""" 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.')