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")
# 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")
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,
description="Solution density in g/ml")
solvate.promote_parameter('salt_concentration', promoted_name='salt_concentration', default=50.0,
description='Salt concentration (Na+, Cl-) in millimolar')
solvate.set_parameters(close_solvent=True)
# This Cube is necessary for the correct work of collection and shard
coll_open = CollectionSetting("OpenCollection", title="Open Collection")