ligands (file): dataset of prepared ligands posed in the protein active site.
protein (file): dataset of the prepared protein structure.
Outputs:
--------
out (.oedb file): file of the protein-ligand complexes with parameters.
"""
# Locally the floe can be invoked by running the terminal command:
# python floes/LigReadPrep.py --ligands ligands.oeb --protein protein.oeb --out prod.oeb
job.classification = [['Molecular Dynamics']]
# job.uuid = "372e1890-d053-4027-970a-85b209e4676f"
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.set_parameters(lig_res_name='LIG')
chargelig = ParallelLigandChargeCube("LigCharge", title="Ligand Charge")
chargelig.promote_parameter('charge_ligands',
promoted_name='charge_ligands',
description="Charge the ligand or not",
default=True)
ligid = IDSettingCube("Ligand Ids")
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",
promoted_name="out",
title="System Output OERecord",
description="OERecord file name")
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")
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')
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)
trajCube = ParallelTrajToOEMolCube("TrajToOEMolCube",
title="Trajectory To OEMols")
IntECube = ParallelTrajInteractionEnergyCube("TrajInteractionEnergyCube",
title="MM Energies")
PBSACube = ParallelTrajPBSACube("TrajPBSACube", title="PBSA Energies")
Optional:
--------
picosec (float): Number of picoseconds to warm up the complex
temperature (decimal): target final temperature in K
pressure (decimal): target final pressure in atm
Outputs:
--------
ofs: Outputs the constant temperature and pressure system
"""
job.classification = [['NPT']]
job.uuid = "4ea1a8ab-5e8b-41c9-9317-3e36b72491fe"
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='System Input File',
description="System input file")
npt = ParallelMDNptCube('npt', title='NPT Simulation')
npt.promote_parameter('time', promoted_name='nanoseconds', default=0.01,
description='Length of MD run in nanoseconds')
npt.promote_parameter('temperature', promoted_name='temperature', default=300.0,
description='Selected temperature in K')
npt.promote_parameter('pressure', promoted_name='pressure', default=1.0,
description='Selected pressure in atm')
npt.promote_parameter('md_engine', promoted_name='md_engine', default='OpenMM',
description='Select the MD Engine')
# Restraints
npt.set_parameters(restraints="ca_protein or (noh ligand)")
# 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)
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
# 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",
promoted_name="in",
title="Input data set of records")
charge_cube.promoted_parameter('max_confs',
promoted_name='in',