def setup_system_and_integrator_files(target, template, temperature,
collision_rate, timestep):
logger.debug(
'Copying system and integrator files for template {}'.format(template))
models_target_dir = os.path.join(default_project_dirnames.models,
target.id)
template_dir = os.path.join(models_target_dir, template)
target_project_dir = os.path.join(fah_projects_dir, target.id)
source_system_filepath = os.path.join(template_dir, 'explicit-system.xml')
source_state_filepath = os.path.join(template_dir, 'explicit-state.xml')
dest_system_filepath = os.path.join(target_project_dir, 'system.xml')
dest_integrator_filepath = os.path.join(target_project_dir,
'integrator.xml')
system = mm.XmlSerializer.deserialize(
read_file_contents_gz_or_not(source_system_filepath))
state = mm.XmlSerializer.deserialize(
read_file_contents_gz_or_not(source_state_filepath))
# Substitute default box vectors in system with those from state.
box_vectors = state.getPeriodicBoxVectors()
system.setDefaultPeriodicBoxVectors(*box_vectors)
# Set PME parameters explicitly to minimize discrepancy between Reference and OpenCL/CUDA if not already set explicitly.
ensure_pme_parameters_are_explicit(system)
# Create new integrator to use.
integrator = mm.LangevinIntegrator(temperature, collision_rate, timestep)
# Make sure MonteCarloBarostat temperature matches set temperature.
forces = {
system.getForce(index).__class__.__name__: system.getForce(index)
for index in range(system.getNumForces())
}
if 'MonteCarloBarostat' in forces:
forces['MonteCarloBarostat'].setTemperature(temperature)
# Serialize System.
with open(dest_system_filepath, 'w') as dest_system_file:
dest_system_file.write(mm.XmlSerializer.serialize(system))
# Serialize Integrator
with open(dest_integrator_filepath, 'w') as dest_integrator_file:
dest_integrator_file.write(mm.XmlSerializer.serialize(integrator))
return system
def setup_system_and_integrator_files(target,
template,
temperature,
collision_rate,
timestep
):
logger.debug('Copying system and integrator files for template {}'.format(template))
models_target_dir = os.path.join(default_project_dirnames.models, target.id)
template_dir = os.path.join(models_target_dir, template)
target_project_dir = os.path.join(fah_projects_dir, target.id)
source_system_filepath = os.path.join(template_dir, 'explicit-system.xml')
source_state_filepath = os.path.join(template_dir, 'explicit-state.xml')
dest_system_filepath = os.path.join(target_project_dir, 'system.xml')
dest_integrator_filepath = os.path.join(target_project_dir, 'integrator.xml')
system = mm.XmlSerializer.deserialize(
read_file_contents_gz_or_not(source_system_filepath)
)
state = mm.XmlSerializer.deserialize(
read_file_contents_gz_or_not(source_state_filepath)
)
# Substitute default box vectors in system with those from state.
box_vectors = state.getPeriodicBoxVectors()
system.setDefaultPeriodicBoxVectors(*box_vectors)
# Set PME parameters explicitly to minimize discrepancy between Reference and OpenCL/CUDA if not already set explicitly.
ensure_pme_parameters_are_explicit(system)
# Create new integrator to use.
integrator = mm.LangevinIntegrator(temperature, collision_rate, timestep)
# Make sure MonteCarloBarostat temperature matches set temperature.
forces = { system.getForce(index).__class__.__name__ : system.getForce(index) for index in range(system.getNumForces()) }
if 'MonteCarloBarostat' in forces:
forces['MonteCarloBarostat'].setTemperature(temperature)
# Serialize System.
with open(dest_system_filepath, 'w') as dest_system_file:
dest_system_file.write(mm.XmlSerializer.serialize(system))
# Serialize Integrator
with open(dest_integrator_filepath, 'w') as dest_integrator_file:
dest_integrator_file.write(mm.XmlSerializer.serialize(integrator))
return system
def generate_fah_run(
target_project_dir,
template,
source_dir,
system,
run_index,
nclones,
temperature,
collision_rate,
timestep,
openmm_platform,
renumbered_resnums,
):
"""
Build Folding@Home RUN and CLONE subdirectories from (possibly compressed) OpenMM serialized XML files.
ARGUMENTS
run (int) - run index
"""
logger.debug("Building RUN %d" % run_index)
try:
# Determine directory and pathnames.
run_dir = os.path.join(target_project_dir, 'RUN%d' % run_index)
run_template_id_filepath = os.path.join(run_dir, 'template.txt')
run_seqid_filepath = os.path.join(run_dir, 'sequence-identity.txt')
run_protein_structure_filepath = os.path.join(run_dir, 'protein.pdb')
run_system_structure_filepath = os.path.join(run_dir, 'system.pdb')
run_final_state_filepath = os.path.join(run_dir,
'state%d.xml' % (nclones - 1))
source_seqid_filepath = os.path.join(source_dir,
'sequence-identity.txt')
source_protein_structure_filepath = os.path.join(
source_dir, 'implicit-refined.pdb.gz')
source_system_structure_filepath = os.path.join(
source_dir, 'explicit-refined.pdb.gz')
source_openmm_state_filepath = os.path.join(source_dir,
'explicit-state.xml')
# Return if this directory has already been set up.
if os.path.exists(run_dir):
if (os.path.exists(run_template_id_filepath)
and os.path.exists(run_seqid_filepath)
and os.path.exists(run_protein_structure_filepath)
and os.path.exists(run_system_structure_filepath)
and os.path.exists(run_final_state_filepath)):
return
else:
# Construct run directory if it does not exist.
if not os.path.exists(run_dir):
os.makedirs(run_dir)
# Write template ID
with open(run_template_id_filepath, 'w') as outfile:
outfile.write(template + '\n')
# Write the protein and system structure pdbs
if 'implicit' in renumbered_resnums:
write_renumbered_structure(
source_protein_structure_filepath,
run_protein_structure_filepath,
renumbered_resnums['implicit'],
)
else:
with open(run_protein_structure_filepath,
'w') as protein_structure_file:
protein_structure_file.write(
read_file_contents_gz_or_not(
source_protein_structure_filepath))
if 'explicit' in renumbered_resnums:
write_renumbered_structure(
source_system_structure_filepath,
run_system_structure_filepath,
renumbered_resnums['explicit'],
)
else:
with open(run_system_structure_filepath,
'w') as system_structure_file:
system_structure_file.write(
read_file_contents_gz_or_not(
source_system_structure_filepath))
state = mm.XmlSerializer.deserialize(
read_file_contents_gz_or_not(source_openmm_state_filepath))
# Write sequence identity.
with open(run_seqid_filepath, 'w') as run_seqid_file:
run_seqid_file.write(
read_file_contents_gz_or_not(source_seqid_filepath))
# Create new integrator to use.
integrator = mm.LangevinIntegrator(temperature, collision_rate,
timestep)
# Create Context so we can randomize velocities.
platform = mm.Platform.getPlatformByName(openmm_platform)
context = mm.Context(system, integrator, platform)
context.setPositions(state.getPositions())
box_vectors = state.getPeriodicBoxVectors()
context.setPeriodicBoxVectors(*box_vectors)
# Create clones with different random initial velocities.
for clone_index in range(nclones):
state_filename = os.path.join(run_dir, 'state%d.xml' % clone_index)
if os.path.exists(state_filename):
continue
context.setVelocitiesToTemperature(temperature)
state = context.getState(getPositions=True,
getVelocities=True,
getForces=True,
getEnergy=True,
getParameters=True,
enforcePeriodicBox=True)
with open(state_filename, 'w') as state_file:
state_file.write(mm.XmlSerializer.serialize(state))
except Exception as e:
import traceback
print(traceback.format_exc())
print(str(e))
def generate_fah_run(target_project_dir,
template,
source_dir,
system,
run_index,
nclones,
temperature,
collision_rate,
timestep,
openmm_platform,
renumbered_resnums,
):
"""
Build Folding@Home RUN and CLONE subdirectories from (possibly compressed) OpenMM serialized XML files.
ARGUMENTS
run (int) - run index
"""
logger.debug("Building RUN %d" % run_index)
try:
# Determine directory and pathnames.
run_dir = os.path.join(target_project_dir, 'RUN%d' % run_index)
run_template_id_filepath = os.path.join(run_dir, 'template.txt')
run_seqid_filepath = os.path.join(run_dir, 'sequence-identity.txt')
run_protein_structure_filepath = os.path.join(run_dir, 'protein.pdb')
run_system_structure_filepath = os.path.join(run_dir, 'system.pdb')
run_final_state_filepath = os.path.join(run_dir, 'state%d.xml' % (nclones - 1))
source_seqid_filepath = os.path.join(source_dir, 'sequence-identity.txt')
source_protein_structure_filepath = os.path.join(source_dir, 'implicit-refined.pdb.gz')
source_system_structure_filepath = os.path.join(source_dir, 'explicit-refined.pdb.gz')
source_openmm_state_filepath = os.path.join(source_dir, 'explicit-state.xml')
# Return if this directory has already been set up.
if os.path.exists(run_dir):
if (
os.path.exists(run_template_id_filepath)
and os.path.exists(run_seqid_filepath)
and os.path.exists(run_protein_structure_filepath)
and os.path.exists(run_system_structure_filepath)
and os.path.exists(run_final_state_filepath)
):
return
else:
# Construct run directory if it does not exist.
if not os.path.exists(run_dir):
os.makedirs(run_dir)
# Write template ID
with open(run_template_id_filepath, 'w') as outfile:
outfile.write(template + '\n')
# Write the protein and system structure pdbs
if 'implicit' in renumbered_resnums:
write_renumbered_structure(
source_protein_structure_filepath,
run_protein_structure_filepath,
renumbered_resnums['implicit'],
)
else:
with open(run_protein_structure_filepath, 'w') as protein_structure_file:
protein_structure_file.write(
read_file_contents_gz_or_not(source_protein_structure_filepath)
)
if 'explicit' in renumbered_resnums:
write_renumbered_structure(
source_system_structure_filepath,
run_system_structure_filepath,
renumbered_resnums['explicit'],
)
else:
with open(run_system_structure_filepath, 'w') as system_structure_file:
system_structure_file.write(
read_file_contents_gz_or_not(source_system_structure_filepath)
)
state = mm.XmlSerializer.deserialize(
read_file_contents_gz_or_not(source_openmm_state_filepath)
)
# Write sequence identity.
with open(run_seqid_filepath, 'w') as run_seqid_file:
run_seqid_file.write(read_file_contents_gz_or_not(source_seqid_filepath))
# Create new integrator to use.
integrator = mm.LangevinIntegrator(temperature, collision_rate, timestep)
# Create Context so we can randomize velocities.
platform = mm.Platform.getPlatformByName(openmm_platform)
context = mm.Context(system, integrator, platform)
context.setPositions(state.getPositions())
box_vectors = state.getPeriodicBoxVectors()
context.setPeriodicBoxVectors(*box_vectors)
# Create clones with different random initial velocities.
for clone_index in range(nclones):
state_filename = os.path.join(run_dir, 'state%d.xml' % clone_index)
if os.path.exists(state_filename):
continue
context.setVelocitiesToTemperature(temperature)
state = context.getState(
getPositions=True,
getVelocities=True,
getForces=True,
getEnergy=True,
getParameters=True,
enforcePeriodicBox=True
)
with open(state_filename, 'w') as state_file:
state_file.write(mm.XmlSerializer.serialize(state))
except Exception as e:
import traceback
print(traceback.format_exc())
print(str(e))
