# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from floe.api import WorkFloe
from MDOrion.TrjAnalysis.cubes_clusterAnalysis import ExtractMDDataCube
from orionplatform.cubes import DatasetReaderCube, DatasetWriterCube
from os import path
job = WorkFloe("Extract Short Trajectory MD Results for Download",
title="Extract Short Trajectory MD Results for Download")
job.description = open(path.join(path.dirname(__file__), 'MDData_desc.rst'),
'r').read()
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")
#!/usr/bin/env python
from floe.api import (WorkFloe, ParallelCubeGroup)
from orionplatform.cubes import DatasetReaderCube, DatasetWriterCube
from MDOrion.TrjAnalysis.cubes_trajProcessing import (
ConformerGatheringData, ParallelConfTrajsToLigTraj,
ParallelConcatenateTrajMMPBSACube)
job = WorkFloe("Testing combining confs Traj OEMols to lig Traj OEMol")
job.description = """
Testing Aggregating conf trajs into one ligand traj OEMol.
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",
from MDOrion.ComplexPrep.cubes import ComplexPrepCube
from MDOrion.System.cubes import (ParallelSolvationCube, MDComponentCube)
from MDOrion.ForceField.cubes import ParallelForceFieldCube
from MDOrion.LigPrep.cubes import (ParallelLigandChargeCube, LigandSetting)
from MDOrion.System.cubes import (IDSettingCube, CollectionSetting,
ParallelRecordSizeCheck)
job = WorkFloe('Solvate and Run Protein-Ligand MD',
title='Solvate and Run Protein-Ligand MD')
job.description = open(
path.join(path.dirname(__file__), 'ProteinLigandMD_desc.rst'), 'r').read()
job.classification = [['Specialized MD']]
job.uuid = "ae561d76-a2b6-4d89-b621-b979f1930b40"
job.tags = [tag for lists in job.classification for tag in lists]
# Ligand setting
iligs = DatasetReaderCube("LigandReader", title="Ligand Reader")
iligs.promote_parameter("data_in",
promoted_name="ligands",
title="Ligand Input Dataset",
description="Ligand Dataset")
ligset = LigandSetting("LigandSetting", title="Ligand Setting")
ligset.promote_parameter('max_md_runs',
promoted_name='max_md_runs',
from MDOrion.TrjAnalysis.cubes_trajProcessing import (
ParallelTrajToOEMolCube, ParallelTrajInteractionEnergyCube,
ParallelTrajPBSACube, ConformerGatheringData, ParallelConfTrajsToLigTraj,
ParallelConcatenateTrajMMPBSACube)
from MDOrion.TrjAnalysis.cubes_clusterAnalysis import (
ParallelClusterOETrajCube, ParallelMakeClusterTrajOEMols,
ParallelMDTrajAnalysisClusterReport, ParallelClusterPopAnalysis,
ParallelTrajAnalysisReportDataset, MDFloeReportCube)
from MDOrion.System.cubes import CollectionSetting
job = WorkFloe('Analyze Protein-Ligand MD', title='Analyze Protein-Ligand MD')
job.description = open(
path.join(path.dirname(__file__), 'AnalyzePLMD_desc.rst'), 'r').read()
job.classification = [['Specialized MD']]
job.uuid = "7438db4d-30b1-478c-afc0-e921f0336c78"
job.tags = [tag for lists in job.classification for tag in lists]
# Ligand setting
iMDInput = DatasetReaderCube("MDInputReader", title="MD Input Reader")
iMDInput.promote_parameter("data_in",
promoted_name="in",
title="MD Input Dataset",
description="MD Input Dataset")
# This Cube is necessary for the correct work of collection and shard
coll_open = CollectionSetting("OpenCollection", title="Open Collection")
coll_open.set_parameters(open=True)
# or its use.
from os import path
from floe.api import WorkFloe
from MDOrion.MDEngines.Gromacs.cubes import (InputGromacs,
GromacsProxyCube,
GromacsRunCube,
WriterRecordCube)
from orionplatform.cubes import DatasetWriterCube
job = WorkFloe('PlainGromacs', title='Plain Gromacs')
job.description = open(path.join(path.dirname(__file__), 'PlainGromacs_desc.rst'), 'r').read()
job.classification = [['General MD']]
job.uuid = "f092b164-7400-403d-8861-b25ff741cab5"
job.tags = [tag for lists in job.classification for tag in lists]
ifs = InputGromacs("Input File", title="Input file")
ifs.promote_parameter('tpr', promoted_name='tpr', default=None)
ifs.promote_parameter("prefix_name", promoted_name="Flask prefix", default="Flask")
ifs.promote_parameter("data_in", promoted_name='in')
proxy = GromacsProxyCube("GromacsProxy", title="Gromacs Proxy Cube")
gmx = GromacsRunCube("GromacsRun", title="Gromacs Run")
gmx.promote_parameter("verbose", promoted_name="verbose", default=False)
ofs = WriterRecordCube("OutputRecords", title="Output Records")
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from floe.api import WorkFloe
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)
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# or its use.
from floe.api import WorkFloe
from cuberecord import (DatasetReaderCube,
DatasetWriterCube)
from {{cookiecutter.module_name}} import MyCube
# Declare and document floe
my_floe = WorkFloe('my_floe', title="My Floe")
my_floe.description = "Outputs the input records unchanged unless the parameter is set to false, in which case nothing " \
"is outputted"
my_floe.classification = [["Examples"]]
my_floe.tags = ["Examples", "I didn't edit the tags"]
# Declare Cubes
input_cube = DatasetReaderCube('input_cube')
switch_cube = MyCube('switch_cube')
output_cube = DatasetWriterCube('output_cube')
# Add cubes to floe
my_floe.add_cube(input_cube)
my_floe.add_cube(switch_cube)
my_floe.add_cube(output_cube)
# Promote parameters
input_cube.promote_parameter('data_in', promoted_name='in', title='Input data set of records')
from MDOrion.TrjAnalysis.cubes_trajProcessing import (
ParallelTrajToOEMolCube, ParallelTrajInteractionEnergyCube,
ParallelTrajPBSACube, ConformerGatheringData, ParallelConfTrajsToLigTraj,
ParallelConcatenateTrajMMPBSACube)
from MDOrion.TrjAnalysis.cubes_clusterAnalysis import (
ParallelClusterOETrajCube, ParallelMakeClusterTrajOEMols,
ParallelMDTrajAnalysisClusterReport, ParallelClusterPopAnalysis,
ParallelTrajAnalysisReportDataset, MDFloeReportCube)
job = WorkFloe('Short Trajectory MD with Analysis',
title='Short Trajectory MD with Analysis')
job.description = open(
path.join(path.dirname(__file__), 'ShortTrajMDWithAnalysis_desc.rst'),
'r').read()
job.classification = [['Specialized MD']]
job.uuid = "c831d03e-c0cb-48b0-aa02-f848da8fd1a6"
job.tags = [tag for lists in job.classification for tag in lists]
# Ligand setting
iligs = DatasetReaderCube("LigandReader", title="Ligand Reader")
iligs.promote_parameter("data_in",
promoted_name="ligands",
title="Ligand Input Dataset",
description="Ligand Dataset")
ligset = LigandSetting("LigandSetting", title="Ligand Setting")
ligset.promote_parameter('max_md_runs',
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable OpenEye offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED. OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall OpenEye be
# liable for any damages or liability in connection with the Sample Code
# 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",
