icolos.core.workflow_steps.ccdc package#
Submodules#
icolos.core.workflow_steps.ccdc.docking module#
- class icolos.core.workflow_steps.ccdc.docking.GoldAdditional(*, configuration: GoldConfiguration = GoldConfiguration(automatic_settings=ConfigAutomaticSettings(autoscale=1.0, autoscale_nops_max=100000, autoscale_nops_min=100), population=ConfigPopulation(popsiz='auto', select_pressure='auto', n_islands='auto', maxops='auto', niche_siz='auto'), genetic_operators=ConfigGeneticOperators(pt_crosswt='auto', allele_mutatewt='auto', migratewt='auto'), flood_fill=None, data_files=ConfigDataFiles(ligand_data_file=[], param_file='DEFAULT', set_ligand_atom_types=1, set_protein_atom_types=0, directory='.', tordist_file='DEFAULT', make_subdirs=0, save_lone_pairs=1, fit_points_file='fit_pts.mol2', read_fitpts=0), flags=ConfigFlags(internal_ligand_h_bonds=0, flip_free_corners=0, match_ring_templates=0, flip_amide_bonds=0, flip_planar_n='1 flip_ring_NRR flip_ring_NHR', flip_pyramidal_n=0, rotate_carboxylic_oh='flip', use_tordist=1, postprocess_bonds=1, rotatable_bond_override_file='DEFAULT', solvate_all=1), termination=ConfigTermination(early_termination=1, n_top_solutions=3, rms_tolerance=1.5), constraints=ConfigConstraints(force_constraints=0), covalent_bonding=ConfigCovalentBonding(covalent=0), save_options=ConfigSaveOptions(save_score_in_file=1, save_protein_torsions=1), fitness_function_settings=ConfigFitnessFunctionSettings(initial_virtual_pt_match_max=3, relative_ligand_energy=1, gold_fitfunc_path='goldscore', start_vdw_linear_cutoff=6, score_param_file='DEFAULT'), protein_data=None), gold_config_file: str = None, docking_score_tag: str = 'Gold.Goldscore.Fitness', grid_ids: List[str] = ['grid0'])[source]#
Bases:
BaseModel- configuration: GoldConfiguration#
- docking_score_tag: str#
- gold_config_file: str#
- grid_ids: List[str]#
- class icolos.core.workflow_steps.ccdc.docking.GoldConfiguration(*, POPULATION: ConfigPopulation = ConfigPopulation(popsiz='auto', select_pressure='auto', n_islands='auto', maxops='auto', niche_siz='auto'), FLAGS: ConfigFlags = ConfigFlags(internal_ligand_h_bonds=0, flip_free_corners=0, match_ring_templates=0, flip_amide_bonds=0, flip_planar_n='1 flip_ring_NRR flip_ring_NHR', flip_pyramidal_n=0, rotate_carboxylic_oh='flip', use_tordist=1, postprocess_bonds=1, rotatable_bond_override_file='DEFAULT', solvate_all=1), TERMINATION: ConfigTermination = ConfigTermination(early_termination=1, n_top_solutions=3, rms_tolerance=1.5), CONSTRAINTS: ConfigConstraints = ConfigConstraints(force_constraints=0), **extra_data: Any)[source]#
Bases:
BaseModel- automatic_settings: ConfigAutomaticSettings#
- constraints: ConfigConstraints#
- covalent_bonding: ConfigCovalentBonding#
- data_files: ConfigDataFiles#
- fitness_function_settings: ConfigFitnessFunctionSettings#
- flags: ConfigFlags#
- flood_fill: ConfigFloodFill#
- genetic_operators: ConfigGeneticOperators#
- population: ConfigPopulation#
- protein_data: ConfigProteinData#
- save_options: ConfigSaveOptions#
- termination: ConfigTermination#
- class icolos.core.workflow_steps.ccdc.docking.StepGold(*, step_id: str, work_dir: str = None, type: str = None, data: ~icolos.core.step_utils.input_preparator.StepData = StepData(compounds=[], generic=<icolos.core.containers.generic.GenericContainer object>, gmx_state=Gromacs Topology object: System: [] | Molecules: [] | FF: amber03 | itp files: [] | posre files []), input: ~icolos.core.step_utils.input_preparator.StepInputParameters = StepInputParameters(compounds=[], generic=[], gmx_state={}, perturbation_map=None, merge=StepMerge(compounds=True, enumerations=False, merge_compounds_by=<StepBaseEnum.INPUT_MERGE_BY_NAME: 'name'>, merge_enumerations_by=<StepBaseEnum.INPUT_MERGE_BY_ID: 'id'>), work_dir=None), writeout: ~typing.List[~icolos.core.step_utils.step_writeout.StepWriteoutParameters] = [], execution: ~icolos.core.workflow_steps.step.StepExecutionParameters = StepExecutionParameters(prefix_execution=None, binary_location=None, pipe_input=None, parallelization=StepExecutionParallelizationParameters(jobs=1, max_length_sublists=None), failure_policy=StepFailurePolicyParameters(n_tries=1, retry_wait_seconds=10), check_backend_availability=False, resources=StepExecutionResourceParameters(partition=<ExecutionPlatformEnum.CORE: 'core'>, time='12:00:00', gres=None, tasks=None, mem=None, cores=None, modules=[], other_args={}, additional_lines=[]), platform=<ExecutionPlatformEnum.LOCAL: 'local'>), settings: ~icolos.core.workflow_steps.step.StepSettingsParameters = StepSettingsParameters(arguments=StepSettingsArgsParameters(flags=[], parameters={}), additional={}), gold_additional: ~icolos.core.workflow_steps.ccdc.docking.GoldAdditional = None)[source]#
Bases:
StepBase,BaseModel- gold_additional: GoldAdditional#