def driver():
# Initialize command-line argument parser.
verbose = True
usage = """
USAGE
%prog --ligand_prmtop PRMTOP --receptor_prmtop PRMTOP { {--ligand_crd CRD | --ligand_mol2 MOL2} {--receptor_crd CRD | --receptor_pdb PDB} | {--complex_crd CRD | --complex_pdb PDB} } [-v | --verbose] [-i | --iterations ITERATIONS] [-o | --online] [-m | --mpi] [--restraints restraint-type] [--doctests] [--randomize_ligand]
EXAMPLES
# Specify AMBER prmtop/crd files for ligand and receptor.
%prog --ligand_prmtop ligand.prmtop --receptor_prmtop receptor.prmtop --ligand_crd ligand.crd --receptor_crd receptor.crd --iterations 1000
# Specify (potentially multi-conformer) mol2 file for ligand and (potentially multi-model) PDB file for receptor.
%prog --ligand_prmtop ligand.prmtop --receptor_prmtop receptor.prmtop --ligand_mol2 ligand.mol2 --receptor_pdb receptor.pdb --iterations 1000
# Specify (potentially multi-model) PDB file for complex, along with flat-bottom restraints (instead of harmonic).
%prog --ligand_prmtop ligand.prmtop --receptor_prmtop receptor.prmtop --complex_pdb complex.pdb --iterations 1000 --restraints flat-bottom
# Specify (potentially multi-model) PDB file for complex, along with flat-bottom restraints (instead of harmonic); randomize ligand positions/orientations at start.
%prog --ligand_prmtop ligand.prmtop --receptor_prmtop receptor.prmtop --complex_pdb complex.pdb --iterations 1000 --restraints flat-bottom --randomize_ligand
NOTES
In atom ordering, receptor comes before ligand atoms.
"""
# Parse command-line arguments.
from optparse import OptionParser
parser = OptionParser(usage=usage)
parser.add_option("--ligand_mol2", dest="ligand_mol2_filename", default=None, help="ligand mol2 file (can contain multiple conformations)", metavar="LIGAND_MOL2")
parser.add_option("--receptor_pdb", dest="receptor_pdb_filename", default=None, help="receptor PDB file (can contain multiple MODELs)", metavar="RECEPTOR_PDB")
parser.add_option("--complex_pdb", dest="complex_pdb_filename", default=None, help="complex PDB file (can contain multiple MODELs)", metavar="COMPLEX_PDB")
parser.add_option("-v", "--verbose", action="store_true", dest="verbose", default=False, help="verbosity flag")
parser.add_option("-i", "--iterations", dest="niterations", default=None, help="number of iterations", metavar="ITERATIONS")
parser.add_option("-o", "--online", dest="online_analysis", default=False, help="perform online analysis")
parser.add_option("-m", "--mpi", action="store_true", dest="mpi", default=False, help="use mpi if possible")
parser.add_option("--restraints", dest="restraint_type", default=None, help="specify ligand restraint type: 'harmonic' or 'flat-bottom' (default: 'harmonic')")
parser.add_option("--output", dest="output_directory", default=None, help="specify output directory---must be unique for each calculation (default: current directory)")
parser.add_option("--doctests", action="store_true", dest="doctests", default=False, help="run doctests first (default: False)")
parser.add_option("--randomize_ligand", action="store_true", dest="randomize_ligand", default=False, help="randomize ligand positions and orientations (default: False)")
parser.add_option("--ignore_signal", action="append", dest="ignore_signals", default=[], help="signals to trap and ignore (default: None)")
parser.add_option("--platform", dest="platform", default="CPU",help="The platform to use when running simulations")
parser.add_option("--gpus_per_node", dest="gpus_per_node", type='int', default=None, help="number of GPUs per node to use for complex simulations during MPI calculations")
# Parse command-line arguments.
(options, args) = parser.parse_args()
if options.doctests:
print "Running doctests for all modules..."
import doctest
# TODO: Test all modules
import yank, oldrepex, alchemy, analyze, utils
(failure_count, test_count) = doctest.testmod(verbose=options.verbose)
if failure_count == 0:
print "All doctests pass."
sys.exit(0)
else:
print "WARNING: There were %d doctest failures." % failure_count
sys.exit(1)
# Check arguments for validity.
if not (options.ligand_mol2_filename):
parser.error("Please supply a ligand in mol2 format")
if not (options.receptor_pdb_filename):
parser.error("Please supply the receptor in pdb format")
if not (options.complex_pdb_filename):
print("Will combine ligand and receptor")
# Initialize MPI if requested.
if options.mpi:
# Initialize MPI.
try:
from mpi4py import MPI # MPI wrapper
hostname = os.uname()[1]
options.mpi = MPI.COMM_WORLD
if not MPI.COMM_WORLD.rank == 0:
options.verbose = False
MPI.COMM_WORLD.barrier()
if MPI.COMM_WORLD.rank == 0: print "Initialized MPI on %d processes." % (MPI.COMM_WORLD.size)
except Exception as e:
print e
parser.error("Could not initialize MPI.")
# Select simulation parameters.
# TODO: Allow user selection or intelligent automated selection of simulation parameters.
# NOTE: Simulation paramters are hard-coded for now.
# NOTE: Simulation parameters will be different for explicit solvent.
import simtk.openmm.app as app
nonbondedMethod = app.NoCutoff
implicitSolvent = app.OBC2
constraints = app.HBonds
removeCMMotion = False
#make ligand, receptor, complex objects
ligand = Mol2SystemBuilder(options.ligand_mol2_filename, "ligand")
receptor = BiomoleculePDBSystemBuilder(options.receptor_pdb_filename,"receptor")
complex = ComplexSystemBuilder(ligand,receptor,"complex")
# DEBUG: Write out ligand, receptor, and complex system objects.
debug = False
if debug:
def write_file(outfile, contents):
outfile = open(outfile, 'w')
outfile.write(contents)
outfile.close()
for name in ['receptor', 'ligand', 'complex']:
system = vars()[name].system
serialized_system = system.__getstate__()
filename = name + '.system.xml'
print "Writing serialized %s to %s..." % (name, filename)
write_file(filename, serialized_system)
# Initialize YANK object.
from yank import Yank
yank = Yank(receptor=receptor.system, ligand=ligand.system, complex=complex.system, complex_positions=[complex.coordinates_as_quantity], output_directory=options.output_directory, verbose=options.verbose)
# Configure YANK object with command-line parameter overrides.
if options.niterations is not None:
yank.niterations = int(options.niterations)
if options.verbose:
yank.verbose = options.verbose
if options.online_analysis:
yank.online_analysis = options.online_analysis
if options.restraint_type is not None:
yank.restraint_type = options.restraint_type
if options.randomize_ligand:
yank.randomize_ligand = True
if options.platform:
yank.platform = openmm.Platform.getPlatformByName(options.platform)
# Hard-coded cpuid:gpuid for Exxact 4xGPU nodes
# TODO: Replace this with something automated
# cpuid_gpuid_mapping = { 0:0, 1:1, 2:2, 3:3 }
#ncpus_per_node = None
# Run calculation.brbz
if options.mpi:
# Run MPI version.
yank.run_mpi(options.mpi, options.gpus_per_node)
else:
# Run serial version.
yank.run()
# Run analysis.
results = yank.analyze()
# Print/write results.
print results
import simtk.unit as units
complex_coordinates = units.Quantity(numpy.zeros([2,3], numpy.float64), units.angstroms)
complex_coordinates[1,0] = 10.0 * units.angstroms
# Create temporary directory for testing.
import tempfile
output_directory = tempfile.mkdtemp()
# Initialize YANK object.
from yank import Yank
yank = Yank(receptor=receptor_system, ligand=ligand_system, complex_coordinates=[complex_coordinates], output_directory=output_directory)
yank.solvent_protocol = yank.vacuum_protocol
yank.complex_protocol = yank.vacuum_protocol
yank.restraint_type = 'flat-bottom'
yank.temperature = temperature
yank.niterations = 100
yank.platform = openmm.Platform.getPlatformByName("Reference")
# Run the simulation.
yank.run()
#
# Analyze the data.
#
results = yank.analyze()
# TODO: Check results against analytical results.
units.angstroms)
complex_coordinates[1, 0] = 10.0 * units.angstroms
# Create temporary directory for testing.
import tempfile
output_directory = tempfile.mkdtemp()
# Initialize YANK object.
from yank import Yank
yank = Yank(receptor=receptor_system,
ligand=ligand_system,
complex_coordinates=[complex_coordinates],
output_directory=output_directory)
yank.solvent_protocol = yank.vacuum_protocol
yank.complex_protocol = yank.vacuum_protocol
yank.restraint_type = 'flat-bottom'
yank.temperature = temperature
yank.niterations = 100
yank.platform = openmm.Platform.getPlatformByName("Reference")
# Run the simulation.
yank.run()
#
# Analyze the data.
#
results = yank.analyze()
# TODO: Check results against analytical results.
def driver():
# Initialize command-line argument parser.
verbose = True
usage = """
USAGE
%prog --ligand_prmtop PRMTOP --receptor_prmtop PRMTOP { {--ligand_crd CRD | --ligand_mol2 MOL2} {--receptor_crd CRD | --receptor_pdb PDB} | {--complex_crd CRD | --complex_pdb PDB} } [-v | --verbose] [-i | --iterations ITERATIONS] [-o | --online] [-m | --mpi] [--restraints restraint-type] [--doctests] [--randomize_ligand]
EXAMPLES
# Specify AMBER prmtop/crd files for ligand and receptor.
%prog --ligand_prmtop ligand.prmtop --receptor_prmtop receptor.prmtop --ligand_crd ligand.crd --receptor_crd receptor.crd --iterations 1000
# Specify (potentially multi-conformer) mol2 file for ligand and (potentially multi-model) PDB file for receptor.
%prog --ligand_prmtop ligand.prmtop --receptor_prmtop receptor.prmtop --ligand_mol2 ligand.mol2 --receptor_pdb receptor.pdb --iterations 1000
# Specify (potentially multi-model) PDB file for complex, along with flat-bottom restraints (instead of harmonic).
%prog --ligand_prmtop ligand.prmtop --receptor_prmtop receptor.prmtop --complex_pdb complex.pdb --iterations 1000 --restraints flat-bottom
# Specify (potentially multi-model) PDB file for complex, along with flat-bottom restraints (instead of harmonic); randomize ligand positions/orientations at start.
%prog --ligand_prmtop ligand.prmtop --receptor_prmtop receptor.prmtop --complex_pdb complex.pdb --iterations 1000 --restraints flat-bottom --randomize_ligand
NOTES
In atom ordering, receptor comes before ligand atoms.
"""
# Parse command-line arguments.
from optparse import OptionParser
parser = OptionParser(usage=usage)
parser.add_option(
"--ligand_mol2",
dest="ligand_mol2_filename",
default=None,
help="ligand mol2 file (can contain multiple conformations)",
metavar="LIGAND_MOL2")
parser.add_option("--receptor_pdb",
dest="receptor_pdb_filename",
default=None,
help="receptor PDB file (can contain multiple MODELs)",
metavar="RECEPTOR_PDB")
parser.add_option("--complex_pdb",
dest="complex_pdb_filename",
default=None,
help="complex PDB file (can contain multiple MODELs)",
metavar="COMPLEX_PDB")
parser.add_option("-v",
"--verbose",
action="store_true",
dest="verbose",
default=False,
help="verbosity flag")
parser.add_option("-i",
"--iterations",
dest="niterations",
default=None,
help="number of iterations",
metavar="ITERATIONS")
parser.add_option("-o",
"--online",
dest="online_analysis",
default=False,
help="perform online analysis")
parser.add_option("-m",
"--mpi",
action="store_true",
dest="mpi",
default=False,
help="use mpi if possible")
parser.add_option(
"--restraints",
dest="restraint_type",
default=None,
help=
"specify ligand restraint type: 'harmonic' or 'flat-bottom' (default: 'harmonic')"
)
parser.add_option(
"--output",
dest="output_directory",
default=None,
help=
"specify output directory---must be unique for each calculation (default: current directory)"
)
parser.add_option("--doctests",
action="store_true",
dest="doctests",
default=False,
help="run doctests first (default: False)")
parser.add_option(
"--randomize_ligand",
action="store_true",
dest="randomize_ligand",
default=False,
help="randomize ligand positions and orientations (default: False)")
parser.add_option("--ignore_signal",
action="append",
dest="ignore_signals",
default=[],
help="signals to trap and ignore (default: None)")
parser.add_option("--platform",
dest="platform",
default="CPU",
help="The platform to use when running simulations")
parser.add_option(
"--gpus_per_node",
dest="gpus_per_node",
type='int',
default=None,
help=
"number of GPUs per node to use for complex simulations during MPI calculations"
)
# Parse command-line arguments.
(options, args) = parser.parse_args()
if options.doctests:
print "Running doctests for all modules..."
import doctest
# TODO: Test all modules
import yank, oldrepex, alchemy, analyze, utils
(failure_count, test_count) = doctest.testmod(verbose=options.verbose)
if failure_count == 0:
print "All doctests pass."
sys.exit(0)
else:
print "WARNING: There were %d doctest failures." % failure_count
sys.exit(1)
# Check arguments for validity.
if not (options.ligand_mol2_filename):
parser.error("Please supply a ligand in mol2 format")
if not (options.receptor_pdb_filename):
parser.error("Please supply the receptor in pdb format")
if not (options.complex_pdb_filename):
print("Will combine ligand and receptor")
# Initialize MPI if requested.
if options.mpi:
# Initialize MPI.
try:
from mpi4py import MPI # MPI wrapper
hostname = os.uname()[1]
options.mpi = MPI.COMM_WORLD
if not MPI.COMM_WORLD.rank == 0:
options.verbose = False
MPI.COMM_WORLD.barrier()
if MPI.COMM_WORLD.rank == 0:
print "Initialized MPI on %d processes." % (
MPI.COMM_WORLD.size)
except Exception as e:
print e
parser.error("Could not initialize MPI.")
# Select simulation parameters.
# TODO: Allow user selection or intelligent automated selection of simulation parameters.
# NOTE: Simulation paramters are hard-coded for now.
# NOTE: Simulation parameters will be different for explicit solvent.
import simtk.openmm.app as app
nonbondedMethod = app.NoCutoff
implicitSolvent = app.OBC2
constraints = app.HBonds
removeCMMotion = False
#make ligand, receptor, complex objects
ligand = Mol2SystemBuilder(options.ligand_mol2_filename, "ligand")
receptor = BiomoleculePDBSystemBuilder(options.receptor_pdb_filename,
"receptor")
complex = ComplexSystemBuilder(ligand, receptor, "complex")
# DEBUG: Write out ligand, receptor, and complex system objects.
debug = False
if debug:
def write_file(outfile, contents):
outfile = open(outfile, 'w')
outfile.write(contents)
outfile.close()
for name in ['receptor', 'ligand', 'complex']:
system = vars()[name].system
serialized_system = system.__getstate__()
filename = name + '.system.xml'
print "Writing serialized %s to %s..." % (name, filename)
write_file(filename, serialized_system)
# Initialize YANK object.
from yank import Yank
yank = Yank(receptor=receptor.system,
ligand=ligand.system,
complex=complex.system,
complex_positions=[complex.coordinates_as_quantity],
output_directory=options.output_directory,
verbose=options.verbose)
# Configure YANK object with command-line parameter overrides.
if options.niterations is not None:
yank.niterations = int(options.niterations)
if options.verbose:
yank.verbose = options.verbose
if options.online_analysis:
yank.online_analysis = options.online_analysis
if options.restraint_type is not None:
yank.restraint_type = options.restraint_type
if options.randomize_ligand:
yank.randomize_ligand = True
if options.platform:
yank.platform = openmm.Platform.getPlatformByName(options.platform)
# Hard-coded cpuid:gpuid for Exxact 4xGPU nodes
# TODO: Replace this with something automated
# cpuid_gpuid_mapping = { 0:0, 1:1, 2:2, 3:3 }
#ncpus_per_node = None
# Run calculation.brbz
if options.mpi:
# Run MPI version.
yank.run_mpi(options.mpi, options.gpus_per_node)
else:
# Run serial version.
yank.run()
# Run analysis.
results = yank.analyze()
# Print/write results.
print results