Parameters:
-----------
complex (file): OEB file of the prepared system
Optional:
--------
picosec (float): Number of picoseconds to warm up the complex
temperature (decimal): target final temperature after warming
Outputs:
--------
ofs: Outputs the constant temperature and volume system
"""
job.classification = [['NVT']]
job.uuid = "f1ec27a4-63a6-4fba-9649-f0ba51a50faa"
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")
nvt = ParallelMDNvtCube('nvt', title='NVT simulation')
nvt.promote_parameter('time', promoted_name='nanoseconds', default=0.01)
nvt.promote_parameter('temperature',
promoted_name='temperature',
default=300.0,
description='Selected temperature in K')
nvt.promote_parameter('md_engine',
An MD production run which has been analyzed in terms of interactions between the
ligand and the active site is clustered in terms of ligand RMSD after fitting the trajectory
based on active site C_alphas.
Required Input Parameters:
--------------------------
Dataset result of an MD Short Trajectory run with traj OEMols and MMPBSA interactions
Outputs:
--------
floe report: html page of the Analysis of each ligand.
out (.oedb file): file of the Analysis results for all ligands.
"""
job.classification = [['Analysis']]
job.uuid = "4de8826b-8902-4037-9f8e-5c1a7d8a793c"
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")
clusCube = ParallelClusterOETrajCube("ClusterOETrajCube")
job = WorkFloe("Floe Report from Analyzed Short Trajectory MD")
job.description = """
Generate a Floe Report from Analyzed and Clustered Short Trajectory MD results
Required Input Parameters:
--------------------------
in: Collection of OERecords (one per ligand) of analyzed, clustered Short Trajectory MD results.
Outputs:
--------
floe report: html page of the Analysis for each ligand.
out (.oedb file): file of the Analysis results for all ligands.
"""
job.uuid = "a21708dd-085b-4494-84db-a45d12c4dded"
ifs = DatasetReaderCube("ifs")
ifs.promote_parameter("data_in",
promoted_name="in",
title="System Input OERecord",
description="OERecord file name")
ofs = DatasetWriterCube('ofs', title='OFS-Success')
ofs.promote_parameter("data_out",
promoted_name="out",
title="System Output OERecord",
description="OERecord file name")
prepDataset = ParallelTrajAnalysisReportDataset('TrajAnalysisReportDataset')
report_gen = ParallelMDTrajAnalysisClusterReport("MDTrajAnalysisClusterReport")
Parameters:
-----------
complex (file): OEB file of the prepared system
Optional:
--------
steps (int): Number of MD steps to minimize the system. If 0 until convergence will be reached
Outputs:
--------
ofs: Outputs the minimized system
"""
job.classification = [['Simulation']]
job.uuid = "57f233a2-751c-43bc-b613-f064ce685468"
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")
min = ParallelMDMinimizeCube('Minimize', title="System Minimization")
min.promote_parameter('steps', promoted_name='steps', default=0)
min.promote_parameter('md_engine',
promoted_name='md_engine',
default='OpenMM',
description='Select the MD Engine')
min.set_parameters(save_md_stage=True)
job.description = """
Analyse the trajectory from Short Trajectory MD in terms of interactions between the
ligand and the active site and in terms of ligand RMSD after fitting the trajectory
based on active site C_alphas.
Required Input Parameters:
--------------------------
in: Collection of OERecords (one per ligand) of Short Trajectory MD results.
Outputs:
--------
floe report: html page of the Analysis for each ligand.
out (.oedb file): file of the Analysis results for all ligands.
"""
job.uuid = "292ef2b7-4ea4-4567-aafa-48bc9650d559"
ifs = DatasetReaderCube("ifs")
ifs.promote_parameter("data_in",
promoted_name="in",
title="System Input OERecord",
description="OERecord file name")
ofs = DatasetWriterCube('ofs', title='OFS-Success')
ofs.promote_parameter("data_out",
promoted_name="out",
title="System Output OERecord",
description="OERecord file name")
trajToOEMol = ParallelTrajToOEMolCube("TrajToOEMolCube")
trajIntE = ParallelTrajInteractionEnergyCube("TrajInteractionEnergyCube")
job.description = """
An MMPBSA analysis is carried out on trajectory OEMols for protein, ligand
and possibly waters.
Required Input Parameters:
--------------------------
.oedb of records containing protein, ligand and possibly water
trajectory OEMols from an MD Short Trajectory run.
Outputs:
--------
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")
job.description = """
Testing PBSALigand Interaction Energies Floe
#
Ex. python floes/up.py --in STMD_TrajIntE.oedb
--out STMD_TrajPBSA.oedb
#
Parameters:
-----------
in (.oedb file): file of the Interaction Energy results with Traj OEMols
#
Outputs:
--------
ofs (.oedb file): file of the MD results with PBSA results.
"""
job.uuid = "c25a9cdb-9f84-4cfe-828e-64300a4f8c64"
ifs = DatasetReaderCube("ifs")
ifs.promote_parameter("data_in",
promoted_name="in",
title="System Input OERecord",
description="OERecord file name")
scube = ParallelTrajPBSACube("TrajPBSACube")
ofs = DatasetWriterCube('ofs', title='OFS-Success')
ofs.promote_parameter("data_out",
promoted_name="out",
title="System Output OERecord",
description="OERecord file name")
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)
trajCube = ParallelTrajToOEMolCube("TrajToOEMolCube",
title="Trajectory To OEMols")
-----------
complex (file): OEB file of the prepared system
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 = "7a72fbf2-655e-45c5-b082-c34ee761b406"
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="Production")
npt.promote_parameter('time',
promoted_name='nanoseconds',
default=0.01,
description='Length of MD run in nanoseconds')
npt.promote_parameter('temperature',
promoted_name='temperature',
# 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)
job.add_cube(target_ligands_input_cube)
job.add_cube(perses_cube)
from MDOrion.System.cubes import (ParallelRecordSizeCheck, CollectionSetting)
from MDOrion.TrjAnalysis.cubes_trajProcessing import (
ParallelTrajToOEMolCube, ParallelTrajInteractionEnergyCube,
ParallelTrajPBSACube)
job = WorkFloe(
"Calculate Trajectory Protein-Ligand MMPBSA Energies from Short Trajectory MD"
)
job.description = """
Analyse the trajectory from Protein-Ligand MD in terms of MMPBSA interaction energies between the
between the ligand and the protein after fitting the trajectory based on active site C_alphas.
"""
job.uuid = "d00de553-5f78-4496-ae96-9c8adc527f53"
# Input MD Dataset
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",
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',
promoted_name='max_md_runs',
default=500,
description='The maximum allowed number of md runs')
ligset.set_parameters(lig_res_name='LIG')
job.description = """
Analyse the trajectory from Short Trajectory MD in terms of interactions between the
ligand and the active site and in terms of ligand RMSD after fitting the trajectory
based on active site C_alphas.
Required Input Parameters:
--------------------------
in: Collection of OERecords (one per ligand) of Short Trajectory MD results.
Outputs:
--------
floe report: html page of the Analysis for each ligand.
out (.oedb file): file of the Analysis results for all ligands.
"""
job.uuid = "673da3f5-3612-4a0d-a964-688e93b1e319"
ifs = DatasetReaderCube("ifs")
ifs.promote_parameter("data_in",
promoted_name="in",
title="System Input OERecord",
description="OERecord file name")
ofs = DatasetWriterCube('ofs', title='OFS-Success')
ofs.promote_parameter("data_out",
promoted_name="out",
title="System Output OERecord",
description="OERecord file name")
# trajCube = ParallelTrajToOEMolCube("TrajToOEMolCube")
trajIntE = ParallelTrajInteractionEnergyCube("TrajInteractionEnergyCube")
Ex. python floes/openmm_complex_prep.py --protein protein.oeb
--ligands ligands.oeb --ofs-data_out complex.oeb
Parameters:
-----------
protein (file): OEB file of the prepared protein
ligands (file): OEB file of the prepared ligands
Outputs:
--------
ofs: Output file
"""
job.classification = [['Simulation']]
job.uuid = "15099639-58e1-4051-af37-05c8d180c78c"
job.tags = [tag for lists in job.classification for tag in lists]
# Ligand setting
iligs = DatasetReaderCube("Ligand Reader", title="Ligand Reader")
iligs.promote_parameter("data_in", promoted_name="ligands", title="Ligand Input File", description="Ligand file name")
chargelig = ParallelLigandChargeCube("LigCharge", title='Ligand Charge')
chargelig.promote_parameter('charge_ligands', promoted_name='charge_ligands',
description="Charge the ligand or not", default=True)
ligset = LigandSetting("LigandSetting")
ligset.promote_parameter('max_md_runs', promoted_name='max_md_runs',
default=500,
description='The maximum allowed number of md runs')
from MDOrion.ForceField.cubes import ParallelForceFieldCube
from MDOrion.System.cubes import (IDSettingCube,
CollectionSetting,
ParallelRecordSizeCheck)
job = WorkFloe('Solvate and Run MD',
title='Solvate and Run MD')
job.description = open(path.join(path.dirname(__file__), 'PlainMD_desc.rst'), 'r').read()
# Locally the floe can be invoked by running the terminal command:
# python floes/PlainMD.py --ligands ligands.oeb --protein protein.oeb --out prod.oeb
job.classification = [['General MD']]
job.uuid = "266481fc-b257-41e9-b2f9-a92bf028b701"
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="solute", title='Solute Input File',
description="Solute input file")
sysid = IDSettingCube("System Ids")
md_comp = MDComponentCube("MD Components")
md_comp.set_parameters(multiple_flasks=True)
# The solvation cube is used to solvate the system and define the ionic strength of the solution
solvate = ParallelSolvationCube("Hydration", title="Hydration")
solvate.promote_parameter('density', promoted_name='density', default=1.03,
-----------
complex (file): OEB file of the prepared system
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')
job.description = """
Testing Floe
#
Ex. python floes/up.py --in STMD_results.oedb
--out ligands_with_trajOEMol.oedb
#
Parameters:
-----------
in (.oedb file): .oedb file of the MD results
#
Outputs:
--------
ofs (.oedb file): file of the MD results with Traj OEMols
"""
job.uuid = "15543564-7170-49da-935a-03310876df61"
ifs = DatasetReaderCube("ifs")
ifs.promote_parameter("data_in", promoted_name="in", title="System Input OERecord", description="OERecord file name")
trajCube = ParallelTrajToOEMolCube("TrajToOEMolCube")
ofs = DatasetWriterCube('ofs', title='OFS-Success')
ofs.promote_parameter("data_out", promoted_name="out", title="System Output OERecord", description="OERecord file name")
job.add_cubes(ifs, trajCube, ofs)
ifs.success.connect(trajCube.intake)
trajCube.success.connect(ofs.intake)
job = WorkFloe("Analysing Trajectory from Short Trajectory MD")
job.description = """
Cluster the trajectory from Short Trajectory MD in terms of ligand RMSD after fitting the trajectory
based on active site C_alphas.
Required Input Parameters:
--------------------------
in: Collection of OERecords (one per ligand) of Short Trajectory MD results.
Outputs:
--------
out (.oedb file): file of the Analysis results for all ligands.
"""
job.uuid = "43f33e3f-0240-4e34-9b8b-da4d5796052a"
ifs = DatasetReaderCube("ifs")
ifs.promote_parameter("data_in",
promoted_name="in",
title="System Input OERecord",
description="OERecord file name")
ofs = DatasetWriterCube('ofs', title='OFS-Success')
ofs.promote_parameter("data_out",
promoted_name="out",
title="System Output OERecord",
description="OERecord file name")
clusCube = ParallelClusterOETrajCube("ClusterOETrajCube")
molHtml = ParallelMDTrajAnalysisClusterReport("MolHtmlCube")
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")
fail = DatasetWriterCube('fail', title='Failures')
fail.promote_parameter("data_out", promoted_name="fail", title="Failures",
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")
data.promote_parameter('out_file_name',
promoted_name='out_file_name',
description="Output File name",
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',
default=500,
description='The maximum allowed number of md runs')
ligset.set_parameters(lig_res_name='LIG')
job.description = """
Testing Protein-Ligand Interaction Energies Floe
#
Ex. python floes/up.py --in STMD_TrajOEMol.oedb
--out STMD_TrajIntE.oedb
#
Parameters:
-----------
in (.oedb file): file of the MD results with Traj OEMols
#
Outputs:
--------
ofs (.oedb file): file of the MD results with Interaction Energy results.
"""
job.uuid = "a73059bd-25e6-47f3-b2d2-56474c439417"
ifs = DatasetReaderCube("ifs")
ifs.promote_parameter("data_in",
promoted_name="in",
title="System Input OERecord",
description="OERecord file name")
scube = ParallelTrajInteractionEnergyCube("TrajInteractionEnergyCube")
ofs = DatasetWriterCube('ofs', title='OFS-Success')
ofs.promote_parameter("data_out",
promoted_name="out",
title="System Output OERecord",
description="OERecord file name")
Required Input Parameters:
--------------------------
ligands (file): dataset of prepared ligands posed in the protein active site.
protein (file): dataset of the prepared protein structure.
Outputs:
--------
out: OERecords (one per ligand) of MD and Analysis results.
floe report: html page of the Analysis of each ligand.
"""
# Locally the floe can be invoked by running the terminal command:
# python floes/ShortTrajMD.py --ligands ligands.oeb --protein protein.oeb --out prod.oeb
job.classification = [['Complex Setup', 'FrosstMD']]
job.uuid = "a60efdb6-6c58-44e6-9449-421c94ace80d"
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 File",
description="Ligand file name")
chargelig = ParallelLigandChargeCube("LigCharge", title="Ligand Charge")
chargelig.promote_parameter('charge_ligands',
promoted_name='charge_ligands',
description="Charge the ligand or not",
default=True)
