filename = get_data_filename('data/gaff.xml')
system_generator = SystemGenerator([gaff_filename, 'amber99sbildn.xml', 'tip3p.xml'])
geometry_engine = FFAllAngleGeometryEngine()
proposal_engine = SmallMoleculeSetProposalEngine(
[initial_smiles, final_smiles], system_generator, residue_name=mol_name)
#generate topology proposal
topology_proposal = proposal_engine.propose(solvated_system, top_old)
#generate new positions with geometry engine
new_positions, _ = geometry_engine.propose(topology_proposal, pos_old, beta)
return topology_proposal, pos_old, new_positions
def generate_vacuum_hybrid_topology(mol_name="naphthalene", ref_mol_name="benzene"):
from topology_proposal import SmallMoleculeSetProposalEngine, TopologyProposal
import simtk.openmm.app as app
from openmoltools import forcefield_generators
from perses.tests.utils import createOEMolFromIUPAC, createSystemFromIUPAC, get_data_filename
m, unsolv_old_system, pos_old, top_old = createSystemFromIUPAC(mol_name)
refmol = createOEMolFromIUPAC(ref_mol_name)
initial_smiles = oechem.OEMolToSmiles(m)
final_smiles = oechem.OEMolToSmiles(refmol)
gaff_xml_filename = get_data_filename("data/gaff.xml")
forcefield = app.ForceField(gaff_xml_filename, 'tip3p.xml')
forcefield.registerTemplateGenerator(forcefield_generators.gaffTemplateGenerator)
solvated_system = forcefield.createSystem(top_old)
gaff_filename = get_data_filename('data/gaff.xml')
system_generator = SystemGenerator([gaff_filename, 'amber99sbildn.xml', 'tip3p.xml'])
geometry_engine = FFAllAngleGeometryEngine()
proposal_engine = SmallMoleculeSetProposalEngine(
[initial_smiles, final_smiles], system_generator, residue_name=mol_name)
#generate topology proposal
topology_proposal = proposal_engine.propose(solvated_system, top_old)
#generate new positions with geometry engine
new_positions, _ = geometry_engine.propose(topology_proposal, pos_old, beta)
return topology_proposal, pos_old, new_positions
def generate_solvated_hybrid_test_topology(current_mol_name="naphthalene", proposed_mol_name="benzene"):
"""
Generate a test solvated topology proposal, current positions, and new positions triplet
from two IUPAC molecule names.
Parameters
----------
current_mol_name : str, optional
name of the first molecule
proposed_mol_name : str, optional
name of the second molecule
Returns
-------
topology_proposal : perses.rjmc.topology_proposal
The topology proposal representing the transformation
current_positions : np.array, unit-bearing
The positions of the initial system
new_positions : np.array, unit-bearing
The positions of the new system
"""
import simtk.openmm.app as app
from openmoltools import forcefield_generators
from perses.tests.utils import createOEMolFromIUPAC, createSystemFromIUPAC, get_data_filename
current_mol, unsolv_old_system, pos_old, top_old = createSystemFromIUPAC(current_mol_name)
proposed_mol = createOEMolFromIUPAC(proposed_mol_name)
initial_smiles = oechem.OEMolToSmiles(current_mol)
final_smiles = oechem.OEMolToSmiles(proposed_mol)
gaff_xml_filename = get_data_filename("data/gaff.xml")
forcefield = app.ForceField(gaff_xml_filename, 'tip3p.xml')
forcefield.registerTemplateGenerator(forcefield_generators.gaffTemplateGenerator)
modeller = app.Modeller(top_old, pos_old)
modeller.addSolvent(forcefield, model='tip3p', padding=9.0*unit.angstrom)
solvated_topology = modeller.getTopology()
solvated_positions = modeller.getPositions()
solvated_system = forcefield.createSystem(solvated_topology, nonbondedMethod=app.PME, removeCMMotion=False)
barostat = openmm.MonteCarloBarostat(1.0*unit.atmosphere, temperature, 50)
solvated_system.addForce(barostat)
gaff_filename = get_data_filename('data/gaff.xml')
system_generator = SystemGenerator([gaff_filename, 'amber99sbildn.xml', 'tip3p.xml'], barostat=barostat, forcefield_kwargs={'removeCMMotion': False, 'nonbondedMethod': app.PME})
geometry_engine = geometry.FFAllAngleGeometryEngine()
proposal_engine = SmallMoleculeSetProposalEngine(
[initial_smiles, final_smiles], system_generator, residue_name=current_mol_name)
#generate topology proposal
topology_proposal = proposal_engine.propose(solvated_system, solvated_topology)
#generate new positions with geometry engine
new_positions, _ = geometry_engine.propose(topology_proposal, solvated_positions, beta)
return topology_proposal, solvated_positions, new_positions
def generate_solvated_hybrid_test_topology(current_mol_name="naphthalene", proposed_mol_name="benzene"):
"""
Generate a test solvated topology proposal, current positions, and new positions triplet
from two IUPAC molecule names.
Parameters
----------
current_mol_name : str, optional
name of the first molecule
proposed_mol_name : str, optional
name of the second molecule
Returns
-------
topology_proposal : perses.rjmc.topology_proposal
The topology proposal representing the transformation
current_positions : np.array, unit-bearing
The positions of the initial system
new_positions : np.array, unit-bearing
The positions of the new system
"""
import simtk.openmm.app as app
from openmoltools import forcefield_generators
from perses.tests.utils import createOEMolFromIUPAC, createSystemFromIUPAC, get_data_filename
current_mol, unsolv_old_system, pos_old, top_old = createSystemFromIUPAC(current_mol_name)
proposed_mol = createOEMolFromIUPAC(proposed_mol_name)
initial_smiles = oechem.OEMolToSmiles(current_mol)
final_smiles = oechem.OEMolToSmiles(proposed_mol)
gaff_xml_filename = get_data_filename("data/gaff.xml")
forcefield = app.ForceField(gaff_xml_filename, 'tip3p.xml')
forcefield.registerTemplateGenerator(forcefield_generators.gaffTemplateGenerator)
modeller = app.Modeller(top_old, pos_old)
modeller.addSolvent(forcefield, model='tip3p', padding=9.0*unit.angstrom)
solvated_topology = modeller.getTopology()
solvated_positions = modeller.getPositions()
solvated_system = forcefield.createSystem(solvated_topology, nonbondedMethod=app.PME, removeCMMotion=False)
barostat = openmm.MonteCarloBarostat(1.0*unit.atmosphere, temperature, 50)
solvated_system.addForce(barostat)
gaff_filename = get_data_filename('data/gaff.xml')
system_generator = SystemGenerator([gaff_filename, 'amber99sbildn.xml', 'tip3p.xml'], barostat=barostat, forcefield_kwargs={'removeCMMotion': False, 'nonbondedMethod': app.PME})
geometry_engine = geometry.FFAllAngleGeometryEngine()
proposal_engine = SmallMoleculeSetProposalEngine(
[initial_smiles, final_smiles], system_generator, residue_name=current_mol_name)
#generate topology proposal
topology_proposal = proposal_engine.propose(solvated_system, solvated_topology)
#generate new positions with geometry engine
new_positions, _ = geometry_engine.propose(topology_proposal, solvated_positions, beta)
return topology_proposal, solvated_positions, new_positions
def generate_vacuum_hostguest_proposal(current_mol_name="B2", proposed_mol_name="MOL"):
"""
Generate a test vacuum topology proposal, current positions, and new positions triplet
from two IUPAC molecule names.
Parameters
----------
current_mol_name : str, optional
name of the first molecule
proposed_mol_name : str, optional
name of the second molecule
Returns
-------
topology_proposal : perses.rjmc.topology_proposal
The topology proposal representing the transformation
current_positions : np.array, unit-bearing
The positions of the initial system
new_positions : np.array, unit-bearing
The positions of the new system
"""
from openmoltools import forcefield_generators
from openmmtools import testsystems
from perses.tests.utils import createOEMolFromIUPAC, createSystemFromIUPAC, get_data_filename
host_guest = testsystems.HostGuestVacuum()
unsolv_old_system, pos_old, top_old = host_guest.system, host_guest.positions, host_guest.topology
ligand_topology = [res for res in top_old.residues()]
current_mol = forcefield_generators.generateOEMolFromTopologyResidue(ligand_topology[1]) # guest is second residue in topology
proposed_mol = createOEMolFromSMILES('C1CC2(CCC1(CC2)C)C')
initial_smiles = oechem.OEMolToSmiles(current_mol)
final_smiles = oechem.OEMolToSmiles(proposed_mol)
gaff_xml_filename = get_data_filename("data/gaff.xml")
forcefield = app.ForceField(gaff_xml_filename, 'tip3p.xml')
forcefield.registerTemplateGenerator(forcefield_generators.gaffTemplateGenerator)
solvated_system = forcefield.createSystem(top_old, removeCMMotion=False)
gaff_filename = get_data_filename('data/gaff.xml')
system_generator = SystemGenerator([gaff_filename, 'amber99sbildn.xml', 'tip3p.xml'], forcefield_kwargs={'removeCMMotion': False, 'nonbondedMethod': app.NoCutoff})
geometry_engine = geometry.FFAllAngleGeometryEngine()
proposal_engine = SmallMoleculeSetProposalEngine(
[initial_smiles, final_smiles], system_generator, residue_name=current_mol_name)
#generate topology proposal
topology_proposal = proposal_engine.propose(solvated_system, top_old, current_mol=current_mol, proposed_mol=proposed_mol)
#generate new positions with geometry engine
new_positions, _ = geometry_engine.propose(topology_proposal, pos_old, beta)
return topology_proposal, pos_old, new_positions
def generate_vacuum_topology_proposal(current_mol_name="benzene", proposed_mol_name="toluene"):
"""
Generate a test vacuum topology proposal, current positions, and new positions triplet
from two IUPAC molecule names.
Parameters
----------
current_mol_name : str, optional
name of the first molecule
proposed_mol_name : str, optional
name of the second molecule
Returns
-------
topology_proposal : perses.rjmc.topology_proposal
The topology proposal representing the transformation
current_positions : np.array, unit-bearing
The positions of the initial system
new_positions : np.array, unit-bearing
The positions of the new system
"""
from openmoltools import forcefield_generators
from perses.tests.utils import createOEMolFromIUPAC, createSystemFromIUPAC, get_data_filename
current_mol, unsolv_old_system, pos_old, top_old = createSystemFromIUPAC(current_mol_name)
proposed_mol = createOEMolFromIUPAC(proposed_mol_name)
initial_smiles = oechem.OEMolToSmiles(current_mol)
final_smiles = oechem.OEMolToSmiles(proposed_mol)
gaff_xml_filename = get_data_filename("data/gaff.xml")
forcefield = app.ForceField(gaff_xml_filename, 'tip3p.xml')
forcefield.registerTemplateGenerator(forcefield_generators.gaffTemplateGenerator)
solvated_system = forcefield.createSystem(top_old, removeCMMotion=False)
gaff_filename = get_data_filename('data/gaff.xml')
system_generator = SystemGenerator([gaff_filename, 'amber99sbildn.xml', 'tip3p.xml'], forcefield_kwargs={'removeCMMotion': False, 'nonbondedMethod': app.NoCutoff})
geometry_engine = geometry.FFAllAngleGeometryEngine()
proposal_engine = SmallMoleculeSetProposalEngine(
[initial_smiles, final_smiles], system_generator, residue_name=current_mol_name)
#generate topology proposal
topology_proposal = proposal_engine.propose(solvated_system, top_old, current_mol=current_mol, proposed_mol=proposed_mol)
#generate new positions with geometry engine
new_positions, _ = geometry_engine.propose(topology_proposal, pos_old, beta)
return topology_proposal, pos_old, new_positions
def oemol_to_omm_ff(oemol, molecule_name):
from perses.rjmc import topology_proposal
from openmoltools import forcefield_generators
gaff_xml_filename = get_data_filename('data/gaff.xml')
system_generator = topology_proposal.SystemGenerator([gaff_xml_filename])
topology = forcefield_generators.generateTopologyFromOEMol(oemol)
system = system_generator.build_system(topology)
positions = extractPositionsFromOEMOL(oemol)
return system, positions, topology
def oemol_to_omm_ff(oemol, molecule_name):
from perses.rjmc import topology_proposal
from openmoltools import forcefield_generators
gaff_xml_filename = get_data_filename('data/gaff.xml')
system_generator = topology_proposal.SystemGenerator([gaff_xml_filename])
topology = forcefield_generators.generateTopologyFromOEMol(oemol)
system = system_generator.build_system(topology)
positions = extractPositionsFromOEMOL(oemol)
return system, positions, topology
def createSystemFromIUPAC(iupac_name):
"""
Create an openmm system out of an oemol
Parameters
----------
iupac_name : str
IUPAC name
Returns
-------
molecule : openeye.OEMol
OEMol molecule
system : openmm.System object
OpenMM system
positions : [n,3] np.array of floats
Positions
topology : openmm.app.Topology object
Topology
"""
# Create OEMol
molecule = createOEMolFromIUPAC(iupac_name)
# Generate a topology.
from openmoltools.forcefield_generators import generateTopologyFromOEMol
topology = generateTopologyFromOEMol(molecule)
# Initialize a forcefield with GAFF.
# TODO: Fix path for `gaff.xml` since it is not yet distributed with OpenMM
from simtk.openmm.app import ForceField
gaff_xml_filename = get_data_filename('data/gaff.xml')
forcefield = ForceField(gaff_xml_filename)
# Generate template and parameters.
from openmoltools.forcefield_generators import generateResidueTemplate
[template, ffxml] = generateResidueTemplate(molecule)
# Register the template.
forcefield.registerResidueTemplate(template)
# Add the parameters.
forcefield.loadFile(StringIO(ffxml))
# Create the system.
system = forcefield.createSystem(topology, removeCMMotion=False)
# Extract positions
positions = extractPositionsFromOEMOL(molecule)
return (molecule, system, positions, topology)
def createSystemFromIUPAC(iupac_name):
"""
Create an openmm system out of an oemol
Parameters
----------
iupac_name : str
IUPAC name
Returns
-------
molecule : openeye.OEMol
OEMol molecule
system : openmm.System object
OpenMM system
positions : [n,3] np.array of floats
Positions
topology : openmm.app.Topology object
Topology
"""
# Create OEMol
molecule = createOEMolFromIUPAC(iupac_name)
# Generate a topology.
from openmoltools.forcefield_generators import generateTopologyFromOEMol
topology = generateTopologyFromOEMol(molecule)
# Initialize a forcefield with GAFF.
# TODO: Fix path for `gaff.xml` since it is not yet distributed with OpenMM
from simtk.openmm.app import ForceField
gaff_xml_filename = get_data_filename('data/gaff.xml')
forcefield = ForceField(gaff_xml_filename)
# Generate template and parameters.
from openmoltools.forcefield_generators import generateResidueTemplate
[template, ffxml] = generateResidueTemplate(molecule)
# Register the template.
forcefield.registerResidueTemplate(template)
# Add the parameters.
forcefield.loadFile(StringIO(ffxml))
# Create the system.
system = forcefield.createSystem(topology, removeCMMotion=False)
# Extract positions
positions = extractPositionsFromOEMOL(molecule)
return (molecule, system, positions, topology)
def prepare_topology_proposal():
from perses.tests.utils import get_data_filename
gaff_xml_filename = get_data_filename("data/gaff.xml")
forcefield = app.ForceField(gaff_xml_filename, 'tip3p.xml',
'amber99sbildn.xml')
forcefield.registerTemplateGenerator(
forcefield_generators.gaffTemplateGenerator)
oemol_list = load_mol_file("p38_ligands.sdf")
mol_a = oemol_list[0]
mol_b = oemol_list[1]
modeller = combine_mol_with_receptor(mol_a, "p38_protein.pdb")
modeller.addSolvent(forcefield, model='tip3p', padding=9.0 * unit.angstrom)
topology = modeller.getTopology()
positions = modeller.getPositions()
system = forcefield.createSystem(topology, nonbondedMethod=app.PME)
def generate_solvated_hybrid_test_topology(mol_name="naphthalene",
ref_mol_name="benzene"):
from perses.rjmc.topology_proposal import SmallMoleculeSetProposalEngine, TopologyProposal
import simtk.openmm.app as app
from openmoltools import forcefield_generators
from perses.tests.utils import createOEMolFromIUPAC, createSystemFromIUPAC, get_data_filename
mol = createOEMolFromIUPAC(mol_name)
m, unsolv_system, pos, top = createSystemFromIUPAC(mol_name)
refmol = createOEMolFromIUPAC(ref_mol_name)
gaff_xml_filename = get_data_filename("data/gaff.xml")
forcefield = app.ForceField(gaff_xml_filename, 'tip3p.xml')
forcefield.registerTemplateGenerator(
forcefield_generators.gaffTemplateGenerator)
#map one of the rings
atom_map = SmallMoleculeSetProposalEngine._get_mol_atom_map(mol, refmol)
#now use the mapped atoms to generate a new and old system with identical atoms mapped. This will result in the
#same molecule with the same positions for lambda=0 and 1, and ensures a contiguous atom map
effective_atom_map = {value: value for value in atom_map.values()}
modeller = app.Modeller(top, pos)
modeller.addSolvent(forcefield, model='tip3p', padding=9.0 * unit.angstrom)
topology = modeller.getTopology()
positions = modeller.getPositions()
system = forcefield.createSystem(topology, nonbondedMethod=app.PME)
n_atoms_old_system = unsolv_system.getNumParticles()
n_atoms_after_solvation = system.getNumParticles()
for i in range(n_atoms_old_system, n_atoms_after_solvation):
effective_atom_map[i] = i
top_proposal = TopologyProposal(new_topology=topology,
new_system=system,
old_topology=topology,
old_system=system,
new_to_old_atom_map=effective_atom_map,
new_chemical_state_key="n1",
old_chemical_state_key='n2')
return top_proposal, positions
def generate_solvated_hybrid_test_topology(mol_name="naphthalene", ref_mol_name="benzene"):
from perses.rjmc.topology_proposal import SmallMoleculeSetProposalEngine, TopologyProposal
import simtk.openmm.app as app
from openmoltools import forcefield_generators
from perses.tests.utils import createOEMolFromIUPAC, createSystemFromIUPAC, get_data_filename
mol = createOEMolFromIUPAC(mol_name)
m, unsolv_system, pos, top = createSystemFromIUPAC(mol_name)
refmol = createOEMolFromIUPAC(ref_mol_name)
gaff_xml_filename = get_data_filename("data/gaff.xml")
forcefield = app.ForceField(gaff_xml_filename, 'tip3p.xml')
forcefield.registerTemplateGenerator(forcefield_generators.gaffTemplateGenerator)
#map one of the rings
atom_map = SmallMoleculeSetProposalEngine._get_mol_atom_map(mol, refmol)
#now use the mapped atoms to generate a new and old system with identical atoms mapped. This will result in the
#same molecule with the same positions for lambda=0 and 1, and ensures a contiguous atom map
effective_atom_map = {value : value for value in atom_map.values()}
modeller = app.Modeller(top, pos)
modeller.addSolvent(forcefield, model='tip3p', padding=9.0*unit.angstrom)
topology = modeller.getTopology()
positions = modeller.getPositions()
system = forcefield.createSystem(topology, nonbondedMethod=app.PME)
n_atoms_old_system = unsolv_system.getNumParticles()
n_atoms_after_solvation = system.getNumParticles()
for i in range(n_atoms_old_system, n_atoms_after_solvation):
effective_atom_map[i] = i
top_proposal = TopologyProposal(new_topology=topology, new_system=system, old_topology=topology, old_system=system, new_to_old_atom_map=effective_atom_map, new_chemical_state_key="n1", old_chemical_state_key='n2')
return top_proposal, positions
def generate_topology_proposal(old_mol_iupac="pentane",
new_mol_iupac="butane"):
"""
Utility function to generate a topologyproposal for tests
Parameters
----------
old_mol_iupac : str, optional
name of old mol, default pentane
new_mol_iupac : str, optional
name of new mol, default butane
Returns
-------
topology_proposal : perses.rjmc.topology_proposal.TopologyProposal
the topology proposal corresponding to the given transformation
old_positions : [n, 3] np.ndarray of float
positions of old mol
new_positions : [m, 3] np.ndarray of float
positions of new mol
"""
from perses.rjmc.topology_proposal import TwoMoleculeSetProposalEngine, SystemGenerator
from perses.rjmc.geometry import FFAllAngleGeometryEngine
from perses.tests.utils import createSystemFromIUPAC, get_data_filename
import openmoltools.forcefield_generators as forcefield_generators
from io import StringIO
from openmmtools.constants import kB
temperature = 300.0 * unit.kelvin
kT = kB * temperature
beta = 1.0 / kT
gaff_filename = get_data_filename("data/gaff.xml")
forcefield_files = [gaff_filename, 'amber99sbildn.xml']
#generate systems and topologies
old_mol, old_system, old_positions, old_topology = createSystemFromIUPAC(
old_mol_iupac)
new_mol, new_system, new_positions, new_topology = createSystemFromIUPAC(
new_mol_iupac)
#set names
old_mol.SetTitle("MOL")
new_mol.SetTitle("MOL")
#generate forcefield and ProposalEngine
#ffxml=forcefield_generators.generateForceFieldFromMolecules([old_mol, new_mol])
system_generator = SystemGenerator(
forcefield_files, forcefield_kwargs={'removeCMMotion': False})
proposal_engine = TwoMoleculeSetProposalEngine(old_mol,
new_mol,
system_generator,
residue_name="pentane")
geometry_engine = FFAllAngleGeometryEngine()
#create a TopologyProposal
topology_proposal = proposal_engine.propose(old_system, old_topology)
new_positions_geometry, _ = geometry_engine.propose(
topology_proposal, old_positions, beta)
return topology_proposal, old_positions, new_positions_geometry
def generate_vacuum_topology_proposal(current_mol_name="benzene", proposed_mol_name="toluene", forcefield_kwargs=None, system_generator_kwargs=None):
"""
Generate a test vacuum topology proposal, current positions, and new positions triplet from two IUPAC molecule names.
Constraints are added to the system by default. To override this, set ``forcefield_kwargs = None``.
Parameters
----------
current_mol_name : str, optional
name of the first molecule
proposed_mol_name : str, optional
name of the second molecule
forcefield_kwargs : dict, optional, default=None
Additional arguments to ForceField in addition to
'removeCMMotion': False, 'nonbondedMethod': app.NoCutoff
system_generator_kwargs : dict, optional, default=None
Dict passed onto SystemGenerator
Returns
-------
topology_proposal : perses.rjmc.topology_proposal
The topology proposal representing the transformation
current_positions : np.array, unit-bearing
The positions of the initial system
new_positions : np.array, unit-bearing
The positions of the new system
"""
from openmoltools import forcefield_generators
from perses.tests.utils import createOEMolFromIUPAC, createSystemFromIUPAC, get_data_filename
gaff_filename = get_data_filename('data/gaff.xml')
default_forcefield_kwargs = {'removeCMMotion': False, 'nonbondedMethod': app.NoCutoff, 'constraints' : app.HBonds}
forcefield_kwargs = default_forcefield_kwargs.update(forcefield_kwargs) if (forcefield_kwargs is not None) else default_forcefield_kwargs
system_generator_kwargs = system_generator_kwargs if (system_generator_kwargs is not None) else dict()
system_generator = SystemGenerator([gaff_filename, 'amber99sbildn.xml', 'tip3p.xml'],
forcefield_kwargs=forcefield_kwargs,
**system_generator_kwargs)
old_oemol = createOEMolFromIUPAC(current_mol_name)
from openmoltools.forcefield_generators import generateTopologyFromOEMol
old_topology = generateTopologyFromOEMol(old_oemol)
old_positions = extractPositionsFromOEMOL(old_oemol)
old_smiles = oechem.OEMolToSmiles(old_oemol)
old_system = system_generator.build_system(old_topology)
new_oemol = createOEMolFromIUPAC(proposed_mol_name)
new_smiles = oechem.OEMolToSmiles(new_oemol)
geometry_engine = geometry.FFAllAngleGeometryEngine()
proposal_engine = SmallMoleculeSetProposalEngine(
[old_smiles, new_smiles], system_generator, residue_name=current_mol_name)
#generate topology proposal
topology_proposal = proposal_engine.propose(old_system, old_topology, current_mol=old_oemol, proposed_mol=new_oemol)
# show atom mapping
filename = str(current_mol_name)+str(proposed_mol_name)+'.pdf'
render_atom_mapping(filename, old_oemol, new_oemol, topology_proposal.new_to_old_atom_map)
#generate new positions with geometry engine
new_positions, _ = geometry_engine.propose(topology_proposal, old_positions, beta)
# DEBUG: Zero out bonds and angles for one system
#print('Zeroing bonds of old system')
#for force in topology_proposal.old_system.getForces():
# if force.__class__.__name__ == 'HarmonicAngleForce':
# for index in range(force.getNumAngles()):
# p1, p2, p3, angle, K = force.getAngleParameters(index)
# K *= 0.0
# force.setAngleParameters(index, p1, p2, p3, angle, K)
# if False and force.__class__.__name__ == 'HarmonicBondForce':
# for index in range(force.getNumBonds()):
# p1, p2, r0, K = force.getBondParameters(index)
# K *= 0.0
# force.setBondParameters(index, p1, p2, r0, K)
# DEBUG : Box vectors
#box_vectors = np.eye(3) * 100 * unit.nanometers
#topology_proposal.old_system.setDefaultPeriodicBoxVectors(box_vectors[0,:], box_vectors[1,:], box_vectors[2,:])
#topology_proposal.new_system.setDefaultPeriodicBoxVectors(box_vectors[0,:], box_vectors[1,:], box_vectors[2,:])
return topology_proposal, old_positions, new_positions
def test_logp_forward_check_for_vacuum_topology_proposal(current_mol_name = 'propane', proposed_mol_name = 'octane', num_iterations = 100, neglect_angles = True):
"""
Generate a test vacuum topology proposal, current positions, and new positions triplet
from two IUPAC molecule names. Assert that the logp_forward < 1e3.
This assertion will fail if the proposal order tool proposed the placement of the a carbon before a previously defined carbon in the alkane.
Parameters
----------
current_mol_name : str, optional
name of the first molecule
proposed_mol_name : str, optional
name of the second molecule
Returns
-------
topology_proposal : perses.rjmc.topology_proposal
The topology proposal representing the transformation
current_positions : np.array, unit-bearing
The positions of the initial system
new_positions : np.array, unit-bearing
The positions of the new system
"""
from openmoltools import forcefield_generators
from perses.tests.utils import createOEMolFromIUPAC, createSystemFromIUPAC, get_data_filename
current_mol, unsolv_old_system, pos_old, top_old = createSystemFromIUPAC(current_mol_name)
proposed_mol = createOEMolFromIUPAC(proposed_mol_name)
initial_smiles = oechem.OEMolToSmiles(current_mol)
final_smiles = oechem.OEMolToSmiles(proposed_mol)
gaff_xml_filename = get_data_filename("data/gaff.xml")
forcefield = app.ForceField(gaff_xml_filename, 'tip3p.xml')
forcefield.registerTemplateGenerator(forcefield_generators.gaffTemplateGenerator)
solvated_system = forcefield.createSystem(top_old, removeCMMotion=False)
gaff_filename = get_data_filename('data/gaff.xml')
system_generator = SystemGenerator([gaff_filename, 'amber99sbildn.xml', 'tip3p.xml'], forcefield_kwargs={'removeCMMotion': False, 'nonbondedMethod': app.NoCutoff})
geometry_engine = geometry.FFAllAngleGeometryEngine(n_bond_divisions=100, n_angle_divisions=180, n_torsion_divisions=360, neglect_angles = neglect_angles)
proposal_engine = SmallMoleculeSetProposalEngine(
[initial_smiles, final_smiles], system_generator, residue_name=current_mol_name)
#generate topology proposal
topology_proposal = proposal_engine.propose(solvated_system, top_old, current_mol=current_mol, proposed_mol=proposed_mol)
# show atom mapping
filename = str(current_mol_name)+str(proposed_mol_name)+'.pdf'
render_atom_mapping(filename,current_mol,proposed_mol,topology_proposal.new_to_old_atom_map)
total_works = []
for _ in range(num_iterations):
#generate new positions with geometry engine
new_positions, logp_forward = geometry_engine.propose(topology_proposal, pos_old, beta)
logp_reverse = geometry_engine.logp_reverse(topology_proposal, new_positions, pos_old, beta)
#now just render forward and backward work
work_fwd = logp_forward + geometry_engine.forward_final_context_reduced_potential - geometry_engine.forward_atoms_with_positions_reduced_potential
work_bkwd = logp_reverse + geometry_engine.reverse_atoms_with_positions_reduced_potential - geometry_engine.reverse_final_context_reduced_potential
total_work = logp_forward - logp_reverse + geometry_engine.forward_final_context_reduced_potential - geometry_engine.reverse_final_context_reduced_potential
total_works.append(total_work)
print("forward, backward works : {}, {}".format(work_fwd, work_bkwd))
print("total_work: {}".format(total_work))
assert abs(work_fwd - work_bkwd - total_work) < 1, "The difference of fwd and backward works is not equal to the total work (within 1kT)"
assert logp_forward < 1e3, "A heavy atom was proposed in an improper order"