def make_replica_pdb_files(topology,replica_positions):
"""
Make PDB files from replica exchange simulation trajectory data
:param topology: OpenMM Topology
:type topology: `Topology() <https://simtk.org/api_docs/openmm/api4_1/python/classsimtk_1_1openmm_1_1app_1_1topology_1_1Topology.html>`_
:param replica_positions: Positions array for the replica exchange data for which we will write PDB files
:type replica_positions: `Quantity() <http://docs.openmm.org/development/api-python/generated/simtk.unit.quantity.Quantity.html>`_ ( np.array( [n_replicas,cgmodel.num_beads,3] ), simtk.unit )
:returns:
- file_list ( List( str ) ) - A list of names for the files that were written
:Example:
>>> from foldamers.cg_model.cgmodel import CGModel
>>> from cg_openmm.simulation.rep_exch import *
>>> cgmodel = CGModel()
>>> replica_energies,replica_positions,replica_state_indices = run_replica_exchange(cgmodel.topology,cgmodel.system,cgmodel.positions)
>>> pdb_file_list = make_replica_pdb_files(cgmodel.topology,replica_positions)
"""
replica_index = 1
file_list = []
for replica_index in range(len(replica_positions)):
replica_trajectory = replica_positions[replica_index]
file_name = str("replica_"+str(replica_index+1)+".pdb")
file = open(file_name,"w")
PDBFile.writeHeader(topology,file=file)
modelIndex=1
for positions in replica_trajectory:
PDBFile.writeModel(topology,positions,file=file,modelIndex=modelIndex)
PDBFile.writeFooter(topology,file=file)
file.close()
file_list.append(file_name)
return(file_list)
def make_state_pdb_files(topology,
output_dir="output",
output_data="output.nc",
checkpoint_data="output_checkpoint.nc",
frame_begin=0,
frame_stride=1,
center=True):
"""
Make pdb files by state from replica exchange simulation trajectory data.
Note: these are discontinuous trajectories with constant temperature state.
:param topology: OpenMM Topology
:type topology: `Topology() <https://simtk.org/api_docs/openmm/api4_1/python/classsimtk_1_1openmm_1_1app_1_1topology_1_1Topology.html>`_
:param output_directory: path to which we will write the output (default='output')
:type output_directory: str
:param output_data: name of output .nc data file (default='output.nc')
:type output_data: str
:param checkpoint_data: name of checkpoint .nc data file (default='output_checkpoint.nc')
:type checkpoint_data: str
:param frame_begin: Frame at which to start writing the pdb trajectory (default=0)
:type frame_begin: int
:param frame_stride: advance by this many frames when writing pdb trajectories (default=1)
:type frame_stride: int
:param center: align the center of mass of each structure in the discontinuous state trajectory (default=True)
:type center: Boolean
:returns:
- file_list ( List( str ) ) - A list of names for the files that were written
"""
file_list = []
output_data_path = os.path.join(output_dir, output_data)
# Get number of states:
reporter = MultiStateReporter(output_data_path, open_mode="r")
states = reporter.read_thermodynamic_states()[0]
sampler_states = reporter.read_sampler_states(iteration=0)
xunit = sampler_states[0].positions[0].unit
for state_index in range(len(states)):
state_trajectory = extract_trajectory(topology,
state_index=state_index,
output_data=output_data_path,
checkpoint_data=checkpoint_data,
frame_begin=frame_begin,
frame_stride=frame_stride)
file_name = f"{output_dir}/state_{state_index+1}.pdb"
file = open(file_name, "w")
PDBFile.writeHeader(topology, file=file)
modelIndex = 1
# TODO: replace this with MDTraj alignment tool
if center == True:
center_x = np.mean(state_trajectory[0, :, 0])
center_y = np.mean(state_trajectory[0, :, 1])
center_z = np.mean(state_trajectory[0, :, 2])
for positions in state_trajectory:
if center == True:
positions[:, 0] += (center_x - np.mean(positions[:, 0]))
positions[:, 1] += (center_y - np.mean(positions[:, 1]))
positions[:, 2] += (center_z - np.mean(positions[:, 2]))
# Add the units consistent with replica_energies
positions *= xunit
PDBFile.writeModel(topology,
positions,
file=file,
modelIndex=modelIndex)
PDBFile.writeFooter(topology, file=file)
file.close()
file_list.append(file_name)
return file_list
