The input dataset is an .oedb file of the aggregated confs MD results with Traj OEMols + IntE + PBSA
"""
# job.uuid = "7cacc2af-cae7-4dc7-8956-fcf539861e3d"
ifs = DatasetReaderCube("ifs")
ifs.promote_parameter("data_in",
promoted_name="in",
title="System Input OERecord",
description="OERecord file name")
confGather = ConformerGatheringData("Gathering Conformer Records")
ligTrajCube = ParallelConfTrajsToLigTraj("ConfTrajsToLigTraj")
ligMMPBSA = ParallelConcatenateTrajMMPBSACube('ConcatenateTrajMMPBSACube')
ofs = DatasetWriterCube('ofs', title='OFS-Success')
ofs.promote_parameter("data_out",
promoted_name="out",
title="System Output OERecord",
description="OERecord file name")
fail = DatasetWriterCube('fail', title='Failures')
fail.promote_parameter("data_out", promoted_name="fail")
job.add_cubes(ifs, confGather, ligTrajCube, ligMMPBSA, ofs, fail)
ifs.success.connect(confGather.intake)
confGather.success.connect(ligTrajCube.intake)
ligTrajCube.success.connect(ligMMPBSA.intake)
ligMMPBSA.success.connect(ofs.intake)
ligMMPBSA.failure.connect(fail.intake)
# Protein Reading cube. The protein prefix parameter is used to select a name for the
# output system files
iprot = DatasetReaderCube("ProteinReader", title="Protein Reader")
iprot.promote_parameter("data_in",
promoted_name="protein",
title='Protein Input Dataset',
description="Protein Dataset")
# Complex cube used to assemble the ligands and the solvated protein
complx = ComplexPrepCube("Complex", title="Complex Preparation")
complx.set_parameters(lig_res_name='LIG')
# Protein Setting
protset = MDComponentCube("ProteinSetting", title="Protein Setting")
ofs = DatasetWriterCube('ofs', title='MD Out')
ofs.promote_parameter("data_out",
promoted_name="out",
title="MD Out",
description="MD Dataset out")
fail = DatasetWriterCube('fail', title='Failures')
fail.promote_parameter("data_out",
promoted_name="fail",
title="Failures",
description="MD Dataset Failures out")
job.add_cubes(iligs, ligset, ligid, iprot, protset, chargelig, complx, ofs,
fail)
iligs.success.connect(ligset.intake)
--------
out (.oedb file): file of the Analysis results for all ligands.
"""
job.uuid = "2717cf39-5bdd-4a1e-880e-5208bb232959"
job.classification = [['Analysis']]
job.tags = [tag for lists in job.classification for tag in lists]
ifs = DatasetReaderCube("ifs")
ifs.promote_parameter("data_in",
promoted_name="in",
title="System Input OERecord",
description="OERecord file name")
ofs = DatasetWriterCube('ofs', title='MD Out')
ofs.promote_parameter("data_out", promoted_name="out")
fail = DatasetWriterCube('fail', title='Failures')
fail.promote_parameter("data_out", promoted_name="fail")
IntECube = ParallelTrajInteractionEnergyCube("TrajInteractionEnergyCube")
PBSACube = ParallelTrajPBSACube("TrajPBSACube")
report = MDFloeReportCube("report", title="Floe Report")
job.add_cubes(ifs, IntECube, PBSACube, ofs, fail)
ifs.success.connect(IntECube.intake)
IntECube.success.connect(PBSACube.intake)
IntECube.failure.connect(fail.intake)
job.classification = [['MD Data']]
job.uuid = "6665ca20-6014-4f3b-8d02-4b5d15b75ee3"
job.tags = [tag for lists in job.classification for tag in lists]
ifs = DatasetReaderCube("SystemReader", title="System Reader")
ifs.promote_parameter(
"data_in",
promoted_name="system",
title='STMDA Input File',
description=
"The Dataset produced by the Short Trajectory MD with Analysis floe")
data = ExtractMDDataCube("MDData", title="Extract MD Data")
data.promote_parameter('out_file_name',
promoted_name='out_file_name',
description="Output File name",
default="md_data.tar.gz")
fail = DatasetWriterCube('fail', title='Failures')
fail.promote_parameter("data_out",
promoted_name="fail",
description="Fail Data Set")
job.add_cubes(ifs, data, fail)
ifs.success.connect(data.intake)
data.failure.connect(fail.intake)
if __name__ == "__main__":
job.run()
from orionplatform.cubes import DatasetReaderCube, DatasetWriterCube
from cubes.perses import PersesCube
# Declare and document floe
job = WorkFloe("Peres Floe", title="Perses Floe")
job.description = ("Run a star-map relative free energy calculation")
job.classification = [['Molecular Dynamics']]
job.uuid = "155b90cf-90fd-4068-8558-3eac7c01c615"
job.tags = [tag for lists in job.classification for tag in lists]
# Declare Cubes
protein_input_cube = DatasetReaderCube("protein_input_cube")
reference_ligand_input_cube = DatasetReaderCube("reference_ligand_input_cube")
target_ligands_input_cube = DatasetReaderCube("target_ligands_input_cube")
perses_cube = PersesCube("perses_cube")
success_output_cube = DatasetWriterCube("success_output_cube", title='success')
failure_output_cube = DatasetWriterCube("failure_output_cube", title='failure')
# Add cubes to floe
job.add_cube(protein_input_cube)
job.add_cube(reference_ligand_input_cube)
job.add_cube(target_ligands_input_cube)
job.add_cube(perses_cube)
job.add_cube(success_output_cube)
job.add_cube(failure_output_cube)
# Promote parameters
protein_input_cube.promote_parameter("data_in",
promoted_name="protein",
title="Protein")
reference_ligand_input_cube.promote_parameter("data_in",
# or its use.
from floe.api import WorkFloe
from orionplatform.cubes import DatasetReaderCube, DatasetWriterCube
from am1bcc_charge.am1bcc_charge import AM1BCCCharge
# Declare and document floe
job = WorkFloe("am1bcc_charge", title="am1bcc charge")
job.description = ("AM1BCC Charge")
job.classification = [["Charge"]]
job.tags = ["Charge"]
# Declare Cubes
input_cube = DatasetReaderCube("input_cube")
charge_cube = MyCube("charge_cube")
output_cube = DatasetWriterCube("output_cube")
# Add cubes to floe
job.add_cube(input_cube)
job.add_cube(charge_cube)
job.add_cube(output_cube)
# Promote parameters
input_cube.promote_parameter("data_in",
promoted_name="in",
title="Input data set of records")
charge_cube.promoted_parameter('max_confs',
promoted_name='in',
title='Maximum number of conformers.')