"""
job.classification = [["Torsion"]]
# Declare cubes
ifs = DatasetReaderCube('ifs')
fraggenCube = ParallelGenerateFragments('fraggenCube')
fraggen_failure = DatasetWriterCube('fraggen_failure')
ofs = DatasetWriterCube('ofs')
cubes = [ifs, fraggenCube, ofs, fraggen_failure]
# Promote parameters
ifs.promote_parameter('data_in', promoted_name='data_in')
ofs.promote_parameter('data_out',
promoted_name='ofs',
description='Floe output',
default='output',
title='Successes')
fraggen_failure.promote_parameter('data_out',
promoted_name='fraggen_failure',
title='Fragment Generation Failures',
description='Fragment Generation Failures',
default='fraggen_failures')
# Add Cubes to Floe
[job.add_cube(c) for c in cubes]
# Connect ports
ifs.success.connect(fraggenCube.intake)
fraggenCube.success.connect(ofs.intake)
fraggenCube.failure.connect(fraggen_failure.intake)
psi4EnergyCube2.set_parameters(opt_method='B3LYP')
psi4EnergyCube2.set_parameters(spe_method='B3LYP')
psi4EnergyCube2.set_parameters(opt_basis='6-31G*')
psi4EnergyCube2.set_parameters(spe_basis='6-31G**')
sysfail = DatasetWriterCube('sysfail')
failfs1 = DatasetWriterCube('failfs1')
failfs2 = DatasetWriterCube('failfs2')
failfs3 = DatasetWriterCube('failfs3')
ofs = DatasetWriterCube('ofs')
torfrags_ofs = DatasetWriterCube('torfrags_ofs')
startconfs_ofs = DatasetWriterCube('startconfs_ofs')
torconfs_ofs = DatasetWriterCube('torconfs_ofs')
qm_conf_ofs = DatasetWriterCube('post_qm_confs')
[
job.add_cube(n) for n in [
ifs, fraggenCube, confgenCube, torsgenCube, psi4EnergyCube1,
psi4EnergyCube2, ofs, failfs1, failfs2, failfs3, fraggen_failure,
confgen_failure, sysfail, torfrags_ofs, startconfs_ofs, torconfs_ofs,
assembler, qm_conf_ofs
]
]
# Promote parameters
ifs.promote_parameter('data_in', promoted_name='ifs')
fraggen_failure.promote_parameter('data_out',
promoted_name='fraggen_failure',
title='Fragment Generation Failures',
description='Fragment Generation Failures',
default='fraggen_failures')
confgenCube.promote_parameter(
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')
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")
job.add_cube(ligid)
# 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")
# The solvation cube is used to solvate the system and define the ionic strength of the solution
solvate = ParallelSolvationCube("Solvation", title="Solvation")
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",
promoted_name="reference_ligand",
title="Reference ligand")
target_ligands_input_cube.promote_parameter("data_in",
promoted_name="target_ligands",
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')
switch_cube.promote_parameter('switch', promoted_name='switch', title="Switch controlling Output")
output_cube.promote_parameter('data_out', promoted_name='out', title='Output File of Molecules')
input_cube.success.connect(switch_cube.intake)
switch_cube.success.connect(output_cube.intake)
if __name__ == "__main__":
my_floe.run()
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.')
charge_cube.promoted_parameter('max_search_time',
promoted_name='in',
title='Search time for conformers.')
