def dispatch_binding(args):
"""
Set up a binding free energy calculation.
Parameters
----------
args : dict
Command-line arguments from docopt.
"""
verbose = args['--verbose']
store_dir = args['--store']
utils.config_root_logger(verbose,
log_file_path=os.path.join(
store_dir, 'prepare.log'))
#
# Determine simulation options.
#
# Specify thermodynamic parameters.
temperature = process_unit_bearing_argument(args, '--temperature',
unit.kelvin)
pressure = process_unit_bearing_argument(args, '--pressure',
unit.atmospheres)
thermodynamic_state = ThermodynamicState(temperature=temperature,
pressure=pressure)
# Create systems according to specified setup/import method.
if args['amber']:
[phases, systems, positions, atom_indices] = setup_binding_amber(args)
elif args['gromacs']:
[phases, systems, positions,
atom_indices] = setup_binding_gromacs(args)
else:
logger.error(
"No valid binding free energy calculation setup command specified: Must be one of ['amber', 'systembuilder']."
)
# Trigger help argument to be returned.
return False
# Report some useful properties.
if verbose:
if 'complex-explicit' in atom_indices:
phase = 'complex-explicit'
else:
phase = 'complex-implicit'
logger.info("TOTAL ATOMS : %9d" %
len(atom_indices[phase]['complex']))
logger.info("receptor : %9d" %
len(atom_indices[phase]['receptor']))
logger.info("ligand : %9d" %
len(atom_indices[phase]['ligand']))
if phase == 'complex-explicit':
logger.info("solvent and ions : %9d" %
len(atom_indices[phase]['solvent']))
# Initialize YANK object.
yank = Yank(store_dir)
# Set options.
options = dict()
if args['--nsteps']:
options['nsteps_per_iteration'] = int(args['--nsteps'])
if args['--iterations']:
options['number_of_iterations'] = int(args['--iterations'])
if args['--equilibrate']:
options['number_of_equilibration_iterations'] = int(
args['--equilibrate'])
if args['--online-analysis']:
options['online_analysis'] = True
if args['--restraints']:
yank.restraint_type = args['--restraints']
if args['--randomize-ligand']:
options['randomize_ligand'] = True
if args['--minimize']:
options['minimize'] = True
# Allow platform to be optionally specified in order for alchemical tests to be carried out.
if args['--platform'] not in [None, 'None']:
options['platform'] = openmm.Platform.getPlatformByName(
args['--platform'])
if args['--precision']:
# We need to modify the Platform object.
if args['--platform'] is None:
raise Exception(
"The --platform argument must be specified in order to specify platform precision."
)
# Set platform precision.
precision = args['--precision']
platform_name = args['--platform']
logger.info(
"Setting %s platform to use precision model '%s'." % platform_name,
precision)
if precision is not None:
if platform_name == 'CUDA':
options['platform'].setPropertyDefaultValue(
'CudaPrecision', precision)
elif platform_name == 'OpenCL':
options['platform'].setPropertyDefaultValue(
'OpenCLPrecision', precision)
elif platform_name == 'CPU':
if precision != 'mixed':
raise Exception(
"CPU platform does not support precision model '%s'; only 'mixed' is supported."
% precision)
elif platform_name == 'Reference':
if precision != 'double':
raise Exception(
"Reference platform does not support precision model '%s'; only 'double' is supported."
% precision)
else:
raise Exception(
"Platform selection logic is outdated and needs to be updated to add platform '%s'."
% platform_name)
# Create new simulation.
yank.create(phases,
systems,
positions,
atom_indices,
thermodynamic_state,
options=options)
# Report success.
return True
def dispatch_binding(args):
"""
Set up a binding free energy calculation.
Parameters
----------
args : dict
Command-line arguments from docopt.
"""
verbose = args['--verbose']
#
# Determine simulation options.
#
# Specify thermodynamic parameters.
temperature = process_unit_bearing_argument(args, '--temperature', unit.kelvin)
pressure = process_unit_bearing_argument(args, '--pressure', unit.atmospheres)
thermodynamic_state = ThermodynamicState(temperature=temperature, pressure=pressure)
# Create systems according to specified setup/import method.
if args['amber']:
[phases, systems, positions, atom_indices] = setup_binding_amber(args)
elif args['systembuilder']:
[phases, systems, positions, atom_indices] = setup_binding_systembuilder(args)
else:
print "No valid binding free energy calculation setup command specified: Must be one of ['amber', 'systembuilder']."
# Trigger help argument to be returned.
return False
# Report some useful properties.
if verbose:
if 'complex-explicit' in atom_indices:
phase = 'complex-explicit'
else:
phase = 'complex-implicit'
print " TOTAL ATOMS : %9d" % len(atom_indices[phase]['complex'])
print " receptor : %9d" % len(atom_indices[phase]['receptor'])
print " ligand : %9d" % len(atom_indices[phase]['ligand'])
if phase == 'complex-explicit':
print " solvent and ions : %9d" % len(atom_indices[phase]['solvent'])
# Initialize YANK object.
yank = Yank(args['--store'], verbose=verbose)
# Set options.
options = dict()
if args['--iterations']:
options['number_of_iterations'] = int(args['--iterations'])
if args['--online-analysis']:
options['online_analysis'] = True
if args['--restraints']:
yank.restraint_type = args['--restraints']
if args['--randomize-ligand']:
options['randomize_ligand'] = True
if args['--minimize']:
options['minimize'] = True
# Create new simulation.
yank.create(phases, systems, positions, atom_indices, thermodynamic_state, options=options)
# Report success.
return True
def dispatch_binding(args):
"""
Set up a binding free energy calculation.
Parameters
----------
args : dict
Command-line arguments from docopt.
"""
verbose = args["--verbose"]
store_dir = args["--store"]
utils.config_root_logger(verbose, log_file_path=os.path.join(store_dir, "prepare.log"))
#
# Determine simulation options.
#
# Specify thermodynamic parameters.
temperature = process_unit_bearing_arg(args, "--temperature", unit.kelvin)
pressure = process_unit_bearing_arg(args, "--pressure", unit.atmospheres)
thermodynamic_state = ThermodynamicState(temperature=temperature, pressure=pressure)
# Create systems according to specified setup/import method.
if args["amber"]:
[phases, systems, positions, atom_indices] = setup_binding_amber(args)
elif args["gromacs"]:
[phases, systems, positions, atom_indices] = setup_binding_gromacs(args)
else:
logger.error(
"No valid binding free energy calculation setup command specified: Must be one of ['amber', 'systembuilder']."
)
# Trigger help argument to be returned.
return False
# Report some useful properties.
if verbose:
if "complex-explicit" in atom_indices:
phase = "complex-explicit"
else:
phase = "complex-implicit"
logger.info("TOTAL ATOMS : %9d" % len(atom_indices[phase]["complex"]))
logger.info("receptor : %9d" % len(atom_indices[phase]["receptor"]))
logger.info("ligand : %9d" % len(atom_indices[phase]["ligand"]))
if phase == "complex-explicit":
logger.info("solvent and ions : %9d" % len(atom_indices[phase]["solvent"]))
# Initialize YANK object.
yank = Yank(store_dir)
# Set options.
options = dict()
if args["--nsteps"]:
options["nsteps_per_iteration"] = int(args["--nsteps"])
if args["--iterations"]:
options["number_of_iterations"] = int(args["--iterations"])
if args["--equilibrate"]:
options["number_of_equilibration_iterations"] = int(args["--equilibrate"])
if args["--online-analysis"]:
options["online_analysis"] = True
if args["--restraints"]:
options["restraint_type"] = args["--restraints"]
if args["--randomize-ligand"]:
options["randomize_ligand"] = True
if args["--minimize"]:
options["minimize"] = True
# Allow platform to be optionally specified in order for alchemical tests to be carried out.
if args["--platform"] not in [None, "None"]:
options["platform"] = openmm.Platform.getPlatformByName(args["--platform"])
if args["--precision"]:
# We need to modify the Platform object.
if args["--platform"] is None:
raise Exception("The --platform argument must be specified in order to specify platform precision.")
# Set platform precision.
precision = args["--precision"]
platform_name = args["--platform"]
logger.info("Setting %s platform to use precision model '%s'." % platform_name, precision)
if precision is not None:
if platform_name == "CUDA":
options["platform"].setPropertyDefaultValue("CudaPrecision", precision)
elif platform_name == "OpenCL":
options["platform"].setPropertyDefaultValue("OpenCLPrecision", precision)
elif platform_name == "CPU":
if precision != "mixed":
raise Exception(
"CPU platform does not support precision model '%s'; only 'mixed' is supported." % precision
)
elif platform_name == "Reference":
if precision != "double":
raise Exception(
"Reference platform does not support precision model '%s'; only 'double' is supported."
% precision
)
else:
raise Exception(
"Platform selection logic is outdated and needs to be updated to add platform '%s'." % platform_name
)
yank.options.cli = options
# Parse YAML configuration file and create YankOptions object
if args["--yaml"]:
yank.options.yaml = YamlBuilder(args["--yaml"]).options
# Create new simulation.
yank.create(phases, systems, positions, atom_indices, thermodynamic_state)
# Report success.
return True
def dispatch_binding(args):
"""
Set up a binding free energy calculation.
Parameters
----------
args : dict
Command-line arguments from docopt.
"""
verbose = args['--verbose']
store_dir = args['--store']
utils.config_root_logger(verbose, log_file_path=os.path.join(store_dir, 'prepare.log'))
#
# Determine simulation options.
#
# Specify thermodynamic parameters.
temperature = process_unit_bearing_arg(args, '--temperature', unit.kelvin)
pressure = process_unit_bearing_arg(args, '--pressure', unit.atmospheres)
thermodynamic_state = ThermodynamicState(temperature=temperature, pressure=pressure)
# Create systems according to specified setup/import method.
if args['amber']:
[phases, systems, positions, atom_indices] = setup_binding_amber(args)
elif args['gromacs']:
[phases, systems, positions, atom_indices] = setup_binding_gromacs(args)
else:
logger.error("No valid binding free energy calculation setup command specified: Must be one of ['amber', 'systembuilder'].")
# Trigger help argument to be returned.
return False
# Report some useful properties.
if verbose:
if 'complex-explicit' in atom_indices:
phase = 'complex-explicit'
else:
phase = 'complex-implicit'
logger.info("TOTAL ATOMS : %9d" % len(atom_indices[phase]['complex']))
logger.info("receptor : %9d" % len(atom_indices[phase]['receptor']))
logger.info("ligand : %9d" % len(atom_indices[phase]['ligand']))
if phase == 'complex-explicit':
logger.info("solvent and ions : %9d" % len(atom_indices[phase]['solvent']))
# Set options.
options = dict()
if args['--nsteps']:
options['nsteps_per_iteration'] = int(args['--nsteps'])
if args['--iterations']:
options['number_of_iterations'] = int(args['--iterations'])
if args['--equilibrate']:
options['number_of_equilibration_iterations'] = int(args['--equilibrate'])
if args['--online-analysis']:
options['online_analysis'] = True
if args['--restraints']:
options['restraint_type'] = args['--restraints']
if args['--randomize-ligand']:
options['randomize_ligand'] = True
if args['--minimize']:
options['minimize'] = True
# Allow platform to be optionally specified in order for alchemical tests to be carried out.
if args['--platform'] not in [None, 'None']:
options['platform'] = openmm.Platform.getPlatformByName(args['--platform'])
if args['--precision']:
# We need to modify the Platform object.
if args['--platform'] is None:
raise Exception("The --platform argument must be specified in order to specify platform precision.")
# Set platform precision.
precision = args['--precision']
platform_name = args['--platform']
logger.info("Setting %s platform to use precision model '%s'." % platform_name, precision)
if precision is not None:
if platform_name == 'CUDA':
options['platform'].setPropertyDefaultValue('CudaPrecision', precision)
elif platform_name == 'OpenCL':
options['platform'].setPropertyDefaultValue('OpenCLPrecision', precision)
elif platform_name == 'CPU':
if precision != 'mixed':
raise Exception("CPU platform does not support precision model '%s'; only 'mixed' is supported." % precision)
elif platform_name == 'Reference':
if precision != 'double':
raise Exception("Reference platform does not support precision model '%s'; only 'double' is supported." % precision)
else:
raise Exception("Platform selection logic is outdated and needs to be updated to add platform '%s'." % platform_name)
# Parse YAML options, CLI options have priority
if args['--yaml']:
options.update(YamlBuilder(args['--yaml']).yank_options)
# Create new simulation.
yank = Yank(store_dir, **options)
yank.create(phases, systems, positions, atom_indices, thermodynamic_state)
# Report success.
return True
def dispatch_binding(args):
"""
Set up a binding free energy calculation.
Parameters
----------
args : dict
Command-line arguments from docopt.
"""
verbose = args['--verbose']
store_dir = args['--store']
utils.config_root_logger(verbose,
log_file_path=os.path.join(
store_dir, 'prepare.log'))
#
# Determine simulation options.
#
# Specify thermodynamic parameters.
temperature = process_unit_bearing_arg(args, '--temperature', unit.kelvin)
pressure = process_unit_bearing_arg(args, '--pressure', unit.atmospheres)
thermodynamic_state = ThermodynamicState(temperature=temperature,
pressure=pressure)
# Create systems according to specified setup/import method.
if args['amber']:
alchemical_phases = setup_binding_amber(args)
elif args['gromacs']:
alchemical_phases = setup_binding_gromacs(args)
else:
logger.error(
"No valid binding free energy calculation setup command specified: Must be one of ['amber', 'systembuilder']."
)
# Trigger help argument to be returned.
return False
# Set options.
options = dict()
if args['--nsteps']:
options['nsteps_per_iteration'] = int(args['--nsteps'])
if args['--iterations']:
options['number_of_iterations'] = int(args['--iterations'])
if args['--equilibrate']:
options['number_of_equilibration_iterations'] = int(
args['--equilibrate'])
if args['--online-analysis']:
options['online_analysis'] = True
if args['--restraints']:
options['restraint_type'] = args['--restraints']
if args['--randomize-ligand']:
options['randomize_ligand'] = True
if args['--minimize']:
options['minimize'] = True
# Allow platform to be optionally specified in order for alchemical tests to be carried out.
if args['--platform'] not in [None, 'None']:
options['platform'] = openmm.Platform.getPlatformByName(
args['--platform'])
if args['--precision']:
# We need to modify the Platform object.
if args['--platform'] is None:
raise Exception(
"The --platform argument must be specified in order to specify platform precision."
)
# Set platform precision.
precision = args['--precision']
platform_name = args['--platform']
logger.info(
"Setting %s platform to use precision model '%s'." % platform_name,
precision)
if precision is not None:
if platform_name == 'CUDA':
options['platform'].setPropertyDefaultValue(
'CudaPrecision', precision)
elif platform_name == 'OpenCL':
options['platform'].setPropertyDefaultValue(
'OpenCLPrecision', precision)
elif platform_name == 'CPU':
if precision != 'mixed':
raise Exception(
"CPU platform does not support precision model '%s'; only 'mixed' is supported."
% precision)
elif platform_name == 'Reference':
if precision != 'double':
raise Exception(
"Reference platform does not support precision model '%s'; only 'double' is supported."
% precision)
else:
raise Exception(
"Platform selection logic is outdated and needs to be updated to add platform '%s'."
% platform_name)
# Parse YAML options, CLI options have priority
if args['--yaml']:
options.update(YamlBuilder(args['--yaml']).yank_options)
# Create new simulation.
yank = Yank(store_dir, **options)
yank.create(thermodynamic_state, *alchemical_phases)
# Dump analysis object
analysis = [[alchemical_phases[0].name, 1],
[alchemical_phases[1].name, -1]]
analysis_script_path = os.path.join(store_dir, 'analysis.yaml')
with open(analysis_script_path, 'w') as f:
yaml.dump(analysis, f)
# Report success.
return True
def dispatch_binding(args):
"""
Set up a binding free energy calculation.
Parameters
----------
args : dict
Command-line arguments from docopt.
"""
verbose = args['--verbose']
# Specify simulation parameters.
nonbondedMethod = getattr(app, args['--nbmethod'])
implicitSolvent = getattr(app, args['--gbsa'])
if args['--constraints'] == None:
args[
'--constraints'] = None # Necessary because there is no 'None' in simtk.openmm.app
constraints = getattr(app, args['--constraints'])
removeCMMotion = False
# Specify thermodynamic parameters.
temperature = process_unit_bearing_argument(args, '--temperature',
unit.kelvin)
pressure = process_unit_bearing_argument(args, '--pressure',
unit.atmospheres)
thermodynamic_state = ThermodynamicState(temperature=temperature,
pressure=pressure)
# Create systems according to specified setup/import method.
if args['amber']:
[phases, systems, positions, atom_indices] = setup_binding_amber(args)
elif args['systembuilder']:
[phases, systems, positions,
atom_indices] = setup_binding_systembuilder(args)
else:
print "No valid binding free energy calculation setup command specified: Must be one of ['amber', 'systembuilder']."
# Trigger help argument to be returned.
return False
# Report some useful properties.
if verbose:
if 'complex-explicit' in atom_indices:
phase = 'complex-explicit'
else:
phase = 'complex-implicit'
print " TOTAL ATOMS : %9d" % len(atom_indices[phase]['complex'])
print " receptor : %9d" % len(atom_indices[phase]['receptor'])
print " ligand : %9d" % len(atom_indices[phase]['ligand'])
if phase == 'complex-explicit':
print " solvent and ions : %9d" % len(
atom_indices[phase]['solvent'])
# Initialize YANK object.
yank = Yank(args['--store'], verbose=verbose)
# Set options.
options = dict()
if args['--iterations']:
options['number_of_iterations'] = int(args['--iterations'])
if args['--online-analysis']:
options['online_analysis'] = True
if args['--restraints']:
yank.restraint_type = args['--restraints']
if args['--randomize-ligand']:
options['randomize_ligand'] = True
if args['--platform'] != 'None':
options['platform'] = openmm.Platform.getPlatformByName(
args['--platform'])
if args['--minimize']:
options['minimize'] = True
# Create new simulation.
yank.create(phases,
systems,
positions,
atom_indices,
thermodynamic_state,
options=options)
# Report success.
return True
def dispatch_binding(args):
"""
Set up a binding free energy calculation.
Parameters
----------
args : dict
Command-line arguments from docopt.
"""
verbose = args["--verbose"]
store_dir = args["--store"]
utils.config_root_logger(verbose, log_file_path=os.path.join(store_dir, "prepare.log"))
#
# Determine simulation options.
#
# Specify thermodynamic parameters.
temperature = process_unit_bearing_arg(args, "--temperature", unit.kelvin)
pressure = process_unit_bearing_arg(args, "--pressure", unit.atmospheres)
thermodynamic_state = ThermodynamicState(temperature=temperature, pressure=pressure)
# Create systems according to specified setup/import method.
if args["amber"]:
alchemical_phases = setup_binding_amber(args)
elif args["gromacs"]:
alchemical_phases = setup_binding_gromacs(args)
else:
logger.error(
"No valid binding free energy calculation setup command specified: Must be one of ['amber', 'systembuilder']."
)
# Trigger help argument to be returned.
return False
# Set options.
options = dict()
if args["--nsteps"]:
options["nsteps_per_iteration"] = int(args["--nsteps"])
if args["--iterations"]:
options["number_of_iterations"] = int(args["--iterations"])
if args["--equilibrate"]:
options["number_of_equilibration_iterations"] = int(args["--equilibrate"])
if args["--online-analysis"]:
options["online_analysis"] = True
if args["--restraints"]:
options["restraint_type"] = args["--restraints"]
if args["--randomize-ligand"]:
options["randomize_ligand"] = True
if args["--minimize"]:
options["minimize"] = True
# Allow platform to be optionally specified in order for alchemical tests to be carried out.
if args["--platform"] not in [None, "None"]:
options["platform"] = openmm.Platform.getPlatformByName(args["--platform"])
if args["--precision"]:
# We need to modify the Platform object.
if args["--platform"] is None:
raise Exception("The --platform argument must be specified in order to specify platform precision.")
# Set platform precision.
precision = args["--precision"]
platform_name = args["--platform"]
logger.info("Setting %s platform to use precision model '%s'." % platform_name, precision)
if precision is not None:
if platform_name == "CUDA":
options["platform"].setPropertyDefaultValue("CudaPrecision", precision)
elif platform_name == "OpenCL":
options["platform"].setPropertyDefaultValue("OpenCLPrecision", precision)
elif platform_name == "CPU":
if precision != "mixed":
raise Exception(
"CPU platform does not support precision model '%s'; only 'mixed' is supported." % precision
)
elif platform_name == "Reference":
if precision != "double":
raise Exception(
"Reference platform does not support precision model '%s'; only 'double' is supported."
% precision
)
else:
raise Exception(
"Platform selection logic is outdated and needs to be updated to add platform '%s'." % platform_name
)
# Parse YAML options, CLI options have priority
if args["--yaml"]:
options.update(YamlBuilder(args["--yaml"]).yank_options)
# Create new simulation.
yank = Yank(store_dir, **options)
yank.create(thermodynamic_state, *alchemical_phases)
# Dump analysis object
analysis = [[alchemical_phases[0].name, 1], [alchemical_phases[1].name, -1]]
analysis_script_path = os.path.join(store_dir, "analysis.yaml")
with open(analysis_script_path, "w") as f:
yaml.dump(analysis, f)
# Report success.
return True
