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 (.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",
# 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 cuberecord import (DatasetReaderCube, 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')
#!/usr/bin/env python from cubes.input_cubes import Test from cubes.compute_cubes import ParallelFastROCSRanking, AccumulateRankings from cubes.output_cubes import TextRankingOutputCube from floe.api import WorkFloe, CubeGroup from floe.api import OEMolIStreamCube from floe.api import OEMolOStreamCube, FileOutputCube # Declare Floe, add metadata for UI job = WorkFloe('FastROCS Test Floe') job.classification=[['Test']] job.tags=[['yippee ki yay mf']] job.title='test FastROCS Server' job.description = """ Read a molecule query and return the FastROCS Server Results """ input_cube = Test('input') request_cube = ParallelFastROCSRanking('request_cube') request_cube.promote_parameter('url', promoted_name='url') accu_cube = AccumulateRankings('accu') accu_cube.promote_parameter('url', promoted_name='url') output_cube = TextRankingOutputCube('results_output') output_cube.promote_parameter('name', promoted_name='name') job.add_cubes(input_cube, request_cube, accu_cube, output_cube) input_cube.success.connect(request_cube.data_input)
# 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 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")