def test_phase_creation():
"""Phases are initialized correctly by Yank.create()."""
phase_name = 'my-solvent-phase'
toluene = testsystems.TolueneImplicit()
protocol = AbsoluteAlchemicalFactory.defaultSolventProtocolImplicit()
atom_indices = find_components(toluene.system, toluene.topology, 'resname TOL')
phase = AlchemicalPhase(phase_name, toluene.system, toluene.topology,
toluene.positions, atom_indices, protocol)
thermodynamic_state = ThermodynamicState(temperature=300.0*unit.kelvin)
# Create new simulation.
with enter_temp_directory():
output_dir = 'output'
utils.config_root_logger(verbose=False)
yank = Yank(store_directory=output_dir)
yank.create(thermodynamic_state, phase)
# Netcdf dataset has been created
nc_path = os.path.join(output_dir, phase_name + '.nc')
assert os.path.isfile(nc_path)
# Read data
try:
nc_file = netcdf.Dataset(nc_path, mode='r')
metadata_group = nc_file.groups['metadata']
serialized_topology = metadata_group.variables['topology'][0]
finally:
nc_file.close()
# Topology has been stored correctly
deserialized_topology = utils.deserialize_topology(serialized_topology)
assert deserialized_topology == mdtraj.Topology.from_openmm(toluene.topology)
def setup_binding_gromacs(args):
"""
Set up ligand binding free energy calculation using gromacs prmtop/inpcrd files.
Parameters
----------
args : dict
Command-line arguments dict from docopt.
Returns
-------
phases : list of str
Phases (thermodynamic legs) of the calculation.
systems : dict
systems[phase] is the OpenMM System reference object for phase 'phase'.
positions : dict
positions[phase] is a set of positions (or list of positions) for initializing replicas.
atom_indices : dict
atom_indices[phase][component] is list of atom indices for component 'component' in phase 'phase'.
"""
verbose = args['--verbose']
# Implicit solvent
if args['--gbsa']:
implicitSolvent = getattr(app, args['--gbsa'])
else:
implicitSolvent = None
# Select nonbonded treatment
# TODO: Carefully check whether input file is periodic or not.
if args['--nbmethod']:
nonbondedMethod = getattr(app, args['--nbmethod'])
else:
nonbondedMethod = None
# Constraints
if args['--constraints']:
constraints = getattr(app, args['--constraints'])
else:
constraints = None
# Cutoff
if args['--cutoff']:
nonbondedCutoff = process_unit_bearing_arg(args, '--cutoff', unit.nanometers)
else:
nonbondedCutoff = None
# COM removal
removeCMMotion = False
# Prepare phases of calculation.
phase_prefixes = ['solvent', 'complex'] # list of calculation phases (thermodynamic legs) to set up
components = ['ligand', 'receptor', 'solvent'] # components of the binding system
systems = dict() # systems[phase] is the System object associated with phase 'phase'
positions = dict() # positions[phase] is a list of coordinates associated with phase 'phase'
atom_indices = dict() # ligand_atoms[phase] is a list of ligand atom indices associated with phase 'phase'
setup_directory = args['--setupdir'] # Directory where prmtop/inpcrd files are to be found
for phase_prefix in phase_prefixes:
if verbose: logger.info("reading phase %s: " % phase_prefix)
# Read gromacs input files.
gro_filename = os.path.join(setup_directory, '%s.gro' % phase_prefix)
top_filename = os.path.join(setup_directory, '%s.top' % phase_prefix)
if verbose: logger.info('reading gromacs .gro file: %s' % gro_filename)
gro = app.GromacsGroFile(gro_filename)
if verbose: logger.info('reading gromacs .top file "%s" using gromacs include directory "%s"' % (top_filename, args['--gromacsinclude']))
top = app.GromacsTopFile(top_filename, unitCellDimensions=gro.getUnitCellDimensions(), includeDir=args['--gromacsinclude'])
# Assume explicit solvent.
# TODO: Modify this if we can have implicit solvent.
is_periodic = True
phase_suffix = 'explicit'
# Adjust nonbondedMethod.
# TODO: Ensure that selected method is appropriate.
if nonbondedMethod == None:
if is_periodic:
nonbondedMethod = app.CutoffPeriodic
else:
nonbondedMethod = app.NoCutoff
# TODO: Check to make sure both prmtop and inpcrd agree on explicit/implicit.
phase = '%s-%s' % (phase_prefix, phase_suffix)
systems[phase] = top.createSystem(nonbondedMethod=nonbondedMethod, nonbondedCutoff=nonbondedCutoff, constraints=constraints, removeCMMotion=removeCMMotion)
positions[phase] = gro.getPositions(asNumpy=True)
# Check to make sure number of atoms match between prmtop and inpcrd.
prmtop_natoms = systems[phase].getNumParticles()
inpcrd_natoms = positions[phase].shape[0]
if prmtop_natoms != inpcrd_natoms:
raise Exception("Atom number mismatch: prmtop %s has %d atoms; inpcrd %s has %d atoms." % (prmtop_filename, prmtop_natoms, inpcrd_filename, inpcrd_natoms))
# Find ligand atoms and receptor atoms.
ligand_dsl = args['--ligand'] # MDTraj DSL that specifies ligand atoms
atom_indices[phase] = find_components(top.topology, ligand_dsl)
phases = systems.keys()
return [phases, systems, positions, atom_indices]
def setup_binding_gromacs(args):
"""
Set up ligand binding free energy calculation using gromacs prmtop/inpcrd files.
Parameters
----------
args : dict
Command-line arguments dict from docopt.
Returns
-------
alchemical_phases : list of AlchemicalPhase
Phases (thermodynamic legs) of the calculation.
"""
verbose = args["--verbose"]
# Implicit solvent
if args["--gbsa"]:
implicitSolvent = getattr(app, args["--gbsa"])
else:
implicitSolvent = None
# Select nonbonded treatment
# TODO: Carefully check whether input file is periodic or not.
if args["--nbmethod"]:
nonbondedMethod = getattr(app, args["--nbmethod"])
else:
nonbondedMethod = None
# Constraints
if args["--constraints"]:
constraints = getattr(app, args["--constraints"])
else:
constraints = None
# Cutoff
if args["--cutoff"]:
nonbondedCutoff = process_unit_bearing_arg(args, "--cutoff", unit.nanometers)
else:
nonbondedCutoff = None
# COM removal
removeCMMotion = False
# Prepare phases of calculation.
phase_prefixes = ["solvent", "complex"] # list of calculation phases (thermodynamic legs) to set up
components = ["ligand", "receptor", "solvent"] # components of the binding system
systems = dict() # systems[phase] is the System object associated with phase 'phase'
topologies = dict() # topologies[phase] is the Topology object associated with phase 'phase'
positions = dict() # positions[phase] is a list of coordinates associated with phase 'phase'
atom_indices = dict() # ligand_atoms[phase] is a list of ligand atom indices associated with phase 'phase'
setup_directory = args["--setupdir"] # Directory where prmtop/inpcrd files are to be found
for phase_prefix in phase_prefixes:
if verbose:
logger.info("reading phase %s: " % phase_prefix)
# Read gromacs input files.
gro_filename = os.path.join(setup_directory, "%s.gro" % phase_prefix)
top_filename = os.path.join(setup_directory, "%s.top" % phase_prefix)
if verbose:
logger.info("reading gromacs .gro file: %s" % gro_filename)
gro = app.GromacsGroFile(gro_filename)
if verbose:
logger.info(
'reading gromacs .top file "%s" using gromacs include directory "%s"'
% (top_filename, args["--gromacsinclude"])
)
top = app.GromacsTopFile(
top_filename, unitCellDimensions=gro.getUnitCellDimensions(), includeDir=args["--gromacsinclude"]
)
# Assume explicit solvent.
# TODO: Modify this if we can have implicit solvent.
is_periodic = True
phase_suffix = "explicit"
# Adjust nonbondedMethod.
# TODO: Ensure that selected method is appropriate.
if nonbondedMethod == None:
if is_periodic:
nonbondedMethod = app.CutoffPeriodic
else:
nonbondedMethod = app.NoCutoff
# TODO: Check to make sure both prmtop and inpcrd agree on explicit/implicit.
phase = "%s-%s" % (phase_prefix, phase_suffix)
systems[phase] = top.createSystem(
nonbondedMethod=nonbondedMethod,
nonbondedCutoff=nonbondedCutoff,
constraints=constraints,
removeCMMotion=removeCMMotion,
)
topologies[phase] = top.topology
positions[phase] = gro.getPositions(asNumpy=True)
# Check to make sure number of atoms match between prmtop and inpcrd.
prmtop_natoms = systems[phase].getNumParticles()
inpcrd_natoms = positions[phase].shape[0]
if prmtop_natoms != inpcrd_natoms:
raise Exception(
"Atom number mismatch: prmtop %s has %d atoms; inpcrd %s has %d atoms."
% (prmtop_filename, prmtop_natoms, inpcrd_filename, inpcrd_natoms)
)
# Find ligand atoms and receptor atoms.
ligand_dsl = args["--ligand"] # MDTraj DSL that specifies ligand atoms
atom_indices[phase] = find_components(systems[phase], top.topology, ligand_dsl)
phases = systems.keys()
alchemical_phases = [None, None]
protocols = {
"complex-explicit": AbsoluteAlchemicalFactory.defaultComplexProtocolExplicit(),
"solvent-explicit": AbsoluteAlchemicalFactory.defaultSolventProtocolImplicit(),
}
for i, name in enumerate(phases):
alchemical_phases[i] = AlchemicalPhase(
name, systems[name], topologies[name], positions[name], atom_indices[name], protocols[name]
)
return alchemical_phases