Index

A

a_type (icolos.core.containers.gmx_state.AtomType attribute) ABFE (icolos.utils.enums.program_parameters.PMXEnum attribute) (icolos.utils.enums.program_parameters.StepPMXEnum attribute) ACPYPE_BINARY (icolos.utils.enums.program_parameters.GromacsEnum attribute) ACQUISITION_BATCH_SIZE (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) ACQUISITION_FUNCTION (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) ACTION (icolos.utils.enums.step_enums.StepDataManipulationEnum attribute) ACTION_ATTACH_CONFORMERS_AS_EXTRA (icolos.utils.enums.step_enums.StepDataManipulationEnum attribute) ACTION_NO_ACTION (icolos.utils.enums.step_enums.StepDataManipulationEnum attribute) add_citation() (in module icolos.utils.general.citation_generator) add_conformer() (icolos.core.containers.compound.Enumeration method) add_conformers() (icolos.core.containers.compound.Enumeration method) add_data() (icolos.utils.general.parallelization.SubtaskContainer method) add_edge() (icolos.core.containers.perturbation_map.PerturbationMap method) add_enumeration() (icolos.core.containers.compound.Compound method) add_enumerations() (icolos.core.containers.compound.Compound method) add_extra_data() (icolos.core.containers.compound.Conformer method) add_file() (icolos.core.containers.generic.GenericContainer method) add_files() (icolos.core.containers.generic.GenericContainer method) add_global() (in module icolos.utils.entry_point_functions.parsing_functions) add_itp() (icolos.core.containers.gmx_state.GromacsState method) ADD_MISSING_ATOMS (icolos.utils.enums.step_enums.StepPdbFixerEnum attribute) ADD_MISSING_HYDROGENS (icolos.utils.enums.step_enums.StepPdbFixerEnum attribute) add_molecule() (icolos.core.containers.gmx_state.GromacsState method) add_node() (icolos.core.containers.perturbation_map.PerturbationMap method) add_posre() (icolos.core.containers.gmx_state.GromacsState method) add_step() (icolos.core.composite_agents.workflow.WorkFlow method) additional (icolos.core.flow_control.iterator.IterSettingsParameters attribute) (icolos.core.workflow_steps.step.StepSettingsParameters attribute) additional_lines (icolos.core.workflow_steps.step.StepExecutionResourceParameters attribute) adv_additional (icolos.core.workflow_steps.autodockvina.docking.StepAutoDockVina attribute) (icolos.core.workflow_steps.autodockvina.target_preparation.StepAutoDockVinaTargetPreparation attribute) ADV_PDBQT (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) (icolos.utils.enums.step_enums.StepAutoDockVinaTargetPreparationEnum attribute) ADV_RECEPTOR_PATH (icolos.utils.enums.step_enums.StepAutoDockVinaEnum attribute) ADV_SEARCH_SPACE (icolos.utils.enums.step_enums.StepAutoDockVinaEnum attribute) ADV_SEARCH_SPACE_CENTER_X (icolos.utils.enums.step_enums.StepAutoDockVinaEnum attribute) ADV_SEARCH_SPACE_CENTER_Y (icolos.utils.enums.step_enums.StepAutoDockVinaEnum attribute) ADV_SEARCH_SPACE_CENTER_Z (icolos.utils.enums.step_enums.StepAutoDockVinaEnum attribute) ADV_SEARCH_SPACE_SIZE_X (icolos.utils.enums.step_enums.StepAutoDockVinaEnum attribute) ADV_SEARCH_SPACE_SIZE_Y (icolos.utils.enums.step_enums.StepAutoDockVinaEnum attribute) ADV_SEARCH_SPACE_SIZE_Z (icolos.utils.enums.step_enums.StepAutoDockVinaEnum attribute) ADV_SEED (icolos.utils.enums.step_enums.StepAutoDockVinaEnum attribute) ADVAdditional (class in icolos.core.workflow_steps.autodockvina.docking) ADVAdditionalTP (class in icolos.core.workflow_steps.autodockvina.target_preparation) ADVConfiguration (class in icolos.core.workflow_steps.autodockvina.docking) ADVExtractBoxTP (class in icolos.core.workflow_steps.autodockvina.target_preparation) ADVSearchSpace (class in icolos.core.workflow_steps.autodockvina.docking) AgentEnvironmentParameters (class in icolos.core.composite_agents.base_agent) AgentEnvironmentParameters.WorkflowExportParameters (class in icolos.core.composite_agents.base_agent) AgentHeaderParameters (class in icolos.core.composite_agents.base_agent) AgentHeaderParameters.AgentLoggingParameters (class in icolos.core.composite_agents.base_agent) AgentHeaderParametersSettings (class in icolos.core.composite_agents.base_agent) AgentLogger (class in icolos.loggers.agentlogger)

aggregation (icolos.core.step_utils.step_writeout.StepWriteoutCompoundParameters attribute) AGGREGATION (icolos.utils.enums.step_enums.StepFilterEnum attribute) ALL (icolos.utils.enums.step_enums.IteratorEnum attribute) allele_mutatewt (icolos.core.step_utils.gold_config.ConfigGeneticOperators attribute) ALP (icolos.utils.enums.program_parameters.KallistoEnum attribute) AMBER_PARAMETRISED_COMPONENTS (icolos.utils.enums.program_parameters.GromacsEnum attribute) AMBERTOOLS_PREFIX (icolos.utils.enums.step_enums.StepGromacsEnum attribute) ANALYSE (icolos.utils.enums.program_parameters.PMXEnum attribute) ANALYSE_HELP (icolos.utils.enums.program_parameters.PMXEnum attribute) ANALYSE_HELP_SUCCESS_STRING (icolos.utils.enums.program_parameters.PMXEnum attribute) analysis_summary() (icolos.core.workflow_steps.pmx.run_analysis.StepPMXRunAnalysis method) ANNOTATION_GRID_FILENAME (icolos.utils.enums.step_enums.StepBaseEnum attribute) ANNOTATION_GRID_ID (icolos.utils.enums.step_enums.StepBaseEnum attribute) ANNOTATION_GRID_PATH (icolos.utils.enums.step_enums.StepBaseEnum attribute) ANNOTATION_TAG_DOCKING_SCORE (icolos.utils.enums.step_enums.StepBaseEnum attribute) ANNOTATION_TAG_G_SCORE (icolos.utils.enums.step_enums.StepBaseEnum attribute) ANTECHAMBER (icolos.utils.enums.program_parameters.GromacsEnum attribute) any_failed() (icolos.utils.general.parallelization.SubtaskContainer method) any_in_file() (in module icolos.utils.general.files_paths) append_structure() (icolos.core.containers.gmx_state.GromacsState method) arbitrary_types_allowed (icolos.core.containers.gmx_state.GromacsState.Config attribute) (icolos.core.containers.perturbation_map.Edge.Config attribute) (icolos.core.containers.perturbation_map.Node.Config attribute) (icolos.core.containers.perturbation_map.PerturbationMap.Config attribute) (icolos.core.step_utils.input_preparator.InputPreparator.Config attribute) (icolos.core.step_utils.input_preparator.StepData.Config attribute) (icolos.core.step_utils.retry.RetryResult.Config attribute) (icolos.core.workflow_steps.gromacs.grompp.StepGMXGrompp.Config attribute) (icolos.core.workflow_steps.gromacs.pdb2gmx.StepGMXPdb2gmx.Config attribute) (icolos.core.workflow_steps.pmx.run_analysis.StepPMXRunAnalysis.Config attribute) (icolos.core.workflow_steps.schrodinger.desmond_exec.StepDesmondExec.Config attribute) (icolos.core.workflow_steps.schrodinger.desmond_preprocessor.StepDesmondSetup.Config attribute) arguments (icolos.core.workflow_steps.step.StepSettingsParameters attribute) as_dict() (icolos.core.flow_control.flow_control.BaseStepConfig method) ASSEMBLE_COMPLEXES (icolos.utils.enums.step_enums.StepDataManipulationEnum attribute) ASSEMBLE_SYSTEMS (icolos.utils.enums.program_parameters.PMXEnum attribute) atom (icolos.core.containers.gmx_state.AtomType attribute) ATOMMAPPING (icolos.utils.enums.program_parameters.PMXEnum attribute) ATOMS (icolos.utils.enums.program_parameters.GromacsEnum attribute) ATOMS_DIRECTIVE (icolos.utils.enums.program_parameters.GromacsEnum attribute) AtomType (class in icolos.core.containers.gmx_state) atomtypes (icolos.core.containers.gmx_state.GromacsState attribute) ATOMTYPES (icolos.utils.enums.program_parameters.GromacsEnum attribute) attach_root_path() (in module icolos.utils.general.files_paths) AUTO (icolos.utils.enums.step_enums.StepGromacsEnum attribute) AutoDockVinaEnum (class in icolos.utils.enums.program_parameters) AutoDockVinaExecutor (class in icolos.utils.execute_external.autodockvina) automatic_settings (icolos.core.workflow_steps.ccdc.docking.GoldConfiguration attribute) AUTOMATIC_SETTINGS (icolos.utils.enums.step_enums.StepGoldEnum attribute) autoscale (icolos.core.step_utils.gold_config.ConfigAutomaticSettings attribute) AUTOSCALE (icolos.utils.enums.step_enums.StepGoldEnum attribute) autoscale_nops_max (icolos.core.step_utils.gold_config.ConfigAutomaticSettings attribute) autoscale_nops_min (icolos.core.step_utils.gold_config.ConfigAutomaticSettings attribute) AWS_BINARY_LOC (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute)

B

base_config (icolos.core.flow_control.flow_control.FlowControlBase attribute) BaseAgent (class in icolos.core.composite_agents.base_agent) BaseAgent.Config (class in icolos.core.composite_agents.base_agent) BaseAgentEnum (class in icolos.utils.enums.composite_agents_enums) BaseLogger (class in icolos.loggers.base_logger) BaseStepConfig (class in icolos.core.flow_control.flow_control) BATCH_SIZE (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) BEST_BUILDCONFIG_OUTPATH (icolos.utils.enums.program_parameters.ModelBuilderEnum attribute) BEST_MODEL_OUTPATH (icolos.utils.enums.program_parameters.ModelBuilderEnum attribute) bidirSnapCoreRmsd (icolos.core.containers.perturbation_map.Edge attribute) binary_location (icolos.core.workflow_steps.step.StepExecutionParameters attribute) (icolos.utils.execute_external.license_token_guard.TokenGuardParameters attribute) BlankLogger (class in icolos.loggers.blank_logger) BLINKING (icolos.utils.general.citation_generator.ConsoleColours attribute) BLOCK_INDENT (icolos.utils.enums.step_enums.StepGoldEnum attribute) BLUE (icolos.utils.general.citation_generator.ConsoleColours attribute) BOLD (icolos.utils.general.citation_generator.ConsoleColours attribute) BONDS (icolos.utils.enums.program_parameters.GromacsEnum attribute) (icolos.utils.enums.program_parameters.KallistoEnum attribute) BOX_WATER_IONS (icolos.utils.enums.program_parameters.PMXEnum attribute) boxd (icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems attribute) (icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping attribute) (icolos.core.workflow_steps.pmx.base.StepPMXBase attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute)

BOXD (icolos.utils.enums.program_parameters.StepPMXEnum attribute) boxshape (icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems attribute) (icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping attribute) (icolos.core.workflow_steps.pmx.base.StepPMXBase attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) BOXSHAPE (icolos.utils.enums.program_parameters.StepPMXEnum attribute) boxWaterIons() (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons method)

C

calculate_file_size() (icolos.core.containers.generic.GenericData method) CANCELLED (icolos.utils.enums.program_parameters.SlurmEnum attribute) category (icolos.core.step_utils.step_writeout.StepWriteoutCompoundParameters attribute) CAVITY_CONFIG_DIR (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) CAVITY_CONFIG_FILE (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) cavity_file (icolos.core.step_utils.gold_config.ConfigFloodFill attribute) CAVITY_FILE (icolos.utils.enums.step_enums.StepGoldEnum attribute) CAVITY_LOCATION (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) center_x (icolos.core.workflow_steps.autodockvina.docking.ADVSearchSpace attribute) center_y (icolos.core.workflow_steps.autodockvina.docking.ADVSearchSpace attribute) center_z (icolos.core.workflow_steps.autodockvina.docking.ADVSearchSpace attribute) CERST_NMR (icolos.utils.enums.program_parameters.CrestEnum attribute) CFG_FIELDS (icolos.utils.enums.step_enums.StepDesmondEnum attribute) cgnr (icolos.core.containers.gmx_state.AtomType attribute) chains (icolos.core.containers.gmx_state.GromacsState attribute) charge (icolos.core.containers.gmx_state.AtomType attribute) CHARGE_METHOD (icolos.utils.enums.step_enums.StepGromacsEnum attribute) (icolos.utils.enums.step_enums.StepPMXSetupEnum attribute) CHARGES (icolos.utils.enums.program_parameters.XTBOutputEnum attribute) check_backend_availability (icolos.core.workflow_steps.step.StepExecutionParameters attribute) check_file_availability() (in module icolos.utils.general.files_paths) CheckFileGenerationEnum (class in icolos.utils.enums.general_utils_enums) chg (icolos.core.containers.perturbation_map.Edge attribute) CLASSIC_CANON_ORDER (icolos.utils.enums.program_parameters.OMEGAEnum attribute) CLASSIC_ENERGY_OUTPUT_TAG (icolos.utils.enums.program_parameters.OMEGAOutputEnum attribute) CLASSIC_EWINDOW (icolos.utils.enums.program_parameters.OMEGAEnum attribute) CLASSIC_FROMCT (icolos.utils.enums.program_parameters.OMEGAEnum attribute) CLASSIC_INPUT (icolos.utils.enums.program_parameters.OMEGAEnum attribute) CLASSIC_MAXCONFS (icolos.utils.enums.program_parameters.OMEGAEnum attribute) CLASSIC_OUTPUT (icolos.utils.enums.program_parameters.OMEGAEnum attribute) CLASSIC_PARAM (icolos.utils.enums.program_parameters.OMEGAEnum attribute) CLASSIC_PREFIX (icolos.utils.enums.program_parameters.OMEGAEnum attribute) CLASSIC_PROGRESS (icolos.utils.enums.program_parameters.OMEGAEnum attribute) CLASSIC_RMS (icolos.utils.enums.program_parameters.OMEGAEnum attribute) CLASSIC_SDENERGY (icolos.utils.enums.program_parameters.OMEGAEnum attribute) CLASSIC_STRICT (icolos.utils.enums.program_parameters.OMEGAEnum attribute) CLASSIC_STRICTSTEREO (icolos.utils.enums.program_parameters.OMEGAEnum attribute) CLASSIC_VERBOSE (icolos.utils.enums.program_parameters.OMEGAEnum attribute) clean_failed_conformers() (icolos.core.containers.compound.Enumeration method) clear() (icolos.utils.general.parallelization.SubtaskContainer method) clear_conformers() (icolos.core.containers.compound.Enumeration method) clear_enumerations() (icolos.core.containers.compound.Compound method) clear_extra_data() (icolos.core.containers.compound.Conformer method) clear_file_dict() (icolos.core.containers.generic.GenericContainer method) clear_molecule() (icolos.core.containers.compound.Enumeration method) clone_compounds() (icolos.core.workflow_steps.step.StepBase method) clone_conformers() (icolos.core.containers.compound.Enumeration method) CLUSTER (icolos.utils.enums.program_parameters.GromacsEnum attribute) CLUSTER_TS (icolos.utils.enums.program_parameters.GromacsEnum attribute) CLUSTERS_NUMBER (icolos.utils.enums.step_enums.StepGromacsEnum attribute) CNS (icolos.utils.enums.program_parameters.KallistoEnum attribute) COFACTOR_IDS (icolos.utils.enums.step_enums.StepPrepwizEnum attribute) COFACTORS (icolos.utils.enums.step_enums.StepGromacsEnum attribute) collect_atomtypes() (icolos.core.containers.gmx_state.GromacsState method) COLLECT_ITERATOR_RESULTS (icolos.utils.enums.step_enums.StepDataManipulationEnum attribute) columns (icolos.core.step_utils.input_preparator.StepInputSource attribute) COM_FILE (icolos.utils.enums.step_enums.StepMacromodelEnum attribute) COM_FILE_DEFAULT (icolos.utils.enums.step_enums.StepMacromodelEnum attribute) COM_FILE_PATH (icolos.utils.enums.step_enums.StepMacromodelEnum attribute) command (icolos.core.workflow_steps.calculation.jazzy.JazzyAdditional attribute) COMPLETED (icolos.utils.enums.program_parameters.SlurmEnum attribute) COMPLEX_PDB (icolos.utils.enums.step_enums.StepGromacsEnum attribute) COMPLEX_TOP (icolos.utils.enums.step_enums.StepGromacsEnum attribute) Compound (class in icolos.core.containers.compound) COMPOUND_ID (icolos.utils.enums.write_out_enums.RunVariablesEnum attribute) compound_ids (icolos.core.step_utils.input_preparator.StepInputEnforceIDs attribute) COMPOUND_NAME (icolos.utils.enums.write_out_enums.RunVariablesEnum attribute) (icolos.utils.enums.write_out_enums.WriteOutEnum attribute) CompoundContainerEnum (class in icolos.utils.enums.compound_enums) compounds (icolos.core.containers.perturbation_map.PerturbationMap attribute) (icolos.core.step_utils.input_merger.StepMerge attribute) (icolos.core.step_utils.input_preparator.StepData attribute) (icolos.core.step_utils.input_preparator.StepInputParameters attribute) (icolos.core.step_utils.step_writeout.StepWriteoutParameters attribute) COMPOUNDS (icolos.utils.enums.step_enums.StepFilterEnum attribute) CompoundTagsEnum (class in icolos.utils.enums.compound_enums) compute_exp_ddG() (icolos.core.workflow_steps.pmx.run_analysis.StepPMXRunAnalysis method) COMPUTE_MCS (icolos.utils.enums.step_enums.StepDataManipulationEnum attribute) conc (icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems attribute) (icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping attribute) (icolos.core.workflow_steps.pmx.base.StepPMXBase attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) CONC (icolos.utils.enums.program_parameters.StepPMXEnum attribute) concatenate() (icolos.core.step_utils.structcat_util.StructcatUtil method) ConfContainer (class in icolos.config_containers.container) config (icolos.core.step_utils.step_writeout.WriteOutHandler attribute) (icolos.scripts.icolos_workflow.IcolosWorkflow attribute) CONFIG (icolos.utils.enums.program_parameters.ModelBuilderEnum attribute) (icolos.utils.enums.step_enums.StepDesmondEnum attribute) ConfigAutomaticSettings (class in icolos.core.step_utils.gold_config) ConfigConstraints (class in icolos.core.step_utils.gold_config)

ConfigCovalentBonding (class in icolos.core.step_utils.gold_config) ConfigDataFiles (class in icolos.core.step_utils.gold_config) ConfigFitnessFunctionSettings (class in icolos.core.step_utils.gold_config) ConfigFlags (class in icolos.core.step_utils.gold_config) ConfigFloodFill (class in icolos.core.step_utils.gold_config) ConfigGeneticOperators (class in icolos.core.step_utils.gold_config) ConfigPopulation (class in icolos.core.step_utils.gold_config) ConfigProteinData (class in icolos.core.step_utils.gold_config) ConfigSaveOptions (class in icolos.core.step_utils.gold_config) ConfigTermination (class in icolos.core.step_utils.gold_config) configuration (icolos.core.workflow_steps.autodockvina.docking.ADVAdditional attribute) (icolos.core.workflow_steps.ccdc.docking.GoldAdditional attribute) CONFIGURATION (icolos.utils.enums.step_enums.StepAutoDockVinaEnum attribute) (icolos.utils.enums.step_enums.StepGlideEnum attribute) (icolos.utils.enums.step_enums.StepGoldEnum attribute) CONFIGURATION_START (icolos.utils.enums.step_enums.StepGoldEnum attribute) Conformer (class in icolos.core.containers.compound) conformer (icolos.core.containers.perturbation_map.Node attribute) CONFORMER_ENERGY_TAG (icolos.utils.enums.compound_enums.CompoundTagsEnum attribute) CONFORMER_ID (icolos.utils.enums.write_out_enums.RunVariablesEnum attribute) CONFORMER_PATH (icolos.utils.enums.program_parameters.ShaepEnum attribute) CONFORMER_STRING (icolos.utils.enums.write_out_enums.RunVariablesEnum attribute) ConformerContainerEnum (class in icolos.utils.enums.compound_enums) CONFORMERS (icolos.utils.enums.step_enums.StepFilterEnum attribute) ConsoleColours (class in icolos.utils.general.citation_generator) constraints (icolos.core.workflow_steps.ccdc.docking.GoldConfiguration attribute) CONSTRAINTS (icolos.utils.enums.step_enums.StepGoldEnum attribute) construct_pipe_arguments() (icolos.core.workflow_steps.gromacs.base.StepGromacsBase method) ContainerCorrupted CONTROL (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) CONTROL_COSMO_INSERTION (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) CONTROL_COSMO_OUT (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) CONTROL_COSMO_REPLACE (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) convert() (icolos.core.step_utils.obabel_structconvert.OBabelStructConvert method) (icolos.core.step_utils.structconvert.StructConvert method) CONVERT_MAE_TO_PDB (icolos.utils.enums.step_enums.StepDataManipulationEnum attribute) convert_to_rdkit_smiles() (in module icolos.utils.smiles) COORD (icolos.utils.enums.program_parameters.CrestOutputEnum attribute) (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) COORD_ORIGINAL (icolos.utils.enums.program_parameters.CrestOutputEnum attribute) CORE (icolos.utils.enums.execution_enums.ExecutionPlatformEnum attribute) cores (icolos.core.workflow_steps.step.StepExecutionResourceParameters attribute) CORES (icolos.utils.enums.execution_enums.ExecutionPlatformEnum attribute) CosmoOutputEnum (class in icolos.utils.enums.program_parameters) COUPLING_GROUP (icolos.utils.enums.step_enums.StepGromacsEnum attribute) COUPLING_GROUPS (icolos.utils.enums.step_enums.StepGromacsEnum attribute) covalent (icolos.core.step_utils.gold_config.ConfigCovalentBonding attribute) covalent_bonding (icolos.core.workflow_steps.ccdc.docking.GoldConfiguration attribute) COVALENT_BONDING (icolos.utils.enums.step_enums.StepGoldEnum attribute) cpt (icolos.core.containers.gmx_state.GromacsState attribute) CRE_MEMBERS (icolos.utils.enums.program_parameters.CrestOutputEnum attribute) CressetExecutor (class in icolos.utils.execute_external.cresset_executor) CREST (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_BEST_XYZ (icolos.utils.enums.program_parameters.CrestOutputEnum attribute) CREST_BTHR (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_CHRG (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_CONFORMERS_SDF (icolos.utils.enums.program_parameters.CrestOutputEnum attribute) CREST_CONFORMERS_XYZ (icolos.utils.enums.program_parameters.CrestOutputEnum attribute) CREST_CROSS (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_DRY (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_ENERGIES (icolos.utils.enums.program_parameters.CrestOutputEnum attribute) CREST_EQV (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_ETHR (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_EWIN (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_G (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_GFF (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_GFN1 (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_GFN2 (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_H (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_HELP_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_NICEPRINT (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_NOCROSS (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_NOZS (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_OPT (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_PRSC (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_PTHR (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_ROTAMERS_XYZ (icolos.utils.enums.program_parameters.CrestOutputEnum attribute) CREST_RTHR (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_SHAKE (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_T (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_TSTEP (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_UHF (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_V3 (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_XNAM (icolos.utils.enums.program_parameters.CrestEnum attribute) CREST_ZS (icolos.utils.enums.program_parameters.CrestEnum attribute) CrestEnum (class in icolos.utils.enums.program_parameters) CrestExecutor (class in icolos.utils.execute_external.crest) CrestOutputEnum (class in icolos.utils.enums.program_parameters) CRITERIA (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) (icolos.utils.enums.step_enums.StepFilterEnum attribute) CT_CONFIG (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) CT_CONFIG_DEFAULTPATH (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) CT_COSMOTHERM (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) CT_COSMOTHERM_CONFIG_FILE (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) CT_COSMOTHERM_FAIL_STRING (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) CT_COSMOTHERM_OUTPUT_FILE (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) CT_COSMOTHERM_TAB_ENDING (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) CYAN (icolos.utils.general.citation_generator.ConsoleColours attribute)

D

D (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) data (icolos.core.flow_control.flow_control.BaseStepConfig attribute) (icolos.core.step_utils.step_writeout.WriteOutHandler attribute) (icolos.core.workflow_steps.calculation.base.StepCalculationBase attribute) (icolos.core.workflow_steps.calculation.boltzmann_weighting.StepBoltzmannWeighting attribute) (icolos.core.workflow_steps.calculation.clustering.StepClustering attribute) (icolos.core.workflow_steps.calculation.cosmo.StepCosmo attribute) (icolos.core.workflow_steps.calculation.cresset_ec.StepCressetEC attribute) (icolos.core.workflow_steps.calculation.esp_sim.StepEspSim attribute) (icolos.core.workflow_steps.calculation.feature_counter.StepFeatureCounter attribute) (icolos.core.workflow_steps.calculation.rms_filter.StepRMSFilter attribute) (icolos.core.workflow_steps.calculation.rmsd.StepRMSD attribute) (icolos.core.workflow_steps.calculation.shaep.StepShaep attribute) (icolos.core.workflow_steps.calculation.turbomole.StepTurbomole attribute) (icolos.core.workflow_steps.confgen.base.StepConfgenBase attribute) (icolos.core.workflow_steps.confgen.crest.StepCREST attribute) (icolos.core.workflow_steps.confgen.omega.StepOmega attribute) (icolos.core.workflow_steps.confgen.xtb.StepXTB attribute) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket attribute) (icolos.core.workflow_steps.gromacs.base.StepGromacsBase attribute) (icolos.core.workflow_steps.gromacs.cluster.StepGMXCluster attribute) (icolos.core.workflow_steps.gromacs.clusters_ts.StepClusterTS attribute) (icolos.core.workflow_steps.gromacs.do_dssp.StepGMXDoDSSP attribute) (icolos.core.workflow_steps.gromacs.editconf.StepGMXEditConf attribute) (icolos.core.workflow_steps.gromacs.genion.StepGMXGenion attribute) (icolos.core.workflow_steps.gromacs.mmpbsa.StepGMXmmpbsa attribute) (icolos.core.workflow_steps.gromacs.rsmd.StepGMXrmsd attribute) (icolos.core.workflow_steps.gromacs.select.StepGMXselect attribute) (icolos.core.workflow_steps.gromacs.solvate.StepGMXSolvate attribute) (icolos.core.workflow_steps.gromacs.trajcat.StepGMXTrjcat attribute) (icolos.core.workflow_steps.gromacs.trjconv.StepGMXTrjconv attribute) (icolos.core.workflow_steps.io.base.StepIOBase attribute) (icolos.core.workflow_steps.io.data_manipulation.StepDataManipulation attribute) (icolos.core.workflow_steps.io.embedder.StepEmbedding attribute) (icolos.core.workflow_steps.io.initialize_compound.StepInitializeCompound attribute) (icolos.core.workflow_steps.openff.openff2gmx.StepOFF2gmx attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) (icolos.core.workflow_steps.prediction.model_building.StepModelBuilder attribute) (icolos.core.workflow_steps.prediction.predictor.StepPredictor attribute) (icolos.core.workflow_steps.schrodinger.fep_analysis.StepFepPlusAnalysis attribute) (icolos.core.workflow_steps.schrodinger.fep_base.StepFEPBase attribute) (icolos.core.workflow_steps.schrodinger.fep_plus_execution.StepFepPlusExec attribute) (icolos.core.workflow_steps.schrodinger.ligprep.StepLigprep attribute) (icolos.core.workflow_steps.schrodinger.macromodel.StepMacromodel attribute) (icolos.core.workflow_steps.schrodinger.prepwizard.StepPrepwizard attribute) (icolos.core.workflow_steps.schrodinger.protein_interaction.StepProteinInteraction attribute) (icolos.core.workflow_steps.schrodinger.residue_scanning.StepResidueScanning attribute) (icolos.core.workflow_steps.step.StepBase attribute) (icolos.core.workflow_steps.structure_prediction.dssp.StepDSSP attribute) (icolos.core.workflow_steps.structure_prediction.pdb_fixer.StepPdbFixer attribute) (icolos.core.workflow_steps.structure_prediction.peptide_embedder.StepPeptideEmbedder attribute)

DATA (icolos.utils.enums.step_enums.StepModelBuilderEnum attribute) data (icolos.utils.general.parallelization.Subtask attribute) data_files (icolos.core.workflow_steps.ccdc.docking.GoldConfiguration attribute) DATA_FILES (icolos.utils.enums.step_enums.StepGoldEnum attribute) DATA_INPUT_COLUMN (icolos.utils.enums.step_enums.StepModelBuilderEnum attribute) DATA_RESPONSE_COLUMN (icolos.utils.enums.step_enums.StepModelBuilderEnum attribute) DATA_TERMINUS (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) DATA_TESTSET_FILE (icolos.utils.enums.step_enums.StepModelBuilderEnum attribute) DATA_TRAININGSET_FILE (icolos.utils.enums.step_enums.StepModelBuilderEnum attribute) ddG (icolos.core.containers.perturbation_map.Edge attribute) ddG_err (icolos.core.containers.perturbation_map.Edge attribute) DEANG (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) DEBUG (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) DEFAULT_MMPBSA_IN (icolos.utils.enums.step_enums.StepGromacsEnum attribute) DEFAULTS (icolos.utils.enums.program_parameters.GromacsEnum attribute) delimiter (icolos.core.step_utils.input_preparator.StepInputSource attribute) DENSE_INPUT (icolos.utils.enums.program_parameters.OMEGAEnum attribute) DENSE_OUTPUT (icolos.utils.enums.program_parameters.OMEGAEnum attribute) DENSE_PARAM (icolos.utils.enums.program_parameters.OMEGAEnum attribute) DENSE_PREFIX (icolos.utils.enums.program_parameters.OMEGAEnum attribute) DENSE_PROGRESS (icolos.utils.enums.program_parameters.OMEGAEnum attribute) DENSE_VERBOSE (icolos.utils.enums.program_parameters.OMEGAEnum attribute) dependent_steps (icolos.core.flow_control.iterator.IterParallelizer attribute) (icolos.core.step_dispatch.dispatcher.IterParallelizer attribute) description (icolos.core.composite_agents.base_agent.AgentHeaderParameters attribute) (icolos.core.composite_agents.scheduler.SchedulerHeaderParameters attribute) (icolos.core.composite_agents.workflow.WorkflowHeaderParameters attribute) DESCRIPTION (icolos.utils.enums.composite_agents_enums.BaseAgentEnum attribute) destination (icolos.core.step_utils.step_writeout.StepWriteoutParameters attribute) DICT (icolos.utils.enums.program_parameters.FepPlusEnum attribute) dict_from_json_file() (in module icolos.utils.general.files_paths) directory (icolos.core.step_utils.gold_config.ConfigDataFiles attribute) dispatcher (icolos.core.flow_control.iterator.StepIterator attribute) DMCS (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) do_cavity (icolos.core.step_utils.gold_config.ConfigFloodFill attribute) DO_DSSP (icolos.utils.enums.program_parameters.GromacsEnum attribute) docking_score_tag (icolos.core.workflow_steps.ccdc.docking.GoldAdditional attribute) done() (icolos.utils.general.parallelization.SubtaskContainer method) DOUBLEBOX (icolos.utils.enums.program_parameters.PMXEnum attribute) DSSPEnum (class in icolos.utils.enums.program_parameters) DYNAMIC_STOP (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute)

E

early_termination (icolos.core.step_utils.gold_config.ConfigTermination attribute) Edge (class in icolos.core.containers.perturbation_map) Edge.Config (class in icolos.core.containers.perturbation_map) EDGE_HEADER_LINE (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) edges (icolos.core.containers.perturbation_map.PerturbationMap attribute) EDITCONF (icolos.utils.enums.program_parameters.GromacsEnum attribute) edr (icolos.core.containers.gmx_state.GromacsState attribute) EEQ (icolos.utils.enums.program_parameters.KallistoEnum attribute) EI (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) ELEMENT (icolos.utils.enums.program_parameters.CosmoOutputEnum attribute) EMBED_AS (icolos.utils.enums.step_enums.StepEmbeddingEnum attribute) EMBED_AS_CONFORMERS (icolos.utils.enums.step_enums.StepEmbeddingEnum attribute) EMBED_AS_ENUMERATIONS (icolos.utils.enums.step_enums.StepEmbeddingEnum attribute) empty() (icolos.core.containers.compound.Compound method) (icolos.core.containers.compound.Conformer method) (icolos.core.containers.compound.Enumeration method) empty_output_dir() (in module icolos.utils.general.files_paths) ENDC (icolos.utils.general.citation_generator.ConsoleColours attribute) enforce_ids (icolos.core.step_utils.input_preparator.StepInputSource attribute) ensure_list() (in module icolos.utils.general.convenience_functions) EntryPointLogger (class in icolos.loggers.entrypoint_logger) Enumeration (class in icolos.core.containers.compound) ENUMERATION_ID (icolos.utils.enums.write_out_enums.RunVariablesEnum attribute) enumeration_ids (icolos.core.step_utils.input_preparator.StepInputEnforceIDs attribute) ENUMERATION_STRING (icolos.utils.enums.write_out_enums.RunVariablesEnum attribute) EnumerationContainerEnum (class in icolos.utils.enums.compound_enums) enumerations (icolos.core.step_utils.input_merger.StepMerge attribute) ENUMERATIONS (icolos.utils.enums.step_enums.StepFilterEnum attribute) environment (icolos.core.composite_agents.base_agent.AgentHeaderParameters attribute) (icolos.core.composite_agents.scheduler.SchedulerHeaderParameters attribute) (icolos.core.composite_agents.workflow.WorkflowHeaderParameters attribute) ENVIRONMENT (icolos.utils.enums.composite_agents_enums.BaseAgentEnum attribute) ENVIRONMENT_EXPORT (icolos.utils.enums.composite_agents_enums.BaseAgentEnum attribute) ENVIRONMENT_EXPORT_KEY (icolos.utils.enums.composite_agents_enums.BaseAgentEnum attribute) ENVIRONMENT_EXPORT_VALUE (icolos.utils.enums.composite_agents_enums.BaseAgentEnum attribute) EPOCHS (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) eps (icolos.core.workflow_steps.fpocket.base.StepFpocketBase attribute) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket attribute) EPS (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) EPSILON (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) ERROR (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) EVALUATE (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) exception (icolos.core.step_utils.retry.RetryResult attribute) EXCEPTION (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) EXEC (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_BINARYLOCATION (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_FAILUREPOLICY (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_FAILUREPOLICY_NTRIES (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_MODE (icolos.utils.enums.program_parameters.StepPMXEnum attribute) EXEC_PARALLELIZATION (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_PARALLELIZATION_CORES (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_PARALLELIZATION_MAXLENSUBLIST (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_PLATFORM (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_PREFIXEXECUTION (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_RESOURCES (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_RESOURCES_ADDITIONAL_LINES (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_RESOURCES_CORES (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_RESOURCES_GRES (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_RESOURCES_MEM (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_RESOURCES_MODULES (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_RESOURCES_OTHER_ARGS (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_RESOURCES_PARTITION (icolos.utils.enums.step_enums.StepBaseEnum attribute) EXEC_RESOURCES_TASKS (icolos.utils.enums.step_enums.StepBaseEnum attribute) execute() (icolos.core.composite_agents.base_agent.BaseAgent method) (icolos.core.composite_agents.scheduler.Scheduler method) (icolos.core.composite_agents.workflow.WorkFlow method) (icolos.core.step_dispatch.dispatcher.StepDispatcher method) (icolos.core.step_utils.obabel_structconvert.OBabelStructConvert method) (icolos.core.step_utils.sdconvert_util.SDConvertUtil method) (icolos.core.step_utils.structconvert.StructConvert method) (icolos.core.workflow_steps.autodockvina.docking.StepAutoDockVina method) (icolos.core.workflow_steps.autodockvina.target_preparation.StepAutoDockVinaTargetPreparation method) (icolos.core.workflow_steps.calculation.boltzmann_weighting.StepBoltzmannWeighting method) (icolos.core.workflow_steps.calculation.clustering.StepClustering method) (icolos.core.workflow_steps.calculation.cosmo.StepCosmo method) (icolos.core.workflow_steps.calculation.cresset_ec.StepCressetEC method) (icolos.core.workflow_steps.calculation.esp_sim.StepEspSim method) (icolos.core.workflow_steps.calculation.feature_counter.StepFeatureCounter method) (icolos.core.workflow_steps.calculation.jazzy.StepJazzy method) (icolos.core.workflow_steps.calculation.kallisto.StepKallisto method) (icolos.core.workflow_steps.calculation.lomap.StepLomap method) (icolos.core.workflow_steps.calculation.panther.StepPanther method) (icolos.core.workflow_steps.calculation.rms_filter.StepRMSFilter method) (icolos.core.workflow_steps.calculation.rmsd.StepRMSD method) (icolos.core.workflow_steps.calculation.shaep.StepShaep method) (icolos.core.workflow_steps.calculation.turbomole.StepTurbomole method) (icolos.core.workflow_steps.ccdc.docking.StepGold method) (icolos.core.workflow_steps.confgen.crest.StepCREST method) (icolos.core.workflow_steps.confgen.omega.StepOmega method) (icolos.core.workflow_steps.confgen.xtb.StepXTB method) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket method) (icolos.core.workflow_steps.gromacs.cluster.StepGMXCluster method) (icolos.core.workflow_steps.gromacs.clusters_ts.StepClusterTS method) (icolos.core.workflow_steps.gromacs.do_dssp.StepGMXDoDSSP method) (icolos.core.workflow_steps.gromacs.editconf.StepGMXEditConf method) (icolos.core.workflow_steps.gromacs.genion.StepGMXGenion method) (icolos.core.workflow_steps.gromacs.grompp.StepGMXGrompp method) (icolos.core.workflow_steps.gromacs.mdrun.StepGMXMDrun method) (icolos.core.workflow_steps.gromacs.mmpbsa.StepGMXmmpbsa method) (icolos.core.workflow_steps.gromacs.pdb2gmx.StepGMXPdb2gmx method) (icolos.core.workflow_steps.gromacs.rsmd.StepGMXrmsd method) (icolos.core.workflow_steps.gromacs.select.StepGMXselect method) (icolos.core.workflow_steps.gromacs.solvate.StepGMXSolvate method) (icolos.core.workflow_steps.gromacs.trajcat.StepGMXTrjcat method) (icolos.core.workflow_steps.gromacs.trjconv.StepGMXTrjconv method) (icolos.core.workflow_steps.io.data_manipulation.StepDataManipulation method) (icolos.core.workflow_steps.io.embedder.StepEmbedding method) (icolos.core.workflow_steps.io.initialize_compound.StepInitializeCompound method) (icolos.core.workflow_steps.openff.openff2gmx.StepOFF2gmx method) (icolos.core.workflow_steps.pmx.abfe.StepPMXabfe method) (icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems method) (icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping method) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons method) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox method) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib method) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop method) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid method) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate method) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations method) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions method) (icolos.core.workflow_steps.pmx.run_analysis.StepPMXRunAnalysis method) (icolos.core.workflow_steps.pmx.run_simulations.StepPMXRunSimulations method) (icolos.core.workflow_steps.pmx.setup_workpath.StepPMXSetup method) (icolos.core.workflow_steps.prediction.model_building.StepModelBuilder method) (icolos.core.workflow_steps.prediction.predictor.StepPredictor method) (icolos.core.workflow_steps.schrodinger.desmond_exec.StepDesmondExec method) (icolos.core.workflow_steps.schrodinger.desmond_preprocessor.StepDesmondSetup method) (icolos.core.workflow_steps.schrodinger.fep_absolute.StepSchrodingerAbsoluteFEP method) (icolos.core.workflow_steps.schrodinger.fep_analysis.StepFepPlusAnalysis method) (icolos.core.workflow_steps.schrodinger.fep_plus_execution.StepFepPlusExec method) (icolos.core.workflow_steps.schrodinger.fep_plus_setup.StepFepPlusSetup method) (icolos.core.workflow_steps.schrodinger.glide.StepGlide method) (icolos.core.workflow_steps.schrodinger.ligprep.StepLigprep method) (icolos.core.workflow_steps.schrodinger.macromodel.StepMacromodel method) (icolos.core.workflow_steps.schrodinger.prepwizard.StepPrepwizard method) (icolos.core.workflow_steps.schrodinger.prime.StepPrime method) (icolos.core.workflow_steps.schrodinger.protein_interaction.StepProteinInteraction method) (icolos.core.workflow_steps.schrodinger.residue_scanning.StepResidueScanning method) (icolos.core.workflow_steps.step.StepBase method) (icolos.core.workflow_steps.structure_prediction.dssp.StepDSSP method) (icolos.core.workflow_steps.structure_prediction.pdb_fixer.StepPdbFixer method) (icolos.core.workflow_steps.structure_prediction.peptide_embedder.StepPeptideEmbedder method) (icolos.scripts.icolos_workflow.IcolosWorkflow method) (icolos.utils.execute_external.autodockvina.AutoDockVinaExecutor method) (icolos.utils.execute_external.cresset_executor.CressetExecutor method) (icolos.utils.execute_external.crest.CrestExecutor method) (icolos.utils.execute_external.execute.Executor method) (icolos.utils.execute_external.execute.ExecutorBase method) (icolos.utils.execute_external.fep_plus.FepPlusExecutor method) (icolos.utils.execute_external.glide.GlideExecutor method) (icolos.utils.execute_external.gold.GoldExecutor method) (icolos.utils.execute_external.gromacs.GromacsExecutor method) (icolos.utils.execute_external.jazzy.JazzyExecutor method) (icolos.utils.execute_external.kallisto.KallistoExecutor method) (icolos.utils.execute_external.ligprep.LigprepExecutor method) (icolos.utils.execute_external.macromodel.MacromodelExecutor method) (icolos.utils.execute_external.omega.OMEGAExecutor method) (icolos.utils.execute_external.openbabel.OpenBabelExecutor method) (icolos.utils.execute_external.pmx.PMXExecutor method) (icolos.utils.execute_external.prime.PrimeExecutor method) (icolos.utils.execute_external.schrodinger.SchrodingerExecutor method) (icolos.utils.execute_external.sdconvert.SDConvertExecutor method) (icolos.utils.execute_external.slurm_executor.SlurmExecutor method) (icolos.utils.execute_external.structcat.StructcatExecutor method) (icolos.utils.execute_external.turbomole.TurbomoleExecutor method) (icolos.utils.execute_external.xtb.XTBExecutor method)

execute_mdrun() (icolos.core.workflow_steps.gromacs.mdrun.StepGMXMDrun method) execute_parallel() (icolos.utils.general.parallelization.Parallelizer method) execute_parallel_simulations() (icolos.core.workflow_steps.gromacs.mdrun.StepGMXMDrun method) execute_workflow() (icolos.core.step_dispatch.dispatcher.StepDispatcher method) execution (icolos.core.flow_control.flow_control.BaseStepConfig attribute) (icolos.core.workflow_steps.calculation.base.StepCalculationBase attribute) (icolos.core.workflow_steps.calculation.boltzmann_weighting.StepBoltzmannWeighting attribute) (icolos.core.workflow_steps.calculation.clustering.StepClustering attribute) (icolos.core.workflow_steps.calculation.cosmo.StepCosmo attribute) (icolos.core.workflow_steps.calculation.cresset_ec.StepCressetEC attribute) (icolos.core.workflow_steps.calculation.esp_sim.StepEspSim attribute) (icolos.core.workflow_steps.calculation.feature_counter.StepFeatureCounter attribute) (icolos.core.workflow_steps.calculation.rms_filter.StepRMSFilter attribute) (icolos.core.workflow_steps.calculation.rmsd.StepRMSD attribute) (icolos.core.workflow_steps.calculation.shaep.StepShaep attribute) (icolos.core.workflow_steps.calculation.turbomole.StepTurbomole attribute) (icolos.core.workflow_steps.confgen.base.StepConfgenBase attribute) (icolos.core.workflow_steps.confgen.crest.StepCREST attribute) (icolos.core.workflow_steps.confgen.omega.StepOmega attribute) (icolos.core.workflow_steps.confgen.xtb.StepXTB attribute) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket attribute) (icolos.core.workflow_steps.gromacs.base.StepGromacsBase attribute) (icolos.core.workflow_steps.gromacs.cluster.StepGMXCluster attribute) (icolos.core.workflow_steps.gromacs.clusters_ts.StepClusterTS attribute) (icolos.core.workflow_steps.gromacs.do_dssp.StepGMXDoDSSP attribute) (icolos.core.workflow_steps.gromacs.editconf.StepGMXEditConf attribute) (icolos.core.workflow_steps.gromacs.genion.StepGMXGenion attribute) (icolos.core.workflow_steps.gromacs.mmpbsa.StepGMXmmpbsa attribute) (icolos.core.workflow_steps.gromacs.rsmd.StepGMXrmsd attribute) (icolos.core.workflow_steps.gromacs.select.StepGMXselect attribute) (icolos.core.workflow_steps.gromacs.solvate.StepGMXSolvate attribute) (icolos.core.workflow_steps.gromacs.trajcat.StepGMXTrjcat attribute) (icolos.core.workflow_steps.gromacs.trjconv.StepGMXTrjconv attribute) (icolos.core.workflow_steps.io.base.StepIOBase attribute) (icolos.core.workflow_steps.io.data_manipulation.StepDataManipulation attribute) (icolos.core.workflow_steps.io.embedder.StepEmbedding attribute) (icolos.core.workflow_steps.io.initialize_compound.StepInitializeCompound attribute) (icolos.core.workflow_steps.openff.openff2gmx.StepOFF2gmx attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) (icolos.core.workflow_steps.prediction.model_building.StepModelBuilder attribute) (icolos.core.workflow_steps.prediction.predictor.StepPredictor attribute) (icolos.core.workflow_steps.schrodinger.fep_analysis.StepFepPlusAnalysis attribute) (icolos.core.workflow_steps.schrodinger.fep_base.StepFEPBase attribute) (icolos.core.workflow_steps.schrodinger.fep_plus_execution.StepFepPlusExec attribute) (icolos.core.workflow_steps.schrodinger.ligprep.StepLigprep attribute) (icolos.core.workflow_steps.schrodinger.macromodel.StepMacromodel attribute) (icolos.core.workflow_steps.schrodinger.prepwizard.StepPrepwizard attribute) (icolos.core.workflow_steps.schrodinger.protein_interaction.StepProteinInteraction attribute) (icolos.core.workflow_steps.schrodinger.residue_scanning.StepResidueScanning attribute) (icolos.core.workflow_steps.step.StepBase attribute) (icolos.core.workflow_steps.structure_prediction.dssp.StepDSSP attribute) (icolos.core.workflow_steps.structure_prediction.pdb_fixer.StepPdbFixer attribute) (icolos.core.workflow_steps.structure_prediction.peptide_embedder.StepPeptideEmbedder attribute) EXECUTION_MODE (icolos.utils.enums.step_enums.StepTurbomoleEnum attribute) execution_successful() (in module icolos.utils.execute_external.execute) ExecutionFailed ExecutionPlatformEnum (class in icolos.utils.enums.execution_enums) Executor (class in icolos.utils.execute_external.execute) ExecutorBase (class in icolos.utils.execute_external.execute) ExecutorEnum (class in icolos.utils.enums.entry_points) export (icolos.core.composite_agents.base_agent.AgentEnvironmentParameters attribute) EXS (icolos.utils.enums.program_parameters.KallistoEnum attribute) extension (icolos.core.step_utils.input_preparator.StepInputSource attribute) EXTRA_DATA_COORDFILE (icolos.utils.enums.compound_enums.ConformerContainerEnum attribute) EXTRA_DATA_COSMOFILE (icolos.utils.enums.compound_enums.ConformerContainerEnum attribute) extract_box (icolos.core.workflow_steps.autodockvina.target_preparation.ADVAdditionalTP attribute) EXTRACT_BOX (icolos.utils.enums.step_enums.StepAutoDockVinaTargetPreparationEnum attribute) EXTRACT_BOX_REFERENCE_LIGAND_FORMAT (icolos.utils.enums.step_enums.StepAutoDockVinaTargetPreparationEnum attribute) EXTRACT_BOX_REFERENCE_LIGAND_FORMAT_PDB (icolos.utils.enums.step_enums.StepAutoDockVinaTargetPreparationEnum attribute) EXTRACT_BOX_REFERENCE_LIGAND_FORMAT_SDF (icolos.utils.enums.step_enums.StepAutoDockVinaTargetPreparationEnum attribute) EXTRACT_BOX_REFERENCE_LIGAND_PATH (icolos.utils.enums.step_enums.StepAutoDockVinaTargetPreparationEnum attribute)

F

FAIL (icolos.utils.general.citation_generator.ConsoleColours attribute) FAILED (icolos.utils.enums.program_parameters.SlurmEnum attribute) (icolos.utils.enums.step_enums.StepTurbomoleEnum attribute) FAILURE (icolos.utils.enums.program_parameters.XTBOutputEnum attribute) (icolos.utils.enums.step_enums.StepJazzyEnum attribute) (icolos.utils.enums.step_enums.StepKallistoEnum attribute) failure_policy (icolos.core.workflow_steps.step.StepExecutionParameters attribute) FEATURE (icolos.utils.enums.step_enums.StepFeatureCounterEnum attribute) FeatureCounterEnum (class in icolos.utils.enums.program_parameters) features (icolos.core.workflow_steps.calculation.kallisto.KallistoAdditional attribute) FEATURES (icolos.utils.enums.step_enums.StepClusteringEnum attribute) (icolos.utils.enums.step_enums.StepKallistoEnum attribute) (icolos.utils.enums.step_enums.StepPredictorEnum attribute) FEP_ABSOLUTE_EXECUTOR (icolos.utils.enums.program_parameters.FepPlusEnum attribute) FEP_EXEC_COMPLETE (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) FEP_EXEC_PARTIAL_COMPLETE (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) FEP_EXECUTOR (icolos.utils.enums.program_parameters.FepPlusEnum attribute) FEP_HELP (icolos.utils.enums.program_parameters.FepPlusEnum attribute) FEP_MAPPER (icolos.utils.enums.program_parameters.FepPlusEnum attribute) FEP_MAPPER_HELP_SUCCESS_STRING (icolos.utils.enums.program_parameters.FepPlusEnum attribute) FEP_MAPPER_OUTPUT (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) FepPlusEnum (class in icolos.utils.enums.program_parameters) FepPlusExecutor (class in icolos.utils.execute_external.fep_plus) ff (icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems attribute) (icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping attribute) (icolos.core.workflow_steps.pmx.base.StepPMXBase attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) FIELD_KEY_BEST_CONFIGURATION (icolos.utils.enums.step_enums.StepModelBuilderEnum attribute) FIELD_KEY_CMS (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) FIELD_KEY_COORDINATES (icolos.utils.enums.step_enums.StepPantherEnum attribute) FIELD_KEY_CPT (icolos.utils.enums.step_enums.StepGromacsEnum attribute) FIELD_KEY_DTR (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) FIELD_KEY_DX (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) FIELD_KEY_EDR (icolos.utils.enums.step_enums.StepGromacsEnum attribute) FIELD_KEY_INPUT_DATA (icolos.utils.enums.step_enums.StepModelBuilderEnum attribute) FIELD_KEY_ITP (icolos.utils.enums.step_enums.StepGromacsEnum attribute) FIELD_KEY_LOG (icolos.utils.enums.step_enums.StepGromacsEnum attribute) FIELD_KEY_MDP (icolos.utils.enums.step_enums.StepGromacsEnum attribute) FIELD_KEY_NDX (icolos.utils.enums.step_enums.StepGromacsEnum attribute) FIELD_KEY_NEGATIVE_IMAGE (icolos.utils.enums.step_enums.StepPantherEnum attribute) (icolos.utils.enums.step_enums.StepShaepEnum attribute) FIELD_KEY_PDB (icolos.utils.enums.step_enums.StepGromacsEnum attribute) FIELD_KEY_PDB_FILE (icolos.utils.enums.step_enums.StepPantherEnum attribute) FIELD_KEY_POSEVIEWER (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) FIELD_KEY_PRODUCTION_MODEL (icolos.utils.enums.step_enums.StepModelBuilderEnum attribute) FIELD_KEY_STRUCTURE (icolos.utils.enums.step_enums.StepGromacsEnum attribute) FIELD_KEY_TOPOL (icolos.utils.enums.step_enums.StepGromacsEnum attribute) FIELD_KEY_TPR (icolos.utils.enums.step_enums.StepGromacsEnum attribute) FIELD_KEY_XTC (icolos.utils.enums.step_enums.StepGromacsEnum attribute) FIELDS (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) (icolos.utils.enums.step_enums.StepGromacsEnum attribute) (icolos.utils.enums.step_enums.StepPantherEnum attribute) FIELDS_PARAMETERS_LIB (icolos.utils.enums.step_enums.StepPantherEnum attribute) FILE_NAME (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) FILE_SIZE_THRESHOLD (icolos.utils.enums.step_enums.StepBaseEnum attribute) (icolos.utils.enums.step_enums.StepGromacsEnum attribute)

FILE_TYPE_PDB (icolos.utils.enums.step_enums.StepBaseEnum attribute) FILETYPE_TXT (icolos.utils.enums.step_enums.StepBaseEnum attribute) FILL_DUMMY_CONFS (icolos.utils.enums.step_enums.StepGlideEnum attribute) FILTER (icolos.utils.enums.step_enums.StepDataManipulationEnum attribute) FILTER_FILE (icolos.utils.enums.step_enums.StepLigprepEnum attribute) FILTER_LEVEL (icolos.utils.enums.step_enums.StepFilterEnum attribute) find_conformer() (icolos.core.containers.compound.Enumeration method) find_enumeration() (icolos.core.containers.compound.Compound method) FIND_MISSING_ATOMS (icolos.utils.enums.step_enums.StepPdbFixerEnum attribute) FIND_MISSING_RESIDUES (icolos.utils.enums.step_enums.StepPdbFixerEnum attribute) find_step_by_step_id() (icolos.core.composite_agents.workflow.WorkFlow method) FIT (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) fit_points_file (icolos.core.step_utils.gold_config.ConfigDataFiles attribute) fitness_function_settings (icolos.core.workflow_steps.ccdc.docking.GoldConfiguration attribute) FITNESS_FUNCTION_SETTINGS (icolos.utils.enums.step_enums.StepGoldEnum attribute) FIXER (icolos.utils.enums.program_parameters.PdbFixerEnum attribute) flags (icolos.core.flow_control.iterator.IterSettingsParameters attribute) (icolos.core.workflow_steps.ccdc.docking.GoldConfiguration attribute) (icolos.core.workflow_steps.step.StepSettingsArgsParameters attribute) FLAGS (icolos.utils.enums.step_enums.StepGoldEnum attribute) flip_amide_bonds (icolos.core.step_utils.gold_config.ConfigFlags attribute) flip_free_corners (icolos.core.step_utils.gold_config.ConfigFlags attribute) flip_planar_n (icolos.core.step_utils.gold_config.ConfigFlags attribute) flip_pyramidal_n (icolos.core.step_utils.gold_config.ConfigFlags attribute) flood_fill (icolos.core.workflow_steps.ccdc.docking.GoldConfiguration attribute) FLOOD_FILL (icolos.utils.enums.step_enums.StepGoldEnum attribute) floodfill_atom_no (icolos.core.step_utils.gold_config.ConfigFloodFill attribute) floodfill_center (icolos.core.step_utils.gold_config.ConfigFloodFill attribute) FLOW_CONTROL_INIT_DICT (icolos.utils.enums.flow_control_enums.FlowControlInitializationEnum attribute) FlowControlBase (class in icolos.core.flow_control.flow_control) FlowControlInitializationEnum (class in icolos.utils.enums.flow_control_enums) FMP_OUTPUT_FILE (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) FMP_STATS (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) FMP_STATS_CALL (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) FORCE_CONSTANTS (icolos.utils.enums.step_enums.StepGromacsEnum attribute) force_constraints (icolos.core.step_utils.gold_config.ConfigConstraints attribute) forcefield (icolos.core.containers.gmx_state.GromacsState attribute) FORCEFIELD (icolos.utils.enums.step_enums.StepGromacsEnum attribute) (icolos.utils.enums.step_enums.StepOpenFFEnum attribute) FORCEFIELD_ITP (icolos.utils.enums.step_enums.StepGromacsEnum attribute) FORMAL_CHARGE_TAG (icolos.utils.enums.compound_enums.CompoundTagsEnum attribute) format (icolos.core.step_utils.input_preparator.StepInputSource attribute) (icolos.core.step_utils.step_writeout.StepWriteoutDestinationParameters attribute) format_ (icolos.core.workflow_steps.fpocket.base.StepFpocketBase attribute) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket attribute) FORMAT_CMS (icolos.utils.enums.step_enums.StepBaseEnum attribute) FORMAT_CSV (icolos.utils.enums.step_enums.StepBaseEnum attribute) FORMAT_DTR (icolos.utils.enums.step_enums.StepBaseEnum attribute) FORMAT_JSON (icolos.utils.enums.step_enums.StepBaseEnum attribute) FORMAT_MOL2 (icolos.utils.enums.step_enums.StepBaseEnum attribute) FORMAT_PDB (icolos.utils.enums.step_enums.StepBaseEnum attribute) FORMAT_PKL (icolos.utils.enums.step_enums.StepBaseEnum attribute) FORMAT_PLAIN (icolos.utils.enums.step_enums.StepBaseEnum attribute) FORMAT_SDF (icolos.utils.enums.step_enums.StepBaseEnum attribute) FORMAT_SMI (icolos.utils.enums.step_enums.StepBaseEnum attribute) FORMAT_SMILES (icolos.utils.enums.step_enums.StepBaseEnum attribute) FORMAT_TXT (icolos.utils.enums.step_enums.StepBaseEnum attribute) FORMAT_XTB (icolos.utils.enums.step_enums.StepBaseEnum attribute) FRACTION_PER_EPOCH (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) FRAGMENTS (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) FRAME_LIST_FILE (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) FREE_ENERGY_SOLVENT_TAGS (icolos.utils.enums.step_enums.StepClusteringEnum attribute) func (icolos.utils.general.parallelization.Parallelizer attribute)

G

GAFF (icolos.utils.enums.step_enums.StepGromacsEnum attribute) gen_tmp_file() (in module icolos.utils.general.files_paths) GENERAL_BLOCK_ANNOTATIONS (icolos.utils.enums.program_parameters.CosmoOutputEnum attribute) GENERAL_BLOCK_PATTERN_STRING (icolos.utils.enums.program_parameters.CosmoOutputEnum attribute) generate_base_topol_file() (icolos.core.containers.gmx_state.GromacsState method) generate_config_file() (icolos.core.workflow_steps.ccdc.docking.StepGold method) generate_from_lomap_output() (icolos.core.containers.perturbation_map.PerturbationMap method) generate_input() (icolos.core.step_utils.input_preparator.InputPreparator method) (icolos.core.workflow_steps.step.StepBase method) generate_output_file() (icolos.core.workflow_steps.gromacs.base.StepGromacsBase method) generate_posre() (icolos.core.containers.gmx_state.GromacsState method) generate_star_map() (icolos.core.containers.perturbation_map.PerturbationMap method) GENERATED_EMPTY (icolos.utils.enums.general_utils_enums.CheckFileGenerationEnum attribute) GENERATED_SUCCESS (icolos.utils.enums.general_utils_enums.CheckFileGenerationEnum attribute) generic (icolos.core.step_utils.input_preparator.StepData attribute) (icolos.core.step_utils.input_preparator.StepInputParameters attribute) (icolos.core.step_utils.step_writeout.StepWriteoutParameters attribute) GenericContainer (class in icolos.core.containers.generic) GenericData (class in icolos.core.containers.generic) genetic_operators (icolos.core.workflow_steps.ccdc.docking.GoldConfiguration attribute) GENETIC_OPERATORS (icolos.utils.enums.step_enums.StepGoldEnum attribute) GENION (icolos.utils.enums.program_parameters.GromacsEnum attribute) GENLIB (icolos.utils.enums.program_parameters.PMXEnum attribute) GENRESTR (icolos.utils.enums.program_parameters.GromacsEnum attribute) GENTOP (icolos.utils.enums.program_parameters.PMXEnum attribute) get() (icolos.config_containers.container.ConfContainer method) get_all_files() (icolos.core.containers.generic.GenericContainer method) get_argument_by_extension() (icolos.core.containers.generic.GenericContainer method) get_arguments() (icolos.core.workflow_steps.step.StepBase method) get_as_dict() (icolos.config_containers.container.ConfContainer method) get_as_string() (icolos.config_containers.container.ConfContainer method) get_charge_for_molecule() (in module icolos.utils.general.molecules) get_compound_by_id() (in module icolos.core.containers.compound) get_compound_by_name() (icolos.core.workflow_steps.step.StepBase method) (in module icolos.core.containers.compound) get_compound_name() (icolos.core.containers.compound.Conformer method) (icolos.core.containers.compound.Enumeration method) get_compound_number() (icolos.core.containers.compound.Compound method) get_compound_object() (icolos.core.containers.compound.Enumeration method) get_compound_stats() (icolos.core.workflow_steps.step.StepBase method) get_compounds() (icolos.core.workflow_steps.step.StepBase method) get_config_version_number() (in module icolos.utils.entry_point_functions.parsing_functions) get_conformer() (icolos.core.containers.perturbation_map.Node method) get_conformer_count() (icolos.core.workflow_steps.io.data_manipulation.StepDataManipulation method) get_conformer_id() (icolos.core.containers.compound.Conformer method) get_conformer_ids() (icolos.core.containers.compound.Enumeration method) get_conformers() (icolos.core.containers.compound.Enumeration method) get_data() (icolos.core.containers.generic.GenericData method) (icolos.core.step_utils.step_writeout.WriteOutHandler method) get_description() (icolos.core.composite_agents.base_agent.BaseAgent method) get_done_tasks() (icolos.utils.general.parallelization.SubtaskContainer method) get_edge_by_id() (icolos.core.containers.perturbation_map.PerturbationMap method) get_edge_id() (icolos.core.containers.perturbation_map.Edge method) get_edges() (icolos.core.containers.perturbation_map.PerturbationMap method) (icolos.core.workflow_steps.pmx.base.StepPMXBase method) get_enumeration_id() (icolos.core.containers.compound.Enumeration method) get_enumeration_ids() (icolos.core.containers.compound.Compound method) get_enumeration_object() (icolos.core.containers.compound.Conformer method) get_enumerations() (icolos.core.containers.compound.Compound method) get_exception_message() (in module icolos.utils.general.icolos_exceptions) get_exception_type() (in module icolos.utils.general.icolos_exceptions) get_extension() (icolos.core.containers.generic.GenericData method) get_extra_data() (icolos.core.containers.compound.Conformer method) get_file_by_index() (icolos.core.containers.generic.GenericContainer method) get_file_by_name() (icolos.core.containers.generic.GenericContainer method) get_file_name() (icolos.core.containers.generic.GenericData method) get_file_names_by_extension() (icolos.core.containers.generic.GenericContainer method) get_file_types() (icolos.core.containers.generic.GenericContainer method) get_files_by_extension() (icolos.core.containers.generic.GenericContainer method) get_flattened_files() (icolos.core.containers.generic.GenericContainer method) get_generic() (icolos.core.workflow_steps.step.StepBase method) get_hub_conformer() (icolos.core.workflow_steps.pmx.base.StepPMXBase method) get_id() (icolos.core.composite_agents.base_agent.BaseAgent method) (icolos.core.containers.generic.GenericData method) get_index_string() (icolos.core.containers.compound.Compound method) (icolos.core.containers.compound.Conformer method) (icolos.core.containers.compound.Enumeration method) get_mdrun_command() (icolos.core.workflow_steps.pmx.run_simulations.StepPMXRunSimulations method) get_molecule() (icolos.core.containers.compound.Conformer method) (icolos.core.containers.compound.Enumeration method) get_name() (icolos.core.containers.compound.Compound method) get_next_file_id() (icolos.core.containers.generic.GenericContainer method) get_node_color() (icolos.core.containers.perturbation_map.Node method) get_node_hash() (icolos.core.containers.perturbation_map.Node method) get_node_id() (icolos.core.containers.perturbation_map.Node method) get_nodes() (icolos.core.containers.perturbation_map.PerturbationMap method) (icolos.core.workflow_steps.pmx.base.StepPMXBase method) get_original_conformer() (icolos.core.workflow_steps.calculation.turbomole.StepTurbomole method) get_original_smile() (icolos.core.containers.compound.Enumeration method) get_perturbation_map() (icolos.core.composite_agents.workflow.WorkFlow method) (icolos.core.workflow_steps.step.StepBase method) get_progress_bar_string() (in module icolos.utils.general.progress_bar) get_protein() (icolos.core.containers.perturbation_map.PerturbationMap method) get_running_tasks() (icolos.utils.general.parallelization.SubtaskContainer method) get_runtime_global_variables() (in module icolos.utils.entry_point_functions.parsing_functions)

get_smile() (icolos.core.containers.compound.Enumeration method) get_step_id() (icolos.core.workflow_steps.step.StepBase method) get_steps() (icolos.core.composite_agents.workflow.WorkFlow method) get_sublists() (icolos.utils.general.parallelization.SubtaskContainer method) get_todo_tasks() (icolos.utils.general.parallelization.SubtaskContainer method) get_topol() (icolos.core.workflow_steps.step.StepBase method) get_version_number() (in module icolos.utils.entry_point_functions.parsing_functions) get_versions_as_strings() (in module icolos.utils.entry_point_functions.parsing_functions) get_workflow_object() (icolos.core.workflow_steps.step.StepBase method) GLIDE (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_AMIDE_MODE (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_ATTACHED (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_CALL (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_DOCKING_SCORE (icolos.utils.enums.step_enums.StepGlideEnum attribute) GLIDE_EXPANDED_SAMPLING (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_GRIDFILE (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_GSCORE (icolos.utils.enums.step_enums.StepGlideEnum attribute) GLIDE_HELP (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_HELP_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_HOST (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_INPUTBLOCK_COMMASEPARATED (icolos.core.workflow_steps.schrodinger.glide.GlideSupportEnum attribute) GLIDE_INPUTBLOCK_VALUEQUOTED (icolos.core.workflow_steps.schrodinger.glide.GlideSupportEnum attribute) GLIDE_LIGANDFILE (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_LOG (icolos.utils.enums.step_enums.StepGlideEnum attribute) GLIDE_LOG_FAIL_STRINGS (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_LOG_FINISHED_STRINGS (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_LOG_SUCCESS_STRING (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_MAEGZ_DEFAULT_EXTENSION (icolos.utils.enums.step_enums.StepGlideEnum attribute) GLIDE_NENHANCED_SAMPLING (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_NJOBS (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_NREQUIRED_CONS (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_OVERWRITE (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_POSE_OUTTYPE (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_POSE_OUTTYPE_LIGANDLIB (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_POSE_OUTTYPE_POSEVIEWER (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_POSES_PER_LIG (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_POSEVIEWER_FILE_KEY (icolos.utils.enums.step_enums.StepGlideEnum attribute) GLIDE_POSTDOCK_NPOSE (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_POSTDOCKSTRAIN (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_PRECISION (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_REWARD_INTRA_HBONDS (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_SDF (icolos.utils.enums.step_enums.StepGlideEnum attribute) GLIDE_SDF_DEFAULT_EXTENSION (icolos.utils.enums.step_enums.StepGlideEnum attribute) GLIDE_SOURCE_FILE_INDEX (icolos.utils.enums.step_enums.StepGlideEnum attribute) GLIDE_TG_WAIT_INTERVAL (icolos.core.workflow_steps.schrodinger.glide.GlideSupportEnum attribute) GLIDE_TG_WAIT_LIMIT (icolos.core.workflow_steps.schrodinger.glide.GlideSupportEnum attribute) GLIDE_TMPLAUNCHDIR (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_USE_CONS (icolos.utils.enums.program_parameters.GlideEnum attribute) GLIDE_WAIT (icolos.utils.enums.program_parameters.GlideEnum attribute) GlideEnum (class in icolos.utils.enums.program_parameters) GlideExecutor (class in icolos.utils.execute_external.glide) GlideSupportEnum (class in icolos.core.workflow_steps.schrodinger.glide) global_settings (icolos.core.composite_agents.base_agent.AgentHeaderParameters attribute) (icolos.core.composite_agents.scheduler.SchedulerHeaderParameters attribute) (icolos.core.composite_agents.workflow.WorkflowHeaderParameters attribute) GLOBAL_SETTINGS (icolos.utils.enums.composite_agents_enums.BaseAgentEnum attribute) global_variables (icolos.core.composite_agents.base_agent.AgentHeaderParameters attribute) (icolos.core.composite_agents.scheduler.SchedulerHeaderParameters attribute) (icolos.core.composite_agents.workflow.WorkflowHeaderParameters attribute) GLOBAL_VARIABLES (icolos.utils.enums.composite_agents_enums.BaseAgentEnum attribute) global_vars (icolos.scripts.icolos_workflow.IcolosWorkflow attribute) gmx_state (icolos.core.step_utils.input_preparator.StepData attribute) (icolos.core.step_utils.input_preparator.StepInputParameters attribute) (icolos.core.step_utils.step_writeout.StepWriteoutParameters attribute) gold_additional (icolos.core.workflow_steps.ccdc.docking.StepGold attribute) GOLD_CALL (icolos.utils.enums.program_parameters.GoldEnum attribute) gold_config_file (icolos.core.workflow_steps.ccdc.docking.GoldAdditional attribute) GOLD_CONFIG_FILE (icolos.utils.enums.step_enums.StepGoldEnum attribute) gold_fitfunc_path (icolos.core.step_utils.gold_config.ConfigFitnessFunctionSettings attribute) GOLD_FITFUNC_PATH (icolos.utils.enums.step_enums.StepGoldEnum attribute) GOLD_HELP (icolos.utils.enums.program_parameters.GoldEnum attribute) GOLD_HELP_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.GoldEnum attribute) GOLD_QUIET (icolos.utils.enums.program_parameters.GoldEnum attribute) GoldAdditional (class in icolos.core.workflow_steps.ccdc.docking) GoldConfiguration (class in icolos.core.workflow_steps.ccdc.docking) GoldEnum (class in icolos.utils.enums.program_parameters) GoldExecutor (class in icolos.utils.execute_external.gold) GoldOutputEnum (class in icolos.utils.enums.program_parameters) GPU (icolos.utils.enums.execution_enums.ExecutionPlatformEnum attribute) GRADIENT_TAG (icolos.utils.enums.program_parameters.XTBOutputEnum attribute) GRAPH (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) GREEDY (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) GREEDY_EPSILON (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) GREEN (icolos.utils.general.citation_generator.ConsoleColours attribute) gres (icolos.core.workflow_steps.step.StepExecutionResourceParameters attribute) GRES (icolos.utils.enums.execution_enums.ExecutionPlatformEnum attribute) grid_ids (icolos.core.workflow_steps.autodockvina.docking.ADVAdditional attribute) (icolos.core.workflow_steps.ccdc.docking.GoldAdditional attribute) GRID_IDS (icolos.utils.enums.step_enums.StepBaseEnum attribute) GROMACS_LOAD (icolos.utils.enums.step_enums.StepGromacsEnum attribute) GromacsEnum (class in icolos.utils.enums.program_parameters) GromacsExecutor (class in icolos.utils.execute_external.gromacs) GromacsState (class in icolos.core.containers.gmx_state) GromacsState.Config (class in icolos.core.containers.gmx_state) GROMPP (icolos.utils.enums.program_parameters.GromacsEnum attribute) guard() (icolos.utils.execute_external.license_token_guard.SchrodingerLicenseTokenGuard method)

H

H2HEAVY (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) H2HPOLAR (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) hash_map (icolos.core.containers.perturbation_map.PerturbationMap attribute) header (icolos.core.composite_agents.base_agent.BaseAgent attribute) (icolos.core.composite_agents.scheduler.Scheduler attribute) (icolos.core.composite_agents.workflow.WorkFlow attribute) HEADER (icolos.utils.enums.composite_agents_enums.BaseAgentEnum attribute) (icolos.utils.general.citation_generator.ConsoleColours attribute) HEADER_SCHEMA (icolos.utils.enums.general_utils_enums.JSONSchemasEnum attribute) HELP (icolos.utils.enums.program_parameters.JazzyEnum attribute) (icolos.utils.enums.program_parameters.KallistoEnum attribute) (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute)

HELP_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.JazzyEnum attribute) (icolos.utils.enums.program_parameters.KallistoEnum attribute) highest_is_best (icolos.core.step_utils.step_writeout.StepWriteoutCompoundAggregationParameters attribute) HIGHEST_IS_BEST (icolos.utils.enums.step_enums.StepFilterEnum attribute) HOST_FLAG (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) hub_conformer (icolos.core.containers.perturbation_map.PerturbationMap attribute) HYBRID_STR_TOP (icolos.utils.enums.program_parameters.PMXEnum attribute)

I

I1 (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) I2 (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) icolos module icolos.config_containers module icolos.config_containers.container module icolos.config_containers.workflow_container module icolos.core module icolos.core.composite_agents module icolos.core.composite_agents.base_agent module icolos.core.composite_agents.scheduler module icolos.core.composite_agents.workflow module icolos.core.containers module icolos.core.containers.compound module icolos.core.containers.generic module icolos.core.containers.gmx_state module icolos.core.containers.perturbation_map module icolos.core.flow_control module icolos.core.flow_control.flow_control module icolos.core.flow_control.iterator module icolos.core.step_dispatch module icolos.core.step_dispatch.dispatcher module icolos.core.step_utils module icolos.core.step_utils.gold_config module icolos.core.step_utils.input_merger module icolos.core.step_utils.input_preparator module icolos.core.step_utils.obabel_structconvert module icolos.core.step_utils.rdkit_utils module icolos.core.step_utils.retry module icolos.core.step_utils.run_variables_resolver module icolos.core.step_utils.sdconvert_util module icolos.core.step_utils.step_writeout module icolos.core.step_utils.structcat_util module icolos.core.step_utils.structconvert module icolos.core.steps_utils module icolos.core.workflow_steps module icolos.core.workflow_steps.autodockvina module icolos.core.workflow_steps.autodockvina.docking module icolos.core.workflow_steps.autodockvina.target_preparation module icolos.core.workflow_steps.calculation module icolos.core.workflow_steps.calculation.base module icolos.core.workflow_steps.calculation.boltzmann_weighting module icolos.core.workflow_steps.calculation.clustering module icolos.core.workflow_steps.calculation.cosmo module icolos.core.workflow_steps.calculation.cresset_ec module icolos.core.workflow_steps.calculation.esp_sim module icolos.core.workflow_steps.calculation.feature_counter module icolos.core.workflow_steps.calculation.jazzy module icolos.core.workflow_steps.calculation.kallisto module icolos.core.workflow_steps.calculation.lomap module icolos.core.workflow_steps.calculation.panther module icolos.core.workflow_steps.calculation.rms_filter module icolos.core.workflow_steps.calculation.rmsd module icolos.core.workflow_steps.calculation.shaep module icolos.core.workflow_steps.calculation.turbomole module icolos.core.workflow_steps.ccdc module icolos.core.workflow_steps.ccdc.docking module icolos.core.workflow_steps.confgen module icolos.core.workflow_steps.confgen.base module icolos.core.workflow_steps.confgen.crest module icolos.core.workflow_steps.confgen.omega module icolos.core.workflow_steps.confgen.xtb module icolos.core.workflow_steps.fpocket module icolos.core.workflow_steps.fpocket.base module icolos.core.workflow_steps.fpocket.mdpocket module icolos.core.workflow_steps.gromacs module icolos.core.workflow_steps.gromacs.base module icolos.core.workflow_steps.gromacs.cluster module icolos.core.workflow_steps.gromacs.clusters_ts module icolos.core.workflow_steps.gromacs.do_dssp module icolos.core.workflow_steps.gromacs.editconf module icolos.core.workflow_steps.gromacs.genion module icolos.core.workflow_steps.gromacs.grompp module icolos.core.workflow_steps.gromacs.mdrun module icolos.core.workflow_steps.gromacs.mmpbsa module icolos.core.workflow_steps.gromacs.pdb2gmx module icolos.core.workflow_steps.gromacs.rsmd module icolos.core.workflow_steps.gromacs.select module icolos.core.workflow_steps.gromacs.solvate module icolos.core.workflow_steps.gromacs.trajcat module icolos.core.workflow_steps.gromacs.trjconv module icolos.core.workflow_steps.io module icolos.core.workflow_steps.io.base module icolos.core.workflow_steps.io.data_manipulation module icolos.core.workflow_steps.io.embedder module icolos.core.workflow_steps.io.initialize_compound module icolos.core.workflow_steps.openff module icolos.core.workflow_steps.openff.openff2gmx module icolos.core.workflow_steps.pmx module icolos.core.workflow_steps.pmx.abfe module icolos.core.workflow_steps.pmx.assemble_systems module icolos.core.workflow_steps.pmx.atomMapping module icolos.core.workflow_steps.pmx.base module icolos.core.workflow_steps.pmx.box_water_ions module icolos.core.workflow_steps.pmx.doublebox module icolos.core.workflow_steps.pmx.genlib module icolos.core.workflow_steps.pmx.gentop module icolos.core.workflow_steps.pmx.ligandHybrid module icolos.core.workflow_steps.pmx.mutate module icolos.core.workflow_steps.pmx.prepare_simulations module icolos.core.workflow_steps.pmx.prepare_transitions module icolos.core.workflow_steps.pmx.run_analysis module icolos.core.workflow_steps.pmx.run_simulations module icolos.core.workflow_steps.pmx.setup_workpath module icolos.core.workflow_steps.prediction module icolos.core.workflow_steps.prediction.model_building module icolos.core.workflow_steps.prediction.predictor module icolos.core.workflow_steps.schrodinger module icolos.core.workflow_steps.schrodinger.base module icolos.core.workflow_steps.schrodinger.desmond_exec module icolos.core.workflow_steps.schrodinger.desmond_preprocessor module icolos.core.workflow_steps.schrodinger.fep_absolute module icolos.core.workflow_steps.schrodinger.fep_analysis module icolos.core.workflow_steps.schrodinger.fep_base module icolos.core.workflow_steps.schrodinger.fep_plus_execution module icolos.core.workflow_steps.schrodinger.fep_plus_setup module icolos.core.workflow_steps.schrodinger.glide module icolos.core.workflow_steps.schrodinger.ligprep module icolos.core.workflow_steps.schrodinger.macromodel module icolos.core.workflow_steps.schrodinger.prepwizard module icolos.core.workflow_steps.schrodinger.prime module icolos.core.workflow_steps.schrodinger.protein_interaction module icolos.core.workflow_steps.schrodinger.residue_scanning module icolos.core.workflow_steps.step module icolos.core.workflow_steps.structure_prediction module icolos.core.workflow_steps.structure_prediction.disicl module icolos.core.workflow_steps.structure_prediction.dssp module icolos.core.workflow_steps.structure_prediction.pdb_fixer module icolos.core.workflow_steps.structure_prediction.peptide_embedder module icolos.loggers module icolos.loggers.agentlogger module icolos.loggers.base_logger module icolos.loggers.blank_logger module icolos.loggers.entrypoint_logger module icolos.loggers.iologger module icolos.loggers.logger_utils module icolos.loggers.steplogger module icolos.scripts module icolos.scripts.executor module

icolos.scripts.icolos_workflow module icolos.scripts.sdf2smi module icolos.scripts.validator module icolos.utils module icolos.utils.constants module icolos.utils.entry_point_functions module icolos.utils.entry_point_functions.logging_helper_functions module icolos.utils.entry_point_functions.parsing_functions module icolos.utils.enums module icolos.utils.enums.composite_agents_enums module icolos.utils.enums.compound_enums module icolos.utils.enums.entry_points module icolos.utils.enums.execution_enums module icolos.utils.enums.flow_control_enums module icolos.utils.enums.general_utils_enums module icolos.utils.enums.input_enums module icolos.utils.enums.logging_enums module icolos.utils.enums.parallelization module icolos.utils.enums.program_parameters module icolos.utils.enums.step_enums module icolos.utils.enums.step_initialization_enum module icolos.utils.enums.write_out_enums module icolos.utils.execute_external module icolos.utils.execute_external.autodockvina module icolos.utils.execute_external.cresset_executor module icolos.utils.execute_external.crest module icolos.utils.execute_external.execute module icolos.utils.execute_external.fep_plus module icolos.utils.execute_external.glide module icolos.utils.execute_external.gold module icolos.utils.execute_external.gromacs module icolos.utils.execute_external.jazzy module icolos.utils.execute_external.kallisto module icolos.utils.execute_external.license_token_guard module icolos.utils.execute_external.ligprep module icolos.utils.execute_external.macromodel module icolos.utils.execute_external.omega module icolos.utils.execute_external.openbabel module icolos.utils.execute_external.pmx module icolos.utils.execute_external.prime module icolos.utils.execute_external.schrodinger module icolos.utils.execute_external.sdconvert module icolos.utils.execute_external.slurm_executor module icolos.utils.execute_external.structcat module icolos.utils.execute_external.turbomole module icolos.utils.execute_external.xtb module icolos.utils.general module icolos.utils.general.arparse_bool_extension module icolos.utils.general.citation_generator module icolos.utils.general.convenience_functions module icolos.utils.general.files_paths module icolos.utils.general.icolos_exceptions module icolos.utils.general.molecules module icolos.utils.general.parallelization module icolos.utils.general.print_log module icolos.utils.general.progress_bar module icolos.utils.general.strings module icolos.utils.smiles module IcolosWorkflow (class in icolos.scripts.icolos_workflow) id (icolos.core.composite_agents.base_agent.AgentHeaderParameters attribute) (icolos.core.composite_agents.scheduler.SchedulerHeaderParameters attribute) (icolos.core.composite_agents.workflow.WorkflowHeaderParameters attribute) ID (icolos.utils.enums.composite_agents_enums.BaseAgentEnum attribute) (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) IDX (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) in_keys() (in module icolos.utils.general.convenience_functions) INCLUDE_LIG_ITP (icolos.utils.enums.step_enums.StepGromacsEnum attribute) increment_tries() (icolos.utils.general.parallelization.Subtask method) INDEX_FLAG (icolos.utils.enums.step_enums.StepGromacsEnum attribute) INDEX_STRING (icolos.utils.enums.write_out_enums.WriteOutEnum attribute) infer_input_type() (in module icolos.utils.general.files_paths) INFO (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) INIT_SAMPLE_FACTOR (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) INITIAL_POOLING_EPOCHS (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) initial_virtual_pt_match_max (icolos.core.step_utils.gold_config.ConfigFitnessFunctionSettings attribute) initialize() (icolos.core.composite_agents.base_agent.BaseAgent method) (icolos.core.composite_agents.scheduler.Scheduler method) (icolos.core.composite_agents.workflow.WorkFlow method) initialize_logging() (in module icolos.utils.entry_point_functions.logging_helper_functions) initialize_step_from_dict() (in module icolos.core.steps_utils) initialized_steps (icolos.core.flow_control.flow_control.FlowControlBase attribute) input (icolos.core.flow_control.flow_control.BaseStepConfig attribute) (icolos.core.workflow_steps.calculation.base.StepCalculationBase attribute) (icolos.core.workflow_steps.calculation.boltzmann_weighting.StepBoltzmannWeighting attribute) (icolos.core.workflow_steps.calculation.clustering.StepClustering attribute) (icolos.core.workflow_steps.calculation.cosmo.StepCosmo attribute) (icolos.core.workflow_steps.calculation.cresset_ec.StepCressetEC attribute) (icolos.core.workflow_steps.calculation.esp_sim.StepEspSim attribute) (icolos.core.workflow_steps.calculation.feature_counter.StepFeatureCounter attribute) (icolos.core.workflow_steps.calculation.rms_filter.StepRMSFilter attribute) (icolos.core.workflow_steps.calculation.rmsd.StepRMSD attribute) (icolos.core.workflow_steps.calculation.shaep.StepShaep attribute) (icolos.core.workflow_steps.calculation.turbomole.StepTurbomole attribute) (icolos.core.workflow_steps.confgen.base.StepConfgenBase attribute) (icolos.core.workflow_steps.confgen.crest.StepCREST attribute) (icolos.core.workflow_steps.confgen.omega.StepOmega attribute) (icolos.core.workflow_steps.confgen.xtb.StepXTB attribute) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket attribute) (icolos.core.workflow_steps.gromacs.base.StepGromacsBase attribute) (icolos.core.workflow_steps.gromacs.cluster.StepGMXCluster attribute) (icolos.core.workflow_steps.gromacs.clusters_ts.StepClusterTS attribute) (icolos.core.workflow_steps.gromacs.do_dssp.StepGMXDoDSSP attribute) (icolos.core.workflow_steps.gromacs.editconf.StepGMXEditConf attribute) (icolos.core.workflow_steps.gromacs.genion.StepGMXGenion attribute) (icolos.core.workflow_steps.gromacs.mmpbsa.StepGMXmmpbsa attribute) (icolos.core.workflow_steps.gromacs.rsmd.StepGMXrmsd attribute) (icolos.core.workflow_steps.gromacs.select.StepGMXselect attribute) (icolos.core.workflow_steps.gromacs.solvate.StepGMXSolvate attribute) (icolos.core.workflow_steps.gromacs.trajcat.StepGMXTrjcat attribute) (icolos.core.workflow_steps.gromacs.trjconv.StepGMXTrjconv attribute) (icolos.core.workflow_steps.io.base.StepIOBase attribute) (icolos.core.workflow_steps.io.data_manipulation.StepDataManipulation attribute) (icolos.core.workflow_steps.io.embedder.StepEmbedding attribute) (icolos.core.workflow_steps.io.initialize_compound.StepInitializeCompound attribute) (icolos.core.workflow_steps.openff.openff2gmx.StepOFF2gmx attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) (icolos.core.workflow_steps.prediction.model_building.StepModelBuilder attribute) (icolos.core.workflow_steps.prediction.predictor.StepPredictor attribute) (icolos.core.workflow_steps.schrodinger.fep_analysis.StepFepPlusAnalysis attribute) (icolos.core.workflow_steps.schrodinger.fep_base.StepFEPBase attribute) (icolos.core.workflow_steps.schrodinger.fep_plus_execution.StepFepPlusExec attribute) (icolos.core.workflow_steps.schrodinger.ligprep.StepLigprep attribute) (icolos.core.workflow_steps.schrodinger.macromodel.StepMacromodel attribute) (icolos.core.workflow_steps.schrodinger.prepwizard.StepPrepwizard attribute) (icolos.core.workflow_steps.schrodinger.protein_interaction.StepProteinInteraction attribute) (icolos.core.workflow_steps.schrodinger.residue_scanning.StepResidueScanning attribute) (icolos.core.workflow_steps.step.StepBase attribute) (icolos.core.workflow_steps.structure_prediction.dssp.StepDSSP attribute) (icolos.core.workflow_steps.structure_prediction.pdb_fixer.StepPdbFixer attribute) (icolos.core.workflow_steps.structure_prediction.peptide_embedder.StepPeptideEmbedder attribute) INPUT (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_COMPOUNDS (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_CSV_COLUMNS (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_CSV_DELIMITER (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_CSV_NAMES_COLUMN (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_CSV_SMILES_COLUMN (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_ENFORCE_COMPOUND_IDS (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_ENFORCE_ENUMERATION_IDS (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_ENFORCE_IDS (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_ENUMERATIONS (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_EXTENSION (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_FIELD (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_FILE (icolos.utils.enums.step_enums.StepGromacsEnum attribute) INPUT_FORMAT (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_GENERIC (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_GMX (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_MERGE (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_MERGE_BY_ID (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_MERGE_BY_NAME (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_MERGE_BY_SMILE (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_MERGE_COMPOUNDS (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_MERGE_COMPOUNDS_BY (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_MERGE_ENUMERATIONS (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_MERGE_ENUMERATIONS_BY (icolos.utils.enums.step_enums.StepBaseEnum attribute) input_receptor_pdb (icolos.core.workflow_steps.autodockvina.target_preparation.ADVAdditionalTP attribute) INPUT_RECEPTOR_PDB (icolos.utils.enums.step_enums.StepAutoDockVinaTargetPreparationEnum attribute) INPUT_SOURCE (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_SOURCE_TYPE (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_SOURCE_TYPE_DIR (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_SOURCE_TYPE_FILE (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_SOURCE_TYPE_PATH (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_SOURCE_TYPE_STEP (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_SOURCE_TYPE_STRING (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_SOURCE_TYPE_URL (icolos.utils.enums.step_enums.StepBaseEnum attribute) INPUT_SOURCES (icolos.utils.enums.step_enums.StepBaseEnum attribute) InputEnum (class in icolos.utils.enums.input_enums) InputMerger (class in icolos.core.step_utils.input_merger) InputPreparator (class in icolos.core.step_utils.input_preparator) InputPreparator.Config (class in icolos.core.step_utils.input_preparator) INTERCHANGE (icolos.utils.enums.step_enums.StepOpenFFEnum attribute) internal_ligand_h_bonds (icolos.core.step_utils.gold_config.ConfigFlags attribute) IOLogger (class in icolos.loggers.iologger) IONS (icolos.utils.enums.program_parameters.GromacsEnum attribute) is_available() (icolos.utils.execute_external.autodockvina.AutoDockVinaExecutor method) (icolos.utils.execute_external.cresset_executor.CressetExecutor method) (icolos.utils.execute_external.crest.CrestExecutor method) (icolos.utils.execute_external.execute.Executor method) (icolos.utils.execute_external.execute.ExecutorBase method) (icolos.utils.execute_external.fep_plus.FepPlusExecutor method) (icolos.utils.execute_external.glide.GlideExecutor method) (icolos.utils.execute_external.gold.GoldExecutor method) (icolos.utils.execute_external.gromacs.GromacsExecutor method) (icolos.utils.execute_external.jazzy.JazzyExecutor method) (icolos.utils.execute_external.kallisto.KallistoExecutor method) (icolos.utils.execute_external.ligprep.LigprepExecutor method) (icolos.utils.execute_external.macromodel.MacromodelExecutor method) (icolos.utils.execute_external.omega.OMEGAExecutor method) (icolos.utils.execute_external.openbabel.OpenBabelExecutor method) (icolos.utils.execute_external.pmx.PMXExecutor method) (icolos.utils.execute_external.prime.PrimeExecutor method) (icolos.utils.execute_external.schrodinger.SchrodingerExecutor method) (icolos.utils.execute_external.sdconvert.SDConvertExecutor method) (icolos.utils.execute_external.slurm_executor.SlurmExecutor method) (icolos.utils.execute_external.structcat.StructcatExecutor method) (icolos.utils.execute_external.turbomole.TurbomoleExecutor method) (icolos.utils.execute_external.xtb.XTBExecutor method) is_valid() (icolos.core.composite_agents.base_agent.BaseAgent method) (icolos.core.composite_agents.scheduler.Scheduler method) (icolos.core.composite_agents.workflow.WorkFlow method) iso_value (icolos.core.workflow_steps.fpocket.base.StepFpocketBase attribute) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket attribute) ISO_VALUE (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) iter_mode (icolos.core.flow_control.iterator.IterSettings attribute) iter_settings (icolos.core.flow_control.iterator.StepIterator attribute) IteratorEnum (class in icolos.utils.enums.step_enums) IterParallelizer (class in icolos.core.flow_control.iterator) (class in icolos.core.step_dispatch.dispatcher) IterSettings (class in icolos.core.flow_control.iterator) IterSettingsParameters (class in icolos.core.flow_control.iterator) ITP1 (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) ITP2 (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) itps (icolos.core.containers.gmx_state.GromacsState attribute)

J

JAZZY (icolos.utils.enums.program_parameters.JazzyEnum attribute) jazzy_additional (icolos.core.workflow_steps.calculation.jazzy.StepJazzy attribute) JazzyAdditional (class in icolos.core.workflow_steps.calculation.jazzy) JazzyEnum (class in icolos.utils.enums.program_parameters) JazzyExecutor (class in icolos.utils.execute_external.jazzy) job_id (icolos.utils.general.parallelization.Subtask attribute) JOBID_STRING (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) JOBNAME_FLAG (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) jobs (icolos.core.flow_control.iterator.IterParallelizer attribute) (icolos.core.step_dispatch.dispatcher.IterParallelizer attribute) (icolos.core.workflow_steps.step.StepExecutionParameters.StepExecutionParallelizationParameters attribute)

JSC_LIST (icolos.utils.enums.program_parameters.FepPlusEnum attribute) JSC_TAIL_FILE (icolos.utils.enums.program_parameters.FepPlusEnum attribute) JSON_NA (icolos.utils.enums.write_out_enums.WriteOutEnum attribute) JSON_NAMES (icolos.utils.enums.input_enums.InputEnum attribute) (icolos.utils.enums.write_out_enums.WriteOutEnum attribute) JSON_RESULTS (icolos.utils.enums.write_out_enums.WriteOutEnum attribute) JSON_SMILES (icolos.utils.enums.input_enums.InputEnum attribute) JSON_VALUES (icolos.utils.enums.write_out_enums.WriteOutEnum attribute) JSON_VALUES_KEY (icolos.utils.enums.write_out_enums.WriteOutEnum attribute) JSONSchemasEnum (class in icolos.utils.enums.general_utils_enums)

K

KALLISTO (icolos.utils.enums.program_parameters.KallistoEnum attribute) kallisto_additional (icolos.core.workflow_steps.calculation.kallisto.StepKallisto attribute) KallistoAdditional (class in icolos.core.workflow_steps.calculation.kallisto) KallistoEnum (class in icolos.utils.enums.program_parameters) KallistoExecutor (class in icolos.utils.execute_external.kallisto)

key (icolos.core.composite_agents.base_agent.AgentEnvironmentParameters.WorkflowExportParameters attribute) (icolos.core.step_utils.step_writeout.StepWriteoutCompoundAggregationParameters attribute) (icolos.core.step_utils.step_writeout.StepWriteoutCompoundParameters attribute) (icolos.core.step_utils.step_writeout.StepWriteoutGenericParameters attribute) (icolos.core.step_utils.step_writeout.StepWriteoutGromacsParameters attribute) KEY_MATCHED (icolos.utils.enums.step_enums.StepDataManipulationEnum attribute)

L

LATENT_DISTANCE (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) LENGTHS (icolos.utils.enums.step_enums.StepGromacsEnum attribute) LEVEL (icolos.utils.enums.step_enums.StepFeatureCounterEnum attribute) LEVEL_CONFORMER (icolos.utils.enums.step_enums.StepFeatureCounterEnum attribute) LEVEL_ENUMERATION (icolos.utils.enums.step_enums.StepFeatureCounterEnum attribute) LICADMIN (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) LICADMIN_STAT (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) LIG (icolos.utils.enums.program_parameters.KallistoEnum attribute) LIG_EXT (icolos.utils.enums.program_parameters.GromacsEnum attribute) LIG_ID (icolos.utils.enums.program_parameters.GromacsEnum attribute) (icolos.utils.enums.step_enums.StepGromacsEnum attribute) LIG_MOLECULE_GRP (icolos.utils.enums.step_enums.StepGromacsEnum attribute) ligand_data_file (icolos.core.step_utils.gold_config.ConfigDataFiles attribute) LIGAND_DATA_FILE (icolos.utils.enums.step_enums.StepGoldEnum attribute) LIGAND_DIR (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) LIGAND_ITP (icolos.utils.enums.step_enums.StepGromacsEnum attribute) LIGAND_MOL2 (icolos.utils.enums.step_enums.StepGromacsEnum attribute) LIGAND_PDB (icolos.utils.enums.step_enums.StepGromacsEnum attribute) LIGANDHYBRID (icolos.utils.enums.program_parameters.PMXEnum attribute) LIGANDS (icolos.utils.enums.step_enums.StepPrepwizEnum attribute) LIGPREP (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_AC (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_BFF (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_EPIK (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_F (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_FF_OPLS3e (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_FF_OPLS_2005 (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_G (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_HELP (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_HELP_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_HOST (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_HOST_LOCALHOST (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_INP_CONFIG (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_INPUT_ISMI (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_LOG_ENDING (icolos.utils.enums.program_parameters.LigprepEnum attribute)

LIGPREP_NJOBS (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_NSTRUCTS (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_OUTPUT_OSD (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_PH (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_PHT (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_S (icolos.utils.enums.program_parameters.LigprepEnum attribute) LIGPREP_TAUTOMER_PROBABILITY (icolos.utils.enums.step_enums.StepLigprepEnum attribute) LIGPREP_VARIANTS (icolos.utils.enums.step_enums.StepLigprepEnum attribute) LIGPREP_WAIT (icolos.utils.enums.program_parameters.LigprepEnum attribute) LigprepEnum (class in icolos.utils.enums.program_parameters) LigprepExecutor (class in icolos.utils.execute_external.ligprep) lines_in_file() (in module icolos.utils.general.files_paths) load_data() (icolos.utils.general.parallelization.SubtaskContainer method) load_topol() (icolos.core.workflow_steps.gromacs.base.StepGromacsBase method) LOCAL (icolos.utils.enums.execution_enums.ExecutionPlatformEnum attribute) log (icolos.core.containers.gmx_state.GromacsState attribute) LOG (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) log() (icolos.loggers.base_logger.BaseLogger method) log_multiline_string() (in module icolos.loggers.logger_utils) log_version_number() (in module icolos.utils.entry_point_functions.parsing_functions) logfile (icolos.core.composite_agents.base_agent.AgentHeaderParameters.AgentLoggingParameters attribute) LOGFILE (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) logger (icolos.core.step_utils.input_preparator.InputPreparator attribute) LOGGER_AGENT (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) LOGGER_BLANK (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) LOGGER_ENTRYPOINT (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) LOGGER_IO (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) LOGGER_STEP (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) logging (icolos.core.composite_agents.base_agent.AgentHeaderParameters attribute) (icolos.core.composite_agents.scheduler.SchedulerHeaderParameters attribute) (icolos.core.composite_agents.workflow.WorkflowHeaderParameters attribute) (icolos.scripts.icolos_workflow.IcolosWorkflow attribute) LOGGING (icolos.utils.enums.composite_agents_enums.BaseAgentEnum attribute) LOGGING_LOGFILE (icolos.utils.enums.composite_agents_enums.BaseAgentEnum attribute) LoggingConfigEnum (class in icolos.utils.enums.logging_enums)

M

MACROCYCLE_EWINDOW (icolos.utils.enums.program_parameters.OMEGAEnum attribute) MACROCYCLE_INPUT (icolos.utils.enums.program_parameters.OMEGAEnum attribute) MACROCYCLE_ITERATION_CYCLE_SIZE (icolos.utils.enums.program_parameters.OMEGAEnum attribute) MACROCYCLE_MAX_ITERATIONS (icolos.utils.enums.program_parameters.OMEGAEnum attribute) MACROCYCLE_MAXCONFS (icolos.utils.enums.program_parameters.OMEGAEnum attribute) MACROCYCLE_OUTPUT (icolos.utils.enums.program_parameters.OMEGAEnum attribute) MACROCYCLE_PARAM (icolos.utils.enums.program_parameters.OMEGAEnum attribute) MACROCYCLE_PREFIX (icolos.utils.enums.program_parameters.OMEGAEnum attribute) MACROCYCLE_REF_TOLERANCE (icolos.utils.enums.program_parameters.OMEGAEnum attribute) MACROCYCLE_RMS (icolos.utils.enums.program_parameters.OMEGAEnum attribute) MACROCYCLE_RMSD_DEDUPLICATE (icolos.utils.enums.program_parameters.OMEGAEnum attribute) MACROMODEL (icolos.utils.enums.program_parameters.MacromodelEnum attribute) MACROMODEL_HELP (icolos.utils.enums.program_parameters.MacromodelEnum attribute) MACROMODEL_HELP_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.MacromodelEnum attribute) MACROMODEL_NJOBS (icolos.utils.enums.program_parameters.MacromodelEnum attribute) MACROMODEL_WAIT (icolos.utils.enums.program_parameters.MacromodelEnum attribute) MacromodelEnum (class in icolos.utils.enums.program_parameters) MacromodelExecutor (class in icolos.utils.execute_external.macromodel) mae2pdb() (icolos.core.step_utils.structconvert.StructConvert method) mae2sdf() (icolos.core.step_utils.sdconvert_util.SDConvertUtil method) MAE_COMPLEX (icolos.utils.enums.step_enums.StepPrimeEnum attribute) MAE_INPUT (icolos.utils.enums.step_enums.StepMacromodelEnum attribute) (icolos.utils.enums.step_enums.StepPrimeEnum attribute) MAE_OUTPUT (icolos.utils.enums.step_enums.StepMacromodelEnum attribute) (icolos.utils.enums.step_enums.StepPrimeEnum attribute) MAESTRO_IN_FILE (icolos.utils.enums.step_enums.StepGlideEnum attribute) MAESTRO_IN_FILE_PATH (icolos.utils.enums.step_enums.StepGlideEnum attribute) main() (in module icolos.scripts.executor) (in module icolos.scripts.sdf2smi) (in module icolos.scripts.validator) MAKE_NDX (icolos.utils.enums.program_parameters.GromacsEnum attribute) MAKE_NDX_COMMAND (icolos.utils.enums.step_enums.StepGromacsEnum attribute) make_subdirs (icolos.core.step_utils.gold_config.ConfigDataFiles attribute) mass (icolos.core.containers.gmx_state.AtomType attribute) match_ring_templates (icolos.core.step_utils.gold_config.ConfigFlags attribute) MATCH_SOURCE (icolos.utils.enums.step_enums.StepDataManipulationEnum attribute) MAX_ITER (icolos.utils.enums.step_enums.StepClusteringEnum attribute) max_length_sublists (icolos.core.workflow_steps.step.StepExecutionParameters.StepExecutionParallelizationParameters attribute) MAX_SAMPLED_FRACTION (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) max_tries (icolos.utils.general.parallelization.SubtaskContainer attribute) maxops (icolos.core.step_utils.gold_config.ConfigPopulation attribute) mcs (icolos.core.containers.perturbation_map.Edge attribute) mdp_prefixes (icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems attribute) (icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping attribute) (icolos.core.workflow_steps.pmx.base.StepPMXBase attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) MDPOCKET_COMMAND (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) MDRUN (icolos.utils.enums.program_parameters.GromacsEnum attribute) MDRUN_EXECUTABLE (icolos.utils.enums.program_parameters.StepPMXEnum attribute) mem (icolos.core.workflow_steps.step.StepExecutionResourceParameters attribute) MEM (icolos.utils.enums.execution_enums.ExecutionPlatformEnum attribute) merge (icolos.core.step_utils.input_preparator.StepInputParameters attribute) (icolos.core.step_utils.step_writeout.StepWriteoutDestinationParameters attribute) merge() (icolos.core.step_utils.input_merger.InputMerger method) merge_compounds_by (icolos.core.step_utils.input_merger.StepMerge attribute) merge_enumerations_by (icolos.core.step_utils.input_merger.StepMerge attribute) MERGED_MODEL_OUTPATH (icolos.utils.enums.program_parameters.ModelBuilderEnum attribute) METHOD (icolos.utils.enums.step_enums.StepEmbeddingEnum attribute) (icolos.utils.enums.step_enums.StepOpenFFEnum attribute) (icolos.utils.enums.step_enums.StepRMSDEnum attribute) (icolos.utils.enums.step_enums.StepRMSFilterEnum attribute) METHOD_ALIGNMOL (icolos.utils.enums.step_enums.StepRMSDEnum attribute) (icolos.utils.enums.step_enums.StepRMSFilterEnum attribute) METHOD_BEST (icolos.utils.enums.step_enums.StepRMSDEnum attribute) (icolos.utils.enums.step_enums.StepRMSFilterEnum attribute) METHOD_RDKIT (icolos.utils.enums.step_enums.StepEmbeddingEnum attribute) migratewt (icolos.core.step_utils.gold_config.ConfigGeneticOperators attribute) min_no_atoms (icolos.core.containers.perturbation_map.Edge attribute) min_samples (icolos.core.workflow_steps.fpocket.base.StepFpocketBase attribute) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket attribute) MIN_SAMPLES (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) MKDSSP (icolos.utils.enums.program_parameters.DSSPEnum attribute) MMGBSA_DG (icolos.utils.enums.step_enums.StepGromacsEnum attribute) MMGBSA_SCORE (icolos.utils.enums.step_enums.StepPrimeEnum attribute) MMPBSA (icolos.utils.enums.program_parameters.GromacsEnum attribute) MMPBSA_IN (icolos.utils.enums.step_enums.StepGromacsEnum attribute) mode (icolos.core.step_utils.step_writeout.StepWriteoutCompoundAggregationParameters attribute) (icolos.core.step_utils.step_writeout.StepWriteoutDestinationParameters attribute) MODEL (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) MODEL_PATH (icolos.utils.enums.step_enums.StepPredictorEnum attribute) ModelBuilderEnum (class in icolos.utils.enums.program_parameters) module icolos icolos.config_containers icolos.config_containers.container icolos.config_containers.workflow_container icolos.core icolos.core.composite_agents icolos.core.composite_agents.base_agent icolos.core.composite_agents.scheduler icolos.core.composite_agents.workflow icolos.core.containers icolos.core.containers.compound icolos.core.containers.generic icolos.core.containers.gmx_state icolos.core.containers.perturbation_map icolos.core.flow_control icolos.core.flow_control.flow_control icolos.core.flow_control.iterator icolos.core.step_dispatch icolos.core.step_dispatch.dispatcher icolos.core.step_utils icolos.core.step_utils.gold_config icolos.core.step_utils.input_merger icolos.core.step_utils.input_preparator icolos.core.step_utils.obabel_structconvert icolos.core.step_utils.rdkit_utils icolos.core.step_utils.retry icolos.core.step_utils.run_variables_resolver icolos.core.step_utils.sdconvert_util icolos.core.step_utils.step_writeout icolos.core.step_utils.structcat_util icolos.core.step_utils.structconvert icolos.core.steps_utils icolos.core.workflow_steps icolos.core.workflow_steps.autodockvina icolos.core.workflow_steps.autodockvina.docking icolos.core.workflow_steps.autodockvina.target_preparation icolos.core.workflow_steps.calculation icolos.core.workflow_steps.calculation.base icolos.core.workflow_steps.calculation.boltzmann_weighting icolos.core.workflow_steps.calculation.clustering icolos.core.workflow_steps.calculation.cosmo icolos.core.workflow_steps.calculation.cresset_ec icolos.core.workflow_steps.calculation.esp_sim icolos.core.workflow_steps.calculation.feature_counter icolos.core.workflow_steps.calculation.jazzy icolos.core.workflow_steps.calculation.kallisto icolos.core.workflow_steps.calculation.lomap icolos.core.workflow_steps.calculation.panther icolos.core.workflow_steps.calculation.rms_filter icolos.core.workflow_steps.calculation.rmsd icolos.core.workflow_steps.calculation.shaep icolos.core.workflow_steps.calculation.turbomole icolos.core.workflow_steps.ccdc icolos.core.workflow_steps.ccdc.docking icolos.core.workflow_steps.confgen icolos.core.workflow_steps.confgen.base icolos.core.workflow_steps.confgen.crest icolos.core.workflow_steps.confgen.omega icolos.core.workflow_steps.confgen.xtb icolos.core.workflow_steps.fpocket icolos.core.workflow_steps.fpocket.base icolos.core.workflow_steps.fpocket.mdpocket icolos.core.workflow_steps.gromacs icolos.core.workflow_steps.gromacs.base icolos.core.workflow_steps.gromacs.cluster icolos.core.workflow_steps.gromacs.clusters_ts icolos.core.workflow_steps.gromacs.do_dssp icolos.core.workflow_steps.gromacs.editconf icolos.core.workflow_steps.gromacs.genion icolos.core.workflow_steps.gromacs.grompp icolos.core.workflow_steps.gromacs.mdrun icolos.core.workflow_steps.gromacs.mmpbsa icolos.core.workflow_steps.gromacs.pdb2gmx icolos.core.workflow_steps.gromacs.rsmd icolos.core.workflow_steps.gromacs.select icolos.core.workflow_steps.gromacs.solvate icolos.core.workflow_steps.gromacs.trajcat icolos.core.workflow_steps.gromacs.trjconv icolos.core.workflow_steps.io icolos.core.workflow_steps.io.base icolos.core.workflow_steps.io.data_manipulation icolos.core.workflow_steps.io.embedder icolos.core.workflow_steps.io.initialize_compound icolos.core.workflow_steps.openff icolos.core.workflow_steps.openff.openff2gmx icolos.core.workflow_steps.pmx icolos.core.workflow_steps.pmx.abfe icolos.core.workflow_steps.pmx.assemble_systems icolos.core.workflow_steps.pmx.atomMapping icolos.core.workflow_steps.pmx.base icolos.core.workflow_steps.pmx.box_water_ions icolos.core.workflow_steps.pmx.doublebox icolos.core.workflow_steps.pmx.genlib icolos.core.workflow_steps.pmx.gentop icolos.core.workflow_steps.pmx.ligandHybrid icolos.core.workflow_steps.pmx.mutate icolos.core.workflow_steps.pmx.prepare_simulations icolos.core.workflow_steps.pmx.prepare_transitions icolos.core.workflow_steps.pmx.run_analysis icolos.core.workflow_steps.pmx.run_simulations icolos.core.workflow_steps.pmx.setup_workpath icolos.core.workflow_steps.prediction icolos.core.workflow_steps.prediction.model_building icolos.core.workflow_steps.prediction.predictor icolos.core.workflow_steps.schrodinger icolos.core.workflow_steps.schrodinger.base icolos.core.workflow_steps.schrodinger.desmond_exec icolos.core.workflow_steps.schrodinger.desmond_preprocessor icolos.core.workflow_steps.schrodinger.fep_absolute icolos.core.workflow_steps.schrodinger.fep_analysis icolos.core.workflow_steps.schrodinger.fep_base icolos.core.workflow_steps.schrodinger.fep_plus_execution icolos.core.workflow_steps.schrodinger.fep_plus_setup icolos.core.workflow_steps.schrodinger.glide icolos.core.workflow_steps.schrodinger.ligprep icolos.core.workflow_steps.schrodinger.macromodel icolos.core.workflow_steps.schrodinger.prepwizard icolos.core.workflow_steps.schrodinger.prime icolos.core.workflow_steps.schrodinger.protein_interaction icolos.core.workflow_steps.schrodinger.residue_scanning icolos.core.workflow_steps.step icolos.core.workflow_steps.structure_prediction icolos.core.workflow_steps.structure_prediction.disicl icolos.core.workflow_steps.structure_prediction.dssp icolos.core.workflow_steps.structure_prediction.pdb_fixer icolos.core.workflow_steps.structure_prediction.peptide_embedder icolos.loggers icolos.loggers.agentlogger icolos.loggers.base_logger icolos.loggers.blank_logger icolos.loggers.entrypoint_logger icolos.loggers.iologger icolos.loggers.logger_utils icolos.loggers.steplogger icolos.scripts icolos.scripts.executor icolos.scripts.icolos_workflow icolos.scripts.sdf2smi icolos.scripts.validator icolos.utils icolos.utils.constants icolos.utils.entry_point_functions icolos.utils.entry_point_functions.logging_helper_functions icolos.utils.entry_point_functions.parsing_functions icolos.utils.enums icolos.utils.enums.composite_agents_enums icolos.utils.enums.compound_enums icolos.utils.enums.entry_points icolos.utils.enums.execution_enums icolos.utils.enums.flow_control_enums icolos.utils.enums.general_utils_enums icolos.utils.enums.input_enums icolos.utils.enums.logging_enums icolos.utils.enums.parallelization icolos.utils.enums.program_parameters icolos.utils.enums.step_enums icolos.utils.enums.step_initialization_enum icolos.utils.enums.write_out_enums icolos.utils.execute_external icolos.utils.execute_external.autodockvina icolos.utils.execute_external.cresset_executor icolos.utils.execute_external.crest icolos.utils.execute_external.execute icolos.utils.execute_external.fep_plus icolos.utils.execute_external.glide icolos.utils.execute_external.gold icolos.utils.execute_external.gromacs icolos.utils.execute_external.jazzy icolos.utils.execute_external.kallisto icolos.utils.execute_external.license_token_guard icolos.utils.execute_external.ligprep icolos.utils.execute_external.macromodel icolos.utils.execute_external.omega icolos.utils.execute_external.openbabel icolos.utils.execute_external.pmx icolos.utils.execute_external.prime icolos.utils.execute_external.schrodinger icolos.utils.execute_external.sdconvert icolos.utils.execute_external.slurm_executor icolos.utils.execute_external.structcat icolos.utils.execute_external.turbomole icolos.utils.execute_external.xtb icolos.utils.general icolos.utils.general.arparse_bool_extension icolos.utils.general.citation_generator icolos.utils.general.convenience_functions icolos.utils.general.files_paths icolos.utils.general.icolos_exceptions icolos.utils.general.molecules icolos.utils.general.parallelization icolos.utils.general.print_log icolos.utils.general.progress_bar icolos.utils.general.strings icolos.utils.smiles

modules (icolos.core.workflow_steps.step.StepExecutionResourceParameters attribute) MOLECULE (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) molecules (icolos.core.containers.gmx_state.GromacsState attribute) MOLECULES (icolos.utils.enums.program_parameters.GromacsEnum attribute) MOLECULETYPES (icolos.utils.enums.program_parameters.GromacsEnum attribute) MORGAN_FP (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) move_up_directory() (in module icolos.utils.general.files_paths) MPI_MDRUN (icolos.utils.enums.program_parameters.GromacsEnum attribute) MPI_THREADS (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) MSJ_FIELDS (icolos.utils.enums.step_enums.StepDesmondEnum attribute) MULTIDIR (icolos.utils.enums.step_enums.StepGromacsEnum attribute) MULTISIM_EXEC (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) MUTATE (icolos.utils.enums.program_parameters.PMXEnum attribute)

N

N1 (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) N2 (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) N_CLUSTERS (icolos.utils.enums.step_enums.StepClusteringEnum attribute) n_islands (icolos.core.step_utils.gold_config.ConfigPopulation attribute) n_iters (icolos.core.flow_control.iterator.IterSettings attribute) N_ITERS (icolos.utils.enums.step_enums.IteratorEnum attribute) N_ROUNDS (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) n_top_solutions (icolos.core.step_utils.gold_config.ConfigTermination attribute) n_tries (icolos.core.workflow_steps.step.StepFailurePolicyParameters attribute) NAME_CA (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) NAME_PREDICTED (icolos.utils.enums.step_enums.StepPredictorEnum attribute) NAME_PREDICTED_DEFAULT (icolos.utils.enums.step_enums.StepPredictorEnum attribute) names (icolos.core.step_utils.input_preparator.StepCSVInputColumnParameters attribute) ndx (icolos.core.containers.gmx_state.GromacsState attribute) NEG_IMAGE_EXT (icolos.utils.enums.step_enums.StepShaepEnum attribute) NEGATIVE_IMAGE_OUTPUT_FILE (icolos.utils.enums.program_parameters.ShaepEnum attribute) negative_images (icolos.core.workflow_steps.calculation.panther.StepPanther attribute) nested_get() (in module icolos.utils.general.convenience_functions) niche_siz (icolos.core.step_utils.gold_config.ConfigPopulation attribute) nname (icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems attribute) (icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping attribute) (icolos.core.workflow_steps.pmx.base.StepPMXBase attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute)

NNAME (icolos.utils.enums.program_parameters.StepPMXEnum attribute) NO_ALIGNMENT (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) NO_CHIRALITY (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) NO_H2H (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) NO_MCS (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) Node (class in icolos.core.containers.perturbation_map) Node.Config (class in icolos.core.containers.perturbation_map) node_connectivity (icolos.core.containers.perturbation_map.Node attribute) node_df (icolos.core.containers.perturbation_map.PerturbationMap attribute) NODE_FAIL (icolos.utils.enums.program_parameters.SlurmEnum attribute) node_from (icolos.core.containers.perturbation_map.Edge attribute) node_hash (icolos.core.containers.perturbation_map.Node attribute) NODE_HEADER_LINE (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) node_id (icolos.core.containers.perturbation_map.Node attribute) node_to (icolos.core.containers.perturbation_map.Edge attribute) nodes (icolos.core.containers.perturbation_map.PerturbationMap attribute) NOT_GENERATED (icolos.utils.enums.general_utils_enums.CheckFileGenerationEnum attribute) number (icolos.core.containers.gmx_state.AtomType attribute) number_poses (icolos.core.workflow_steps.autodockvina.docking.ADVConfiguration attribute) NUMBER_POSES (icolos.utils.enums.step_enums.StepAutoDockVinaEnum attribute)

O

O1 (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) O2 (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) OA (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) OB (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) OBABEL (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_INPUTFORMAT_PDB (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_INPUTFORMAT_PDBQT (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_INPUTFORMAT_SDF (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_INPUTFORMAT_XYZ (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_M (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_O (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_OUTPUT_FORMAT_PDB (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_OUTPUT_FORMAT_PDBQT (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_OUTPUT_FORMAT_SDF (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_OUTPUT_FORMAT_XYZ (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_P (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_PARTIALCHARGE (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_PARTIALCHARGE_GASTEIGER (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_X (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBABEL_X_R (icolos.utils.enums.program_parameters.OpenBabelEnum attribute) OBabelStructConvert (class in icolos.core.step_utils.obabel_structconvert) OFFITP (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) OITP (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) OMEGA (icolos.utils.enums.program_parameters.OMEGAEnum attribute) OMEGA_HELP (icolos.utils.enums.program_parameters.OMEGAEnum attribute) OMEGA_HELP_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.OMEGAEnum attribute) OMEGA_MODE_CLASSIC (icolos.utils.enums.program_parameters.OMEGAEnum attribute) OMEGA_MODE_DENSE (icolos.utils.enums.program_parameters.OMEGAEnum attribute)

OMEGA_MODE_MACROCYCLE (icolos.utils.enums.program_parameters.OMEGAEnum attribute) OMEGA_MODE_POSE (icolos.utils.enums.program_parameters.OMEGAEnum attribute) OMEGA_MODE_ROCS (icolos.utils.enums.program_parameters.OMEGAEnum attribute) OMEGAEnum (class in icolos.utils.enums.program_parameters) OMEGAExecutor (class in icolos.utils.execute_external.omega) OMEGAOutputEnum (class in icolos.utils.enums.program_parameters) OPDB1 (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) OPDB2 (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) OPDBM1 (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) OPDBM2 (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) OpenBabelEnum (class in icolos.utils.enums.program_parameters) OpenBabelExecutor (class in icolos.utils.execute_external.openbabel) OpenBabelOutputEnum (class in icolos.utils.enums.program_parameters) OPENFF (icolos.utils.enums.step_enums.StepGromacsEnum attribute) OPTBUILD_ENTRY_POINT (icolos.utils.enums.program_parameters.ModelBuilderEnum attribute) ORACLE_CONFIG (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) ORACLE_LABEL (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) ORACLE_TYPE (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) ORANGE (icolos.utils.general.citation_generator.ConsoleColours attribute) ORDER_ASCENDING (icolos.utils.enums.step_enums.StepRMSFilterEnum attribute) ORDER_BY (icolos.utils.enums.step_enums.StepRMSFilterEnum attribute) origin (icolos.core.step_utils.gold_config.ConfigFloodFill attribute) other_args (icolos.core.workflow_steps.step.StepExecutionResourceParameters attribute) OUTPUT_FILE (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) (icolos.utils.enums.step_enums.StepPantherEnum attribute) output_receptor_pdbqt (icolos.core.workflow_steps.autodockvina.target_preparation.ADVAdditionalTP attribute) OUTPUT_RECEPTOR_PDBQT (icolos.utils.enums.step_enums.StepAutoDockVinaTargetPreparationEnum attribute) OUTPUT_SDF_NAME (icolos.utils.enums.program_parameters.OMEGAOutputEnum attribute) OUTPUT_SIMILARITY (icolos.utils.enums.program_parameters.ShaepEnum attribute)

P

PAIRS (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) PANTHER_CONFIG (icolos.utils.enums.program_parameters.PantherEnum attribute) PANTHER_CONFIG_DIR (icolos.utils.enums.step_enums.StepPantherEnum attribute) PANTHER_CONFIG_FILE (icolos.utils.enums.step_enums.StepPantherEnum attribute) PANTHER_ENTRYPOINT (icolos.utils.enums.program_parameters.PantherEnum attribute) PANTHER_LOCATION (icolos.utils.enums.step_enums.StepPantherEnum attribute) PANTHER_OUTPUT_FILE (icolos.utils.enums.program_parameters.PantherEnum attribute) PANTHER_PTYHON2 (icolos.utils.enums.program_parameters.PantherEnum attribute) PantherEnum (class in icolos.utils.enums.program_parameters) parallel_execution (icolos.core.step_dispatch.dispatcher.StepDispatcher attribute) parallelization (icolos.core.workflow_steps.step.StepExecutionParameters attribute) ParallelizationEnum (class in icolos.utils.enums.parallelization) parallelize (icolos.core.flow_control.iterator.IterParallelizer attribute) (icolos.core.step_dispatch.dispatcher.IterParallelizer attribute) Parallelizer (class in icolos.utils.general.parallelization) parallelizer_settings (icolos.core.flow_control.iterator.IterSettings attribute) param_file (icolos.core.step_utils.gold_config.ConfigDataFiles attribute) PARAM_METHOD (icolos.utils.enums.step_enums.StepGromacsEnum attribute) parameters (icolos.core.flow_control.iterator.IterSettingsParameters attribute) (icolos.core.workflow_steps.step.StepSettingsArgsParameters attribute) parametrise_mols() (icolos.core.workflow_steps.openff.openff2gmx.StepOFF2gmx method) PARMED (icolos.utils.enums.step_enums.StepOpenFFEnum attribute) parse() (icolos.core.containers.gmx_state.GromacsState method) parse_global() (in module icolos.utils.entry_point_functions.parsing_functions) parse_header() (in module icolos.utils.entry_point_functions.parsing_functions) parse_map_file() (icolos.core.containers.perturbation_map.PerturbationMap method) parse_results() (icolos.core.workflow_steps.gromacs.mmpbsa.StepGMXmmpbsa method) parse_setuppy() (in module icolos.utils.general.convenience_functions) partition (icolos.core.workflow_steps.step.StepExecutionResourceParameters attribute) PARTITION (icolos.utils.enums.execution_enums.ExecutionPlatformEnum attribute) PATH (icolos.utils.enums.program_parameters.FepPlusEnum attribute) PATH_CONFIG_DEBUG (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) PATH_CONFIG_DEFAULT (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) PATH_CONFIG_TUTORIAL (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) PATH_CONFIG_VERBOSE (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) PATTERN (icolos.utils.enums.program_parameters.CosmoOutputEnum attribute) PDB (icolos.utils.enums.program_parameters.PMXEnum attribute) (icolos.utils.enums.write_out_enums.WriteOutEnum attribute) PDB2GMX (icolos.utils.enums.program_parameters.GromacsEnum attribute) PDB2GMX_FAIL_ID_STRING (icolos.utils.enums.program_parameters.GromacsEnum attribute) pdb2mae() (icolos.core.step_utils.structconvert.StructConvert method) PdbFixerEnum (class in icolos.utils.enums.program_parameters) PENDING (icolos.utils.enums.program_parameters.SlurmEnum attribute) PERSISTENCE_MODE (icolos.utils.enums.program_parameters.ModelBuilderEnum attribute) PERSISTENCE_MODE_PLAINSKLEARN (icolos.utils.enums.program_parameters.ModelBuilderEnum attribute) PERSISTENCE_MODE_SKLEARNWITHOPTUNAAZ (icolos.utils.enums.program_parameters.ModelBuilderEnum attribute) perturbation_map (icolos.core.composite_agents.workflow.WorkflowData attribute) (icolos.core.step_utils.input_preparator.StepInputParameters attribute) PerturbationMap (class in icolos.core.containers.perturbation_map) PerturbationMap.Config (class in icolos.core.containers.perturbation_map) pH (icolos.core.workflow_steps.autodockvina.target_preparation.ADVAdditionalTP attribute) PH (icolos.utils.enums.step_enums.StepAutoDockVinaTargetPreparationEnum attribute) PI (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) pickle_topol() (icolos.core.workflow_steps.gromacs.base.StepGromacsBase method) pipe_input (icolos.core.workflow_steps.step.StepExecutionParameters attribute) PIPE_INPUT (icolos.utils.enums.step_enums.StepBaseEnum attribute) platform (icolos.core.workflow_steps.step.StepExecutionParameters attribute) PMXAtomMappingEnum (class in icolos.utils.enums.program_parameters) PMXEnum (class in icolos.utils.enums.program_parameters) PMXExecutor (class in icolos.utils.execute_external.pmx) PMXLigandHybridEnum (class in icolos.utils.enums.program_parameters) pname (icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems attribute) (icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping attribute) (icolos.core.workflow_steps.pmx.base.StepPMXBase attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute)

PNAME (icolos.utils.enums.program_parameters.StepPMXEnum attribute) popsiz (icolos.core.step_utils.gold_config.ConfigPopulation attribute) population (icolos.core.workflow_steps.ccdc.docking.GoldConfiguration attribute) POPULATION (icolos.utils.enums.step_enums.StepGoldEnum attribute) POSE_INPUT (icolos.utils.enums.program_parameters.OMEGAEnum attribute) POSE_OUTPUT (icolos.utils.enums.program_parameters.OMEGAEnum attribute) POSE_PREFIX (icolos.utils.enums.program_parameters.OMEGAEnum attribute) POSE_PROGRESS (icolos.utils.enums.program_parameters.OMEGAEnum attribute) POSE_VERBOSE (icolos.utils.enums.program_parameters.OMEGAEnum attribute) POSEVIEWER (icolos.utils.enums.step_enums.StepPrimeEnum attribute) POSEVIEWER_FILE_KEY (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) posre (icolos.core.containers.gmx_state.GromacsState attribute) POSRE_LIG (icolos.utils.enums.step_enums.StepGromacsEnum attribute) POSTFIX (icolos.utils.enums.write_out_enums.RunVariablesEnum attribute) postprocess_bonds (icolos.core.step_utils.gold_config.ConfigFlags attribute) PREFIX (icolos.utils.enums.write_out_enums.RunVariablesEnum attribute) PREFIX_ENERGIES_XYZ (icolos.utils.enums.program_parameters.CrestOutputEnum attribute) prefix_execution (icolos.core.workflow_steps.step.StepExecutionParameters attribute) (icolos.utils.execute_external.license_token_guard.TokenGuardParameters attribute) prepare_batch_script() (icolos.utils.execute_external.slurm_executor.SlurmExecutor method) prepare_jobs() (icolos.core.workflow_steps.gromacs.mdrun.StepGMXMDrun method) prepare_simulation() (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations method) PREPARE_SIMULATIONS (icolos.utils.enums.program_parameters.PMXEnum attribute) PREPARE_TRANSITIONS (icolos.utils.enums.program_parameters.PMXEnum attribute) prepare_transitions() (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions method) PREPROCESS_MSJ (icolos.utils.enums.step_enums.StepDesmondEnum attribute) PREPWIZARD (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) PREPWIZARD_CALL (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) PREV_STEP (icolos.utils.enums.program_parameters.StepPMXEnum attribute) PRIMARY_COMPONENTS (icolos.utils.enums.program_parameters.GromacsEnum attribute) PRIME_HELP (icolos.utils.enums.program_parameters.PrimeEnum attribute) PRIME_HELP_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.PrimeEnum attribute) PRIME_MMGBSA (icolos.utils.enums.program_parameters.PrimeEnum attribute) PRIME_MMGBSA_TOTAL_ENERGY (icolos.utils.enums.program_parameters.PrimeEnum attribute) PRIME_MMGBSA_TOTAL_ENERGY_NS (icolos.utils.enums.program_parameters.PrimeEnum attribute) PRIME_NJOBS (icolos.utils.enums.program_parameters.PrimeEnum attribute) PRIME_OUTTYPE (icolos.utils.enums.program_parameters.PrimeEnum attribute) PRIME_OUTTYPE_LIGAND (icolos.utils.enums.program_parameters.PrimeEnum attribute) PRIME_WAIT (icolos.utils.enums.program_parameters.PrimeEnum attribute) PrimeEnum (class in icolos.utils.enums.program_parameters) PrimeExecutor (class in icolos.utils.execute_external.prime) print_citations() (in module icolos.utils.general.citation_generator) print_log_file() (in module icolos.utils.general.print_log) process_write_out() (icolos.core.workflow_steps.step.StepBase method) PRODUCTION_CFG (icolos.utils.enums.step_enums.StepDesmondEnum attribute) PRODUCTION_MSJ (icolos.utils.enums.step_enums.StepDesmondEnum attribute) properties (icolos.core.containers.gmx_state.GromacsState attribute) PROPERTIES (icolos.utils.enums.step_enums.StepBoltzmannWeightingEnum attribute) PROPERTIES_INPUT (icolos.utils.enums.step_enums.StepBoltzmannWeightingEnum attribute) PROPERTIES_OUTPUT (icolos.utils.enums.step_enums.StepBoltzmannWeightingEnum attribute) PROPERTY_NUM_AROMATIC_RINGS (icolos.utils.enums.program_parameters.FeatureCounterEnum attribute) PROPERTY_NUM_RINGS (icolos.utils.enums.program_parameters.FeatureCounterEnum attribute) PROPS (icolos.utils.enums.step_enums.StepGromacsEnum attribute) protein (icolos.core.containers.perturbation_map.PerturbationMap attribute) PROTEIN (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) protein_data (icolos.core.workflow_steps.ccdc.docking.GoldConfiguration attribute) PROTEIN_DATA (icolos.utils.enums.step_enums.StepGoldEnum attribute) protein_datafile (icolos.core.step_utils.gold_config.ConfigProteinData attribute) PROTEIN_DATAFILE (icolos.utils.enums.step_enums.StepGoldEnum attribute) PROTEIN_INTERACTION (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) PROTEIN_INTERACTION_CALL (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) PROTEIN_OTHER (icolos.utils.enums.step_enums.StepGromacsEnum attribute) PROTEIN_PDB (icolos.utils.enums.step_enums.StepGromacsEnum attribute) PROTEIN_TOP (icolos.utils.enums.step_enums.StepGromacsEnum attribute) PROX (icolos.utils.enums.program_parameters.KallistoEnum attribute) pt_crosswt (icolos.core.step_utils.gold_config.ConfigGeneticOperators attribute)

R

radius (icolos.core.step_utils.gold_config.ConfigFloodFill attribute) RANDOM (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) RANDOM_FOREST_REGRESSOR (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) randomize_smiles() (in module icolos.utils.smiles) RBFE (icolos.utils.enums.program_parameters.StepPMXEnum attribute) RDKIT_NAME (icolos.utils.enums.write_out_enums.WriteOutEnum attribute) RDKIT_PROTONATE (icolos.utils.enums.step_enums.StepEmbeddingEnum attribute) read_fitpts (icolos.core.step_utils.gold_config.ConfigDataFiles attribute) rearrange_input() (icolos.utils.general.parallelization.Parallelizer method) RECEPTOR (icolos.utils.enums.step_enums.StepDataManipulationEnum attribute) (icolos.utils.enums.step_enums.StepPrimeEnum attribute) RECEPTOR_MAEGZ (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) receptor_path (icolos.core.workflow_steps.autodockvina.docking.ADVConfiguration attribute) RED (icolos.utils.general.citation_generator.ConsoleColours attribute) REFERENCE_DG (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) reference_ligand_format (icolos.core.workflow_steps.autodockvina.target_preparation.ADVExtractBoxTP attribute) reference_ligand_path (icolos.core.workflow_steps.autodockvina.target_preparation.ADVExtractBoxTP attribute) relative_ligand_energy (icolos.core.step_utils.gold_config.ConfigFitnessFunctionSettings attribute) REMARK_TAG (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) (icolos.utils.enums.program_parameters.GoldEnum attribute) REMOVE_CHAINS (icolos.utils.enums.step_enums.StepPdbFixerEnum attribute) remove_folder() (in module icolos.utils.general.files_paths) REMOVE_RES (icolos.utils.enums.step_enums.StepPrepwizEnum attribute) remove_temporary_files (icolos.core.composite_agents.base_agent.AgentHeaderParametersSettings attribute) (icolos.core.flow_control.iterator.IterSettings attribute) REPLACE_NONSTANDARD_RESIDUES (icolos.utils.enums.step_enums.StepPdbFixerEnum attribute) replicas (icolos.core.containers.perturbation_map.PerturbationMap attribute) REPLICAS (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) (icolos.utils.enums.step_enums.StepGromacsEnum attribute) (icolos.utils.enums.step_enums.StepPMXSetupEnum attribute) res (icolos.core.containers.gmx_state.AtomType attribute) reset_all_ids() (icolos.core.containers.compound.Compound method) reset_conformer_ids() (icolos.core.containers.compound.Enumeration method) reset_enumeration_ids() (icolos.core.containers.compound.Compound method) resi (icolos.core.containers.gmx_state.AtomType attribute) resolve() (icolos.core.step_utils.run_variables_resolver.RunVariablesResolver method) resolve_compound_level() (icolos.core.step_utils.run_variables_resolver.RunVariablesResolver method) resolve_conformer_level() (icolos.core.step_utils.run_variables_resolver.RunVariablesResolver method) resolve_enumeration_level() (icolos.core.step_utils.run_variables_resolver.RunVariablesResolver method) resource (icolos.core.step_utils.step_writeout.StepWriteoutDestinationParameters attribute) resources (icolos.core.workflow_steps.step.StepExecutionParameters attribute) RESTRAINTS (icolos.utils.enums.step_enums.StepGromacsEnum attribute) result (icolos.core.step_utils.retry.RetryResult attribute) RESULT_DGA (icolos.utils.enums.program_parameters.JazzyEnum attribute) RESULT_DGP (icolos.utils.enums.program_parameters.JazzyEnum attribute) RESULT_DGTOT (icolos.utils.enums.program_parameters.JazzyEnum attribute) RESULT_LINE_IDENTIFIER (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) RESULT_LINE_POS_RMSDTOBEST_LB (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) RESULT_LINE_POS_RMSDTOBEST_UB (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) RESULT_LINE_POS_SCORE (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) RESULT_SA (icolos.utils.enums.program_parameters.JazzyEnum attribute)

RESULT_SDC (icolos.utils.enums.program_parameters.JazzyEnum attribute) RESULT_SDX (icolos.utils.enums.program_parameters.JazzyEnum attribute) RESULT_SMILES (icolos.utils.enums.program_parameters.JazzyEnum attribute) RESULT_STATUS (icolos.utils.enums.program_parameters.JazzyEnum attribute) RESULT_STATUS_SUCCESS (icolos.utils.enums.program_parameters.JazzyEnum attribute) results_all (icolos.core.workflow_steps.pmx.run_analysis.StepPMXRunAnalysis attribute) results_summary (icolos.core.workflow_steps.pmx.run_analysis.StepPMXRunAnalysis attribute) RETRAIN (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) RETRIES (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) retry() (in module icolos.core.step_utils.retry) retry_wait_seconds (icolos.core.workflow_steps.step.StepFailurePolicyParameters attribute) RetryResult (class in icolos.core.step_utils.retry) RetryResult.Config (class in icolos.core.step_utils.retry) RETURN_N (icolos.utils.enums.step_enums.StepFilterEnum attribute) RINGSONLY (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) RMS (icolos.utils.enums.program_parameters.GromacsEnum attribute) (icolos.utils.enums.program_parameters.KallistoEnum attribute) rms_tolerance (icolos.core.step_utils.gold_config.ConfigTermination attribute) RMSD_TAG (icolos.utils.enums.step_enums.StepRMSDEnum attribute) ROCS_INPUT (icolos.utils.enums.program_parameters.OMEGAEnum attribute) ROCS_OUTPUT (icolos.utils.enums.program_parameters.OMEGAEnum attribute) ROCS_PARAM (icolos.utils.enums.program_parameters.OMEGAEnum attribute) ROCS_PREFIX (icolos.utils.enums.program_parameters.OMEGAEnum attribute) ROCS_PROGRESS (icolos.utils.enums.program_parameters.OMEGAEnum attribute) ROCS_VERBOSE (icolos.utils.enums.program_parameters.OMEGAEnum attribute) rotatable_bond_override_file (icolos.core.step_utils.gold_config.ConfigFlags attribute) rotate_carboxylic_oh (icolos.core.step_utils.gold_config.ConfigFlags attribute) RUN_ANALYSIS (icolos.utils.enums.program_parameters.PMXEnum attribute) run_analysis() (icolos.core.workflow_steps.pmx.run_analysis.StepPMXRunAnalysis method) run_multidir_sim() (icolos.core.workflow_steps.gromacs.mdrun.StepGMXMDrun method) RUN_SIMULATIONS (icolos.utils.enums.program_parameters.PMXEnum attribute) run_single_tpr() (icolos.core.workflow_steps.gromacs.mdrun.StepGMXMDrun method) run_type (icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems attribute) (icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping attribute) (icolos.core.workflow_steps.pmx.base.StepPMXBase attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) RUN_TYPE (icolos.utils.enums.program_parameters.StepPMXEnum attribute) RUNNING (icolos.utils.enums.program_parameters.SlurmEnum attribute) RUNTIME_GLOBAL_VARIABLE_CONFIGDIR (icolos.utils.enums.entry_points.ExecutorEnum attribute) RUNTIME_GLOBAL_VARIABLE_ENTRYPOINTDIR (icolos.utils.enums.entry_points.ExecutorEnum attribute) RUNTIME_GLOBAL_VARIABLE_PACKAGEDIR (icolos.utils.enums.entry_points.ExecutorEnum attribute) RUNTIME_GLOBAL_VARIABLE_WORKDIR (icolos.utils.enums.entry_points.ExecutorEnum attribute) RunVariablesEnum (class in icolos.utils.enums.write_out_enums) RunVariablesResolver (class in icolos.core.step_utils.run_variables_resolver)

S

SAVE_DIR (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) save_lone_pairs (icolos.core.step_utils.gold_config.ConfigDataFiles attribute) save_options (icolos.core.workflow_steps.ccdc.docking.GoldConfiguration attribute) SAVE_OPTIONS (icolos.utils.enums.step_enums.StepGoldEnum attribute) save_protein_torsions (icolos.core.step_utils.gold_config.ConfigSaveOptions attribute) save_score_in_file (icolos.core.step_utils.gold_config.ConfigSaveOptions attribute) SBATCH (icolos.utils.enums.program_parameters.SlurmEnum attribute) SCDUMA (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) SCDUMD (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) SCDUMM (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) Scheduler (class in icolos.core.composite_agents.scheduler) SCHEDULER (icolos.utils.enums.composite_agents_enums.SchedulerEnum attribute) Scheduler.Config (class in icolos.core.composite_agents.scheduler) SchedulerEnum (class in icolos.utils.enums.composite_agents_enums) SchedulerHeaderParameters (class in icolos.core.composite_agents.scheduler) SCHRODINGER_MODULE (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SchrodingerExecutablesEnum (class in icolos.utils.enums.program_parameters) SchrodingerExecutor (class in icolos.utils.execute_external.schrodinger) SchrodingerLicenseTokenGuard (class in icolos.utils.execute_external.license_token_guard) SchrodingerLicenseTokenGuard.Config (class in icolos.utils.execute_external.license_token_guard) SCORE (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) score_param_file (icolos.core.step_utils.gold_config.ConfigFitnessFunctionSettings attribute) SDCONVERT (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDCONVERT_A (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDCONVERT_CALL (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDCONVERT_FORMAT_MAE (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDCONVERT_FORMAT_MM (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDCONVERT_FORMAT_PDB (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDCONVERT_FORMAT_SD (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDCONVERT_HELP (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDCONVERT_HELP_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDCONVERT_I (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDCONVERT_NOAROM (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDCONVERT_NOSTEREO (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDCONVERT_O (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDCONVERT_TITLE (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) SDConvertExecutor (class in icolos.utils.execute_external.sdconvert) SDConvertUtil (class in icolos.core.step_utils.sdconvert_util) SDF (icolos.utils.enums.write_out_enums.WriteOutEnum attribute) sdf2mae() (icolos.core.step_utils.sdconvert_util.SDConvertUtil method) sdf2pdb() (icolos.core.step_utils.obabel_structconvert.OBabelStructConvert method) (icolos.core.step_utils.sdconvert_util.SDConvertUtil method) (icolos.core.step_utils.structconvert.StructConvert method) SDF_INPUT (icolos.utils.enums.step_enums.StepPrimeEnum attribute) SDF_OUTPUT (icolos.utils.enums.step_enums.StepMacromodelEnum attribute) (icolos.utils.enums.step_enums.StepPrimeEnum attribute) search_space (icolos.core.workflow_steps.autodockvina.docking.ADVConfiguration attribute) seed (icolos.core.workflow_steps.autodockvina.docking.ADVConfiguration attribute) SELECT (icolos.utils.enums.program_parameters.GromacsEnum attribute) select_pressure (icolos.core.step_utils.gold_config.ConfigPopulation attribute) selected_tags (icolos.core.step_utils.step_writeout.StepWriteoutCompoundParameters attribute) SELECTION_TEXT (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) SERIAL (icolos.utils.enums.execution_enums.ExecutionPlatformEnum attribute) set_compound_number() (icolos.core.containers.compound.Compound method) set_compound_object() (icolos.core.containers.compound.Enumeration method) set_conformer() (icolos.core.containers.perturbation_map.Node method) set_conformer_id() (icolos.core.containers.compound.Conformer method) set_cpt() (icolos.core.containers.gmx_state.GromacsState method) set_data() (icolos.core.containers.generic.GenericData method) (icolos.core.step_utils.step_writeout.WriteOutHandler method) set_description() (icolos.core.composite_agents.base_agent.BaseAgent method) set_edr() (icolos.core.containers.gmx_state.GromacsState method) set_enumeration_id() (icolos.core.containers.compound.Enumeration method) set_enumeration_object() (icolos.core.containers.compound.Conformer method) set_extension() (icolos.core.containers.generic.GenericData method) set_file_name() (icolos.core.containers.generic.GenericData method) set_id() (icolos.core.composite_agents.base_agent.BaseAgent method) (icolos.core.containers.generic.GenericData method) set_job_id() (icolos.utils.general.parallelization.Subtask method) set_ligand_atom_types (icolos.core.step_utils.gold_config.ConfigDataFiles attribute) set_log() (icolos.core.containers.gmx_state.GromacsState method) set_max_tries() (icolos.utils.general.parallelization.SubtaskContainer method) set_molecule() (icolos.core.containers.compound.Conformer method) (icolos.core.containers.compound.Enumeration method) set_name() (icolos.core.containers.compound.Compound method) set_ndx() (icolos.core.containers.gmx_state.GromacsState method) set_node_id() (icolos.core.containers.perturbation_map.Node method) set_original_smile() (icolos.core.containers.compound.Enumeration method) set_perturbation_map() (icolos.core.composite_agents.workflow.WorkFlow method) set_protein_atom_types (icolos.core.step_utils.gold_config.ConfigDataFiles attribute) set_smile() (icolos.core.containers.compound.Enumeration method) set_status() (icolos.utils.general.parallelization.Subtask method) set_status_failed() (icolos.utils.general.parallelization.Subtask method) set_status_success() (icolos.utils.general.parallelization.Subtask method) set_step_id() (icolos.core.workflow_steps.step.StepBase method) set_structure() (icolos.core.containers.gmx_state.GromacsState method) set_topol() (icolos.core.containers.gmx_state.GromacsState method) set_tpr() (icolos.core.containers.gmx_state.GromacsState method) set_trajectory() (icolos.core.containers.gmx_state.GromacsState method) set_workflow_data() (icolos.core.step_utils.step_writeout.WriteOutHandler method) set_workflow_object() (icolos.core.workflow_steps.step.StepBase method) settings (icolos.core.flow_control.flow_control.BaseStepConfig attribute) (icolos.core.flow_control.iterator.IterSettings attribute) (icolos.core.workflow_steps.calculation.base.StepCalculationBase attribute) (icolos.core.workflow_steps.calculation.boltzmann_weighting.StepBoltzmannWeighting attribute) (icolos.core.workflow_steps.calculation.clustering.StepClustering attribute) (icolos.core.workflow_steps.calculation.cosmo.StepCosmo attribute) (icolos.core.workflow_steps.calculation.cresset_ec.StepCressetEC attribute) (icolos.core.workflow_steps.calculation.esp_sim.StepEspSim attribute) (icolos.core.workflow_steps.calculation.feature_counter.StepFeatureCounter attribute) (icolos.core.workflow_steps.calculation.rms_filter.StepRMSFilter attribute) (icolos.core.workflow_steps.calculation.rmsd.StepRMSD attribute) (icolos.core.workflow_steps.calculation.shaep.StepShaep attribute) (icolos.core.workflow_steps.calculation.turbomole.StepTurbomole attribute) (icolos.core.workflow_steps.confgen.base.StepConfgenBase attribute) (icolos.core.workflow_steps.confgen.crest.StepCREST attribute) (icolos.core.workflow_steps.confgen.omega.StepOmega attribute) (icolos.core.workflow_steps.confgen.xtb.StepXTB attribute) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket attribute) (icolos.core.workflow_steps.gromacs.base.StepGromacsBase attribute) (icolos.core.workflow_steps.gromacs.cluster.StepGMXCluster attribute) (icolos.core.workflow_steps.gromacs.clusters_ts.StepClusterTS attribute) (icolos.core.workflow_steps.gromacs.do_dssp.StepGMXDoDSSP attribute) (icolos.core.workflow_steps.gromacs.editconf.StepGMXEditConf attribute) (icolos.core.workflow_steps.gromacs.genion.StepGMXGenion attribute) (icolos.core.workflow_steps.gromacs.mmpbsa.StepGMXmmpbsa attribute) (icolos.core.workflow_steps.gromacs.rsmd.StepGMXrmsd attribute) (icolos.core.workflow_steps.gromacs.select.StepGMXselect attribute) (icolos.core.workflow_steps.gromacs.solvate.StepGMXSolvate attribute) (icolos.core.workflow_steps.gromacs.trajcat.StepGMXTrjcat attribute) (icolos.core.workflow_steps.gromacs.trjconv.StepGMXTrjconv attribute) (icolos.core.workflow_steps.io.base.StepIOBase attribute) (icolos.core.workflow_steps.io.data_manipulation.StepDataManipulation attribute) (icolos.core.workflow_steps.io.embedder.StepEmbedding attribute) (icolos.core.workflow_steps.io.initialize_compound.StepInitializeCompound attribute) (icolos.core.workflow_steps.openff.openff2gmx.StepOFF2gmx attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) (icolos.core.workflow_steps.prediction.model_building.StepModelBuilder attribute) (icolos.core.workflow_steps.prediction.predictor.StepPredictor attribute) (icolos.core.workflow_steps.schrodinger.fep_analysis.StepFepPlusAnalysis attribute) (icolos.core.workflow_steps.schrodinger.fep_base.StepFEPBase attribute) (icolos.core.workflow_steps.schrodinger.fep_plus_execution.StepFepPlusExec attribute) (icolos.core.workflow_steps.schrodinger.ligprep.StepLigprep attribute) (icolos.core.workflow_steps.schrodinger.macromodel.StepMacromodel attribute) (icolos.core.workflow_steps.schrodinger.prepwizard.StepPrepwizard attribute) (icolos.core.workflow_steps.schrodinger.protein_interaction.StepProteinInteraction attribute) (icolos.core.workflow_steps.schrodinger.residue_scanning.StepResidueScanning attribute) (icolos.core.workflow_steps.step.StepBase attribute) (icolos.core.workflow_steps.structure_prediction.dssp.StepDSSP attribute) (icolos.core.workflow_steps.structure_prediction.pdb_fixer.StepPdbFixer attribute) (icolos.core.workflow_steps.structure_prediction.peptide_embedder.StepPeptideEmbedder attribute) SETTINGS (icolos.utils.enums.step_enums.StepBaseEnum attribute) SETTINGS_ADDITIONAL (icolos.utils.enums.step_enums.StepBaseEnum attribute) SETTINGS_ARGUMENTS (icolos.utils.enums.step_enums.StepBaseEnum attribute) SETTINGS_ARGUMENTS_FLAGS (icolos.utils.enums.step_enums.StepBaseEnum attribute) SETTINGS_ARGUMENTS_PARAMETERS (icolos.utils.enums.step_enums.StepBaseEnum attribute) SETUP_MSJ_FIELDS (icolos.utils.enums.step_enums.StepDesmondEnum attribute) SHAEP_EXECUTABLE (icolos.utils.enums.program_parameters.ShaepEnum attribute) ShaepEnum (class in icolos.utils.enums.program_parameters) SHIFT (icolos.utils.enums.program_parameters.KallistoEnum attribute) SILENT (icolos.utils.enums.program_parameters.KallistoEnum attribute) SIM_COMPLETE (icolos.utils.enums.step_enums.StepGromacsEnum attribute) sim_type (icolos.core.workflow_steps.pmx.run_simulations.StepPMXRunSimulations attribute) SIM_TYPE (icolos.utils.enums.program_parameters.StepPMXEnum attribute) sim_types (icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems attribute) (icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping attribute) (icolos.core.workflow_steps.pmx.base.StepPMXBase attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) SIM_TYPES (icolos.utils.enums.program_parameters.StepPMXEnum attribute) SIMILARITY (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) SIMULATION_PROTOCOL (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) SINGLE (icolos.utils.enums.step_enums.IteratorEnum attribute) single_directory (icolos.core.composite_agents.base_agent.AgentHeaderParametersSettings attribute) (icolos.core.flow_control.iterator.IterSettings attribute) size_x (icolos.core.workflow_steps.autodockvina.docking.ADVSearchSpace attribute) size_y (icolos.core.workflow_steps.autodockvina.docking.ADVSearchSpace attribute) size_z (icolos.core.workflow_steps.autodockvina.docking.ADVSearchSpace attribute) SLURM (icolos.utils.enums.execution_enums.ExecutionPlatformEnum attribute) SlurmEnum (class in icolos.utils.enums.program_parameters) SlurmExecutor (class in icolos.utils.execute_external.slurm_executor) smiles (icolos.core.step_utils.input_preparator.StepCSVInputColumnParameters attribute) SMILES (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) snapCoreRmsd (icolos.core.containers.perturbation_map.Edge attribute) SOAP_VECTOR (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) softbond (icolos.core.containers.perturbation_map.Edge attribute) SOLVATE (icolos.utils.enums.program_parameters.GromacsEnum attribute) solvate_all (icolos.core.step_utils.gold_config.ConfigFlags attribute) SOLVENT_BLOCK_BODY_ANNOTATIONS (icolos.utils.enums.program_parameters.CosmoOutputEnum attribute) SOLVENT_BLOCK_BODY_START_PATTERN (icolos.utils.enums.program_parameters.CosmoOutputEnum attribute) SOLVENT_BLOCK_CURRENT_FRACTION_VALUE (icolos.utils.enums.program_parameters.CosmoOutputEnum attribute) SOLVENT_BLOCK_HEADER_COMPOUNDS_PATTERN (icolos.utils.enums.program_parameters.CosmoOutputEnum attribute) SOLVENT_BLOCK_HEADER_MOLFRACTION_PATTERN (icolos.utils.enums.program_parameters.CosmoOutputEnum attribute) SOLVENT_BLOCK_PATTERN_STRING (icolos.utils.enums.program_parameters.CosmoOutputEnum attribute) SOLVENT_BLOCK_START_PATTERN (icolos.utils.enums.program_parameters.CosmoOutputEnum attribute) SOLVENT_REPLACEHOLDER (icolos.utils.enums.program_parameters.CosmoOutputEnum attribute) SOLVENT_TRANSLATE_SOLVENT (icolos.utils.enums.program_parameters.CosmoOutputEnum attribute) SOLVENTS (icolos.utils.enums.program_parameters.GromacsEnum attribute) SORT (icolos.utils.enums.program_parameters.KallistoEnum attribute) sort_conformers() (icolos.core.containers.compound.Enumeration method) source (icolos.core.step_utils.input_preparator.StepInputSource attribute) source_field (icolos.core.step_utils.input_preparator.StepInputSource attribute) SOURCE_FIELD_COMPOUNDS (icolos.utils.enums.input_enums.InputEnum attribute) source_type (icolos.core.step_utils.input_preparator.StepInputSource attribute) SPLIT (icolos.utils.enums.program_parameters.PMXLigandHybridEnum attribute) start_vdw_linear_cutoff (icolos.core.step_utils.gold_config.ConfigFitnessFunctionSettings attribute) STATE (icolos.utils.enums.program_parameters.SlurmEnum attribute) states (icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems attribute) (icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping attribute) (icolos.core.workflow_steps.pmx.base.StepPMXBase attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) status (icolos.core.containers.perturbation_map.Edge attribute) (icolos.utils.general.parallelization.Subtask attribute) STATUS_FAILED (icolos.utils.enums.parallelization.ParallelizationEnum attribute) STATUS_READY (icolos.utils.enums.parallelization.ParallelizationEnum attribute) STATUS_RUNNING (icolos.utils.enums.parallelization.ParallelizationEnum attribute) STATUS_SUCCESS (icolos.utils.enums.parallelization.ParallelizationEnum attribute) STD_CPT (icolos.utils.enums.step_enums.StepGromacsEnum attribute) STD_EDR (icolos.utils.enums.step_enums.StepGromacsEnum attribute) STD_INDEX (icolos.utils.enums.step_enums.StepGromacsEnum attribute) STD_LOG (icolos.utils.enums.step_enums.StepGromacsEnum attribute) STD_STRUCTURE (icolos.utils.enums.step_enums.StepGromacsEnum attribute) STD_TOPOL (icolos.utils.enums.step_enums.StepGromacsEnum attribute) STD_TPR (icolos.utils.enums.step_enums.StepGromacsEnum attribute) STD_TRR (icolos.utils.enums.step_enums.StepGromacsEnum attribute) STD_XTC (icolos.utils.enums.step_enums.StepGromacsEnum attribute) STEP_ACTIVE_LEARNING (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_AUTODOCKVINA_DOCKING (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_AUTODOCKVINA_TARGET_PREPARATION (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_BOLTZMANN_WEIGHTING (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_CLUSTER (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_CLUSTERING (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_COSMO (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_CREST (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_DATA_MANIPULATION (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_DESMOND (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_DESMOND_SETUP (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_DISPATCHER (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_DO_DSSP (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_DSSP (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_EDITCONF (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_EMBEDDING (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_ESP_SIM (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_FEATURE_COUNTER (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_FEP_ABSOLUTE (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_FEP_PLUS_ANALYSIS (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_FEP_PLUS_EXEC (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_FEP_PLUS_SETUP (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_FILTER (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_GENION (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_GLIDE (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_GMX_MMPBSA (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_GMX_RMSD (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_GOLD_DOCKING (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_GROMPP (icolos.utils.enums.step_enums.StepBaseEnum attribute) step_id (icolos.core.flow_control.flow_control.BaseStepConfig attribute) (icolos.core.workflow_steps.calculation.base.StepCalculationBase attribute) (icolos.core.workflow_steps.calculation.boltzmann_weighting.StepBoltzmannWeighting attribute) (icolos.core.workflow_steps.calculation.clustering.StepClustering attribute) (icolos.core.workflow_steps.calculation.cosmo.StepCosmo attribute) (icolos.core.workflow_steps.calculation.cresset_ec.StepCressetEC attribute) (icolos.core.workflow_steps.calculation.esp_sim.StepEspSim attribute) (icolos.core.workflow_steps.calculation.feature_counter.StepFeatureCounter attribute) (icolos.core.workflow_steps.calculation.rms_filter.StepRMSFilter attribute) (icolos.core.workflow_steps.calculation.rmsd.StepRMSD attribute) (icolos.core.workflow_steps.calculation.shaep.StepShaep attribute) (icolos.core.workflow_steps.calculation.turbomole.StepTurbomole attribute) (icolos.core.workflow_steps.confgen.base.StepConfgenBase attribute) (icolos.core.workflow_steps.confgen.crest.StepCREST attribute) (icolos.core.workflow_steps.confgen.omega.StepOmega attribute) (icolos.core.workflow_steps.confgen.xtb.StepXTB attribute) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket attribute) (icolos.core.workflow_steps.gromacs.base.StepGromacsBase attribute) (icolos.core.workflow_steps.gromacs.cluster.StepGMXCluster attribute) (icolos.core.workflow_steps.gromacs.clusters_ts.StepClusterTS attribute) (icolos.core.workflow_steps.gromacs.do_dssp.StepGMXDoDSSP attribute) (icolos.core.workflow_steps.gromacs.editconf.StepGMXEditConf attribute) (icolos.core.workflow_steps.gromacs.genion.StepGMXGenion attribute) (icolos.core.workflow_steps.gromacs.mmpbsa.StepGMXmmpbsa attribute) (icolos.core.workflow_steps.gromacs.rsmd.StepGMXrmsd attribute) (icolos.core.workflow_steps.gromacs.select.StepGMXselect attribute) (icolos.core.workflow_steps.gromacs.solvate.StepGMXSolvate attribute) (icolos.core.workflow_steps.gromacs.trajcat.StepGMXTrjcat attribute) (icolos.core.workflow_steps.gromacs.trjconv.StepGMXTrjconv attribute) (icolos.core.workflow_steps.io.base.StepIOBase attribute) (icolos.core.workflow_steps.io.data_manipulation.StepDataManipulation attribute) (icolos.core.workflow_steps.io.embedder.StepEmbedding attribute) (icolos.core.workflow_steps.io.initialize_compound.StepInitializeCompound attribute) (icolos.core.workflow_steps.openff.openff2gmx.StepOFF2gmx attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) (icolos.core.workflow_steps.prediction.model_building.StepModelBuilder attribute) (icolos.core.workflow_steps.prediction.predictor.StepPredictor attribute) (icolos.core.workflow_steps.schrodinger.fep_analysis.StepFepPlusAnalysis attribute) (icolos.core.workflow_steps.schrodinger.fep_base.StepFEPBase attribute) (icolos.core.workflow_steps.schrodinger.fep_plus_execution.StepFepPlusExec attribute) (icolos.core.workflow_steps.schrodinger.ligprep.StepLigprep attribute) (icolos.core.workflow_steps.schrodinger.macromodel.StepMacromodel attribute) (icolos.core.workflow_steps.schrodinger.prepwizard.StepPrepwizard attribute) (icolos.core.workflow_steps.schrodinger.protein_interaction.StepProteinInteraction attribute) (icolos.core.workflow_steps.schrodinger.residue_scanning.StepResidueScanning attribute) (icolos.core.workflow_steps.step.StepBase attribute) (icolos.core.workflow_steps.structure_prediction.dssp.StepDSSP attribute) (icolos.core.workflow_steps.structure_prediction.pdb_fixer.StepPdbFixer attribute) (icolos.core.workflow_steps.structure_prediction.peptide_embedder.StepPeptideEmbedder attribute)

STEP_INIT_DICT (icolos.utils.enums.step_initialization_enum.StepInitializationEnum attribute) STEP_INITIALIZATION (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_ITERATOR (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_JAZZY (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_KALLISTO (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_LIGPREP (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_LOMAP (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_MACROMODEL (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_MDPOCKET (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_MDRUN (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_MODEL_BUILDING (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_OMEGA (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PANTHER (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PDB2GMX (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PDB_FIXER (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PEPTIDE_EMBEDDER (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PKA_PREDICTION (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_ABFE_SETUP (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_ANALYSE (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_ASSEMBLE_SYSTEMS (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_ATOMMAPPING (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_BOX_WATER_IONS (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_DOUBLEBOX (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_GENLIB (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_GENTOP (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_LIGANDHYBRID (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_MUTATE (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_PREPARE_SIMULATIONS (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_PREPARE_TRANSITIONS (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_RUN_ANALYSIS (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_RUN_SIMULATIONS (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PMX_SETUP (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PREDICTION (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PREPWIZARD (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PRIME (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PROSPECTIVE_REINVENT (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_PROTEIN_INTERACTIONS (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_RESIDUE_SCANNING (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_RMSD (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_RMSFILTER (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_SCHEMA (icolos.utils.enums.general_utils_enums.JSONSchemasEnum attribute) STEP_SHAEP (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_SOLVATE (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_TRJCAT (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_TRJCONV (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_TS_CLUSTER (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_TURBOMOLE (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_TYPE (icolos.utils.enums.step_enums.StepBaseEnum attribute) STEP_XTB (icolos.utils.enums.step_enums.StepBaseEnum attribute) StepActiveLearningEnum (class in icolos.utils.enums.step_enums) StepAutoDockVina (class in icolos.core.workflow_steps.autodockvina.docking) StepAutoDockVinaEnum (class in icolos.utils.enums.step_enums) StepAutoDockVinaTargetPreparation (class in icolos.core.workflow_steps.autodockvina.target_preparation) StepAutoDockVinaTargetPreparationEnum (class in icolos.utils.enums.step_enums) StepBase (class in icolos.core.workflow_steps.step) StepBase.Config (class in icolos.core.workflow_steps.step) StepBaseEnum (class in icolos.utils.enums.step_enums) StepBoltzmannWeighting (class in icolos.core.workflow_steps.calculation.boltzmann_weighting) StepBoltzmannWeightingEnum (class in icolos.utils.enums.step_enums) StepCalculationBase (class in icolos.core.workflow_steps.calculation.base) StepCavExploreEnum (class in icolos.utils.enums.step_enums) StepClustering (class in icolos.core.workflow_steps.calculation.clustering) StepClusteringEnum (class in icolos.utils.enums.step_enums) StepClusterTS (class in icolos.core.workflow_steps.gromacs.clusters_ts) StepConfgenBase (class in icolos.core.workflow_steps.confgen.base) StepCosmo (class in icolos.core.workflow_steps.calculation.cosmo) StepCressetEC (class in icolos.core.workflow_steps.calculation.cresset_ec) StepCressetEnum (class in icolos.utils.enums.step_enums) StepCREST (class in icolos.core.workflow_steps.confgen.crest) StepCSVInputColumnParameters (class in icolos.core.step_utils.input_preparator) StepData (class in icolos.core.step_utils.input_preparator) StepData.Config (class in icolos.core.step_utils.input_preparator) StepDataManipulation (class in icolos.core.workflow_steps.io.data_manipulation) StepDataManipulationEnum (class in icolos.utils.enums.step_enums) StepDesmondEnum (class in icolos.utils.enums.step_enums) StepDesmondExec (class in icolos.core.workflow_steps.schrodinger.desmond_exec) StepDesmondExec.Config (class in icolos.core.workflow_steps.schrodinger.desmond_exec) StepDesmondSetup (class in icolos.core.workflow_steps.schrodinger.desmond_preprocessor) StepDesmondSetup.Config (class in icolos.core.workflow_steps.schrodinger.desmond_preprocessor) StepDispatcher (class in icolos.core.step_dispatch.dispatcher) StepDSSP (class in icolos.core.workflow_steps.structure_prediction.dssp) StepDSSPEnum (class in icolos.utils.enums.step_enums) StepEmbedding (class in icolos.core.workflow_steps.io.embedder) StepEmbeddingEnum (class in icolos.utils.enums.step_enums) StepEspSim (class in icolos.core.workflow_steps.calculation.esp_sim) StepExecutionParameters (class in icolos.core.workflow_steps.step) StepExecutionParameters.StepExecutionParallelizationParameters (class in icolos.core.workflow_steps.step) StepExecutionResourceParameters (class in icolos.core.workflow_steps.step) StepFailed StepFailurePolicyParameters (class in icolos.core.workflow_steps.step) StepFeatureCounter (class in icolos.core.workflow_steps.calculation.feature_counter) StepFeatureCounterEnum (class in icolos.utils.enums.step_enums) StepFEPBase (class in icolos.core.workflow_steps.schrodinger.fep_base) StepFepPlusAnalysis (class in icolos.core.workflow_steps.schrodinger.fep_analysis) StepFepPlusEnum (class in icolos.utils.enums.step_enums) StepFepPlusExec (class in icolos.core.workflow_steps.schrodinger.fep_plus_execution) StepFepPlusExec.Config (class in icolos.core.workflow_steps.schrodinger.fep_plus_execution) StepFepPlusSetup (class in icolos.core.workflow_steps.schrodinger.fep_plus_setup) StepFilterEnum (class in icolos.utils.enums.step_enums) StepFpocketBase (class in icolos.core.workflow_steps.fpocket.base) StepGlide (class in icolos.core.workflow_steps.schrodinger.glide) StepGlide.Config (class in icolos.core.workflow_steps.schrodinger.glide) StepGlideEnum (class in icolos.utils.enums.step_enums) StepGMXCluster (class in icolos.core.workflow_steps.gromacs.cluster) StepGMXDoDSSP (class in icolos.core.workflow_steps.gromacs.do_dssp) StepGMXEditConf (class in icolos.core.workflow_steps.gromacs.editconf) StepGMXGenion (class in icolos.core.workflow_steps.gromacs.genion) StepGMXGrompp (class in icolos.core.workflow_steps.gromacs.grompp) StepGMXGrompp.Config (class in icolos.core.workflow_steps.gromacs.grompp) StepGMXMDrun (class in icolos.core.workflow_steps.gromacs.mdrun) StepGMXmmpbsa (class in icolos.core.workflow_steps.gromacs.mmpbsa) StepGMXPdb2gmx (class in icolos.core.workflow_steps.gromacs.pdb2gmx) StepGMXPdb2gmx.Config (class in icolos.core.workflow_steps.gromacs.pdb2gmx) StepGMXrmsd (class in icolos.core.workflow_steps.gromacs.rsmd) StepGMXselect (class in icolos.core.workflow_steps.gromacs.select) StepGMXSolvate (class in icolos.core.workflow_steps.gromacs.solvate) StepGMXTrjcat (class in icolos.core.workflow_steps.gromacs.trajcat) StepGMXTrjconv (class in icolos.core.workflow_steps.gromacs.trjconv) StepGold (class in icolos.core.workflow_steps.ccdc.docking) StepGoldEnum (class in icolos.utils.enums.step_enums) StepGoldTargetPreparationEnum (class in icolos.utils.enums.step_enums) StepGromacsBase (class in icolos.core.workflow_steps.gromacs.base) StepGromacsEnum (class in icolos.utils.enums.step_enums) STEPID (icolos.utils.enums.step_enums.StepBaseEnum attribute) StepInitializationEnum (class in icolos.utils.enums.step_initialization_enum) StepInitializeCompound (class in icolos.core.workflow_steps.io.initialize_compound) StepInputEnforceIDs (class in icolos.core.step_utils.input_preparator) StepInputParameters (class in icolos.core.step_utils.input_preparator) StepInputSource (class in icolos.core.step_utils.input_preparator) StepIOBase (class in icolos.core.workflow_steps.io.base) StepIterator (class in icolos.core.flow_control.iterator) StepJazzy (class in icolos.core.workflow_steps.calculation.jazzy) StepJazzyEnum (class in icolos.utils.enums.step_enums) StepKallisto (class in icolos.core.workflow_steps.calculation.kallisto) StepKallistoEnum (class in icolos.utils.enums.step_enums) StepLigprep (class in icolos.core.workflow_steps.schrodinger.ligprep) StepLigprep.Config (class in icolos.core.workflow_steps.schrodinger.ligprep) StepLigprepEnum (class in icolos.utils.enums.step_enums) StepLogger (class in icolos.loggers.steplogger) StepLomap (class in icolos.core.workflow_steps.calculation.lomap) StepMacromodel (class in icolos.core.workflow_steps.schrodinger.macromodel) StepMacromodel.Config (class in icolos.core.workflow_steps.schrodinger.macromodel) StepMacromodelEnum (class in icolos.utils.enums.step_enums) StepMDpocket (class in icolos.core.workflow_steps.fpocket.mdpocket) StepMerge (class in icolos.core.step_utils.input_merger) StepModelBuilder (class in icolos.core.workflow_steps.prediction.model_building) StepModelBuilderEnum (class in icolos.utils.enums.step_enums) StepOFF2gmx (class in icolos.core.workflow_steps.openff.openff2gmx) StepOmega (class in icolos.core.workflow_steps.confgen.omega) StepOpenFFEnum (class in icolos.utils.enums.step_enums) StepPanther (class in icolos.core.workflow_steps.calculation.panther) StepPantherEnum (class in icolos.utils.enums.step_enums) StepPdbFixer (class in icolos.core.workflow_steps.structure_prediction.pdb_fixer) StepPdbFixerEnum (class in icolos.utils.enums.step_enums) StepPeptideEmbedder (class in icolos.core.workflow_steps.structure_prediction.peptide_embedder) StepPMXabfe (class in icolos.core.workflow_steps.pmx.abfe) StepPMXAssembleSystems (class in icolos.core.workflow_steps.pmx.assemble_systems) StepPMXatomMapping (class in icolos.core.workflow_steps.pmx.atomMapping) StepPMXBase (class in icolos.core.workflow_steps.pmx.base) StepPMXBoxWaterIons (class in icolos.core.workflow_steps.pmx.box_water_ions) StepPMXdoublebox (class in icolos.core.workflow_steps.pmx.doublebox) StepPMXEnum (class in icolos.utils.enums.program_parameters) StepPMXgenlib (class in icolos.core.workflow_steps.pmx.genlib) StepPMXgentop (class in icolos.core.workflow_steps.pmx.gentop) StepPMXligandHybrid (class in icolos.core.workflow_steps.pmx.ligandHybrid) StepPMXmutate (class in icolos.core.workflow_steps.pmx.mutate) StepPMXPrepareSimulations (class in icolos.core.workflow_steps.pmx.prepare_simulations) StepPMXPrepareTransitions (class in icolos.core.workflow_steps.pmx.prepare_transitions) StepPMXRunAnalysis (class in icolos.core.workflow_steps.pmx.run_analysis) StepPMXRunAnalysis.Config (class in icolos.core.workflow_steps.pmx.run_analysis) StepPMXRunSimulations (class in icolos.core.workflow_steps.pmx.run_simulations) StepPMXSetup (class in icolos.core.workflow_steps.pmx.setup_workpath) StepPMXSetupEnum (class in icolos.utils.enums.step_enums) StepPredictor (class in icolos.core.workflow_steps.prediction.predictor) StepPredictorEnum (class in icolos.utils.enums.step_enums) StepPrepwizard (class in icolos.core.workflow_steps.schrodinger.prepwizard) StepPrepwizEnum (class in icolos.utils.enums.step_enums) StepPrime (class in icolos.core.workflow_steps.schrodinger.prime) StepPrime.Config (class in icolos.core.workflow_steps.schrodinger.prime) StepPrimeEnum (class in icolos.utils.enums.step_enums) StepProteinInteraction (class in icolos.core.workflow_steps.schrodinger.protein_interaction) StepResidueScanning (class in icolos.core.workflow_steps.schrodinger.residue_scanning) StepRMSD (class in icolos.core.workflow_steps.calculation.rmsd) StepRMSDEnum (class in icolos.utils.enums.step_enums) StepRMSFilter (class in icolos.core.workflow_steps.calculation.rms_filter) StepRMSFilterEnum (class in icolos.utils.enums.step_enums) steps (icolos.core.composite_agents.workflow.WorkFlow attribute) STEPS (icolos.utils.enums.composite_agents_enums.BaseAgentEnum attribute) STEPS_SCHEMA (icolos.utils.enums.general_utils_enums.JSONSchemasEnum attribute) StepSchrodingerAbsoluteFEP (class in icolos.core.workflow_steps.schrodinger.fep_absolute) StepSchrodingerBase (class in icolos.core.workflow_steps.schrodinger.base) StepSettingsArgsParameters (class in icolos.core.workflow_steps.step) StepSettingsParameters (class in icolos.core.workflow_steps.step) StepShaep (class in icolos.core.workflow_steps.calculation.shaep) StepShaepEnum (class in icolos.utils.enums.step_enums) StepTurbomole (class in icolos.core.workflow_steps.calculation.turbomole) StepTurbomoleEnum (class in icolos.utils.enums.step_enums) StepWriteoutCompoundAggregationParameters (class in icolos.core.step_utils.step_writeout) StepWriteoutCompoundParameters (class in icolos.core.step_utils.step_writeout) StepWriteoutDestinationParameters (class in icolos.core.step_utils.step_writeout) StepWriteoutGenericParameters (class in icolos.core.step_utils.step_writeout) StepWriteoutGromacsParameters (class in icolos.core.step_utils.step_writeout) StepWriteoutParameters (class in icolos.core.step_utils.step_writeout) StepXTB (class in icolos.core.workflow_steps.confgen.xtb) STM (icolos.utils.enums.program_parameters.KallistoEnum attribute) str2bool() (in module icolos.utils.general.arparse_bool_extension) STRICT (icolos.utils.enums.program_parameters.StepPMXEnum attribute) strict_execution (icolos.core.containers.perturbation_map.PerturbationMap attribute) StringFile (class in icolos.core.step_utils.input_preparator) stringify() (in module icolos.utils.general.strings) StringPath (class in icolos.core.step_utils.input_preparator) STRUCT_SPLIT (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCT_SPLIT_BASE (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) STRUCT_SPLIT_CALL (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCTCAT (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCTCAT_CALL (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCTCAT_FORMAT_MAE (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCTCAT_FORMAT_MOL2 (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCTCAT_FORMAT_PDB (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCTCAT_FORMAT_SD (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCTCAT_FORMAT_SDF (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCTCAT_HELP (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCTCAT_HELP_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCTCAT_I (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCTCAT_MAEGZ_OUTFILE (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) STRUCTCAT_O (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCTCAT_SDF_OUTFILE (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) StructcatExecutor (class in icolos.utils.execute_external.structcat) StructcatUtil (class in icolos.core.step_utils.structcat_util) StructConvert (class in icolos.core.step_utils.structconvert) STRUCTCONVERT (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) STRUCTCONVERT_CALL (icolos.utils.enums.program_parameters.SchrodingerExecutablesEnum attribute) structures (icolos.core.containers.gmx_state.GromacsState attribute) Subtask (class in icolos.utils.general.parallelization) SubtaskContainer (class in icolos.utils.general.parallelization) subtasks (icolos.utils.general.parallelization.SubtaskContainer attribute) success (icolos.core.step_utils.retry.RetryResult attribute) SUCCESS (icolos.utils.enums.program_parameters.XTBOutputEnum attribute) (icolos.utils.enums.step_enums.StepCressetEnum attribute) (icolos.utils.enums.step_enums.StepJazzyEnum attribute) (icolos.utils.enums.step_enums.StepKallistoEnum attribute) (icolos.utils.enums.step_enums.StepTurbomoleEnum attribute) SUPPORT_VECTOR_REGRESSOR (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) SURROGATE_MODEL_TYPE (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) SWAP (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) system (icolos.core.containers.gmx_state.GromacsState attribute) SYSTEM (icolos.utils.enums.program_parameters.GromacsEnum attribute)

T

TAG_ESP_SIMILARITY (icolos.utils.enums.program_parameters.ShaepEnum attribute) TAG_SHAPE_SIMILARITY (icolos.utils.enums.program_parameters.ShaepEnum attribute) TANIMOTO (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) TANIMOTO_TRUE_BELIEVER (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) target_field (icolos.core.step_utils.input_preparator.StepInputSource attribute) TARGET_FIELD_COMPOUNDS (icolos.utils.enums.input_enums.InputEnum attribute) TARGET_FIELD_CONFORMERS (icolos.utils.enums.input_enums.InputEnum attribute) tasks (icolos.core.workflow_steps.step.StepExecutionResourceParameters attribute) TC_GRPS (icolos.utils.enums.step_enums.StepGromacsEnum attribute) termination (icolos.core.workflow_steps.ccdc.docking.GoldConfiguration attribute) TERMINATION (icolos.utils.enums.step_enums.StepGoldEnum attribute) TERMINATIONS (icolos.utils.enums.program_parameters.GromacsEnum attribute) TG (icolos.utils.enums.step_enums.TokenGuardEnum attribute) TG_BINARY_LOCATION (icolos.utils.enums.step_enums.TokenGuardEnum attribute) TG_PREFIX_EXECUTION (icolos.utils.enums.step_enums.TokenGuardEnum attribute) TG_TOKEN_POOLS (icolos.utils.enums.step_enums.TokenGuardEnum attribute) TG_WAIT_INTERVAL_SECONDS (icolos.utils.enums.step_enums.TokenGuardEnum attribute) TG_WAIT_LIMIT_SECONDS (icolos.utils.enums.step_enums.TokenGuardEnum attribute) therm_cycle_branches (icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems attribute) (icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping attribute) (icolos.core.workflow_steps.pmx.base.StepPMXBase attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) THREADS (icolos.utils.enums.step_enums.StepGromacsEnum attribute) threshold (icolos.core.workflow_steps.fpocket.base.StepFpocketBase attribute) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket attribute) THRESHOLD (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) (icolos.utils.enums.step_enums.StepRMSFilterEnum attribute) time (icolos.core.workflow_steps.step.StepExecutionResourceParameters attribute) TIME (icolos.utils.enums.execution_enums.ExecutionPlatformEnum attribute) TIME_LIMIT_PER_TASK (icolos.utils.enums.step_enums.StepGlideEnum attribute) TIMEOUT (icolos.utils.enums.program_parameters.PMXAtomMappingEnum attribute) times_tried (icolos.utils.general.parallelization.Subtask attribute) TM_CONFIG_BASENAME (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_CONFIG_COSMO (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_CONFIG_DIR (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_CONFIG_ENDING (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_COSMOPREP (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_COSMOPREP_SUCCESS_STRING (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_DEFINE (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_DEFINE_SUCCESS_STRING (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_JOBEX (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_JOBEX_C (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_JOBEX_FAIL_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_JOBEX_GCART (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_JOBEX_SUCCESS_STRING (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_OUTPUT_COORDFILE (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_OUTPUT_COSMOFILE (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_OUTPUT_FINAL_SDF (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_OUTPUT_FINAL_XYZ (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_RIDFT (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_RIDFT_FAIL_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_RIDFT_SUCCESS_STRING (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_T2X (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_T2X_C (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_TURBOTMPDIR (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_X2T (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TM_X2T_SUCCESS_STRING (icolos.utils.enums.program_parameters.TurbomoleEnum attribute) TMP_INPUT_CONFIG (icolos.utils.enums.step_enums.StepModelBuilderEnum attribute) TMP_INPUT_DATA (icolos.utils.enums.step_enums.StepModelBuilderEnum attribute) TMP_OUTPUT_BEST_MODEL (icolos.utils.enums.step_enums.StepModelBuilderEnum attribute) TMP_OUTPUT_BEST_PARAMETERS (icolos.utils.enums.step_enums.StepModelBuilderEnum attribute) TMP_OUTPUT_PRODUCTION_MODEL (icolos.utils.enums.step_enums.StepModelBuilderEnum attribute) to_mol() (in module icolos.utils.smiles) to_smiles() (in module icolos.core.step_utils.rdkit_utils) (in module icolos.utils.smiles) token_guard (icolos.core.workflow_steps.schrodinger.base.StepSchrodingerBase attribute) (icolos.core.workflow_steps.schrodinger.fep_analysis.StepFepPlusAnalysis attribute) (icolos.core.workflow_steps.schrodinger.fep_base.StepFEPBase attribute) (icolos.core.workflow_steps.schrodinger.fep_plus_execution.StepFepPlusExec attribute) (icolos.core.workflow_steps.schrodinger.ligprep.StepLigprep attribute) (icolos.core.workflow_steps.schrodinger.macromodel.StepMacromodel attribute) (icolos.core.workflow_steps.schrodinger.prepwizard.StepPrepwizard attribute) (icolos.core.workflow_steps.schrodinger.residue_scanning.StepResidueScanning attribute)

TOKEN_GUARD (icolos.utils.enums.step_enums.StepBaseEnum attribute) token_guard (icolos.utils.execute_external.license_token_guard.SchrodingerLicenseTokenGuard attribute) token_pools (icolos.utils.execute_external.license_token_guard.TokenGuardParameters attribute) TOKEN_STR (icolos.utils.enums.step_enums.StepDesmondEnum attribute) TokenGuardEnum (class in icolos.utils.enums.step_enums) TokenGuardParameters (class in icolos.utils.execute_external.license_token_guard) top_lines (icolos.core.containers.gmx_state.GromacsState attribute) TOP_N_PER_SOLVENT (icolos.utils.enums.step_enums.StepClusteringEnum attribute) topol (icolos.core.workflow_steps.gromacs.grompp.StepGMXGrompp attribute) (icolos.core.workflow_steps.gromacs.mdrun.StepGMXMDrun attribute) tordist_file (icolos.core.step_utils.gold_config.ConfigDataFiles attribute) total (icolos.core.containers.perturbation_map.Edge attribute) TOTAL_ENERGY_TAG (icolos.utils.enums.program_parameters.XTBOutputEnum attribute) tprs (icolos.core.containers.gmx_state.GromacsState attribute) TRAJ_TYPE (icolos.utils.enums.step_enums.StepCavExploreEnum attribute) trajectories (icolos.core.containers.gmx_state.GromacsState attribute) tries (icolos.core.step_utils.retry.RetryResult attribute) TRJCAT (icolos.utils.enums.program_parameters.GromacsEnum attribute) TRJCONV (icolos.utils.enums.program_parameters.GromacsEnum attribute) TS (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) TurbomoleEnum (class in icolos.utils.enums.program_parameters) TurbomoleExecutor (class in icolos.utils.execute_external.turbomole) type (icolos.core.flow_control.flow_control.BaseStepConfig attribute) (icolos.core.step_utils.step_writeout.StepWriteoutDestinationParameters attribute) (icolos.core.workflow_steps.calculation.base.StepCalculationBase attribute) (icolos.core.workflow_steps.calculation.boltzmann_weighting.StepBoltzmannWeighting attribute) (icolos.core.workflow_steps.calculation.clustering.StepClustering attribute) (icolos.core.workflow_steps.calculation.cosmo.StepCosmo attribute) (icolos.core.workflow_steps.calculation.cresset_ec.StepCressetEC attribute) (icolos.core.workflow_steps.calculation.esp_sim.StepEspSim attribute) (icolos.core.workflow_steps.calculation.feature_counter.StepFeatureCounter attribute) (icolos.core.workflow_steps.calculation.rms_filter.StepRMSFilter attribute) (icolos.core.workflow_steps.calculation.rmsd.StepRMSD attribute) (icolos.core.workflow_steps.calculation.shaep.StepShaep attribute) (icolos.core.workflow_steps.calculation.turbomole.StepTurbomole attribute) (icolos.core.workflow_steps.confgen.base.StepConfgenBase attribute) (icolos.core.workflow_steps.confgen.crest.StepCREST attribute) (icolos.core.workflow_steps.confgen.omega.StepOmega attribute) (icolos.core.workflow_steps.confgen.xtb.StepXTB attribute) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket attribute) (icolos.core.workflow_steps.gromacs.base.StepGromacsBase attribute) (icolos.core.workflow_steps.gromacs.cluster.StepGMXCluster attribute) (icolos.core.workflow_steps.gromacs.clusters_ts.StepClusterTS attribute) (icolos.core.workflow_steps.gromacs.do_dssp.StepGMXDoDSSP attribute) (icolos.core.workflow_steps.gromacs.editconf.StepGMXEditConf attribute) (icolos.core.workflow_steps.gromacs.genion.StepGMXGenion attribute) (icolos.core.workflow_steps.gromacs.mmpbsa.StepGMXmmpbsa attribute) (icolos.core.workflow_steps.gromacs.rsmd.StepGMXrmsd attribute) (icolos.core.workflow_steps.gromacs.select.StepGMXselect attribute) (icolos.core.workflow_steps.gromacs.solvate.StepGMXSolvate attribute) (icolos.core.workflow_steps.gromacs.trajcat.StepGMXTrjcat attribute) (icolos.core.workflow_steps.gromacs.trjconv.StepGMXTrjconv attribute) (icolos.core.workflow_steps.io.base.StepIOBase attribute) (icolos.core.workflow_steps.io.data_manipulation.StepDataManipulation attribute) (icolos.core.workflow_steps.io.embedder.StepEmbedding attribute) (icolos.core.workflow_steps.io.initialize_compound.StepInitializeCompound attribute) (icolos.core.workflow_steps.openff.openff2gmx.StepOFF2gmx attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) (icolos.core.workflow_steps.prediction.model_building.StepModelBuilder attribute) (icolos.core.workflow_steps.prediction.predictor.StepPredictor attribute) (icolos.core.workflow_steps.schrodinger.fep_analysis.StepFepPlusAnalysis attribute) (icolos.core.workflow_steps.schrodinger.fep_base.StepFEPBase attribute) (icolos.core.workflow_steps.schrodinger.fep_plus_execution.StepFepPlusExec attribute) (icolos.core.workflow_steps.schrodinger.ligprep.StepLigprep attribute) (icolos.core.workflow_steps.schrodinger.macromodel.StepMacromodel attribute) (icolos.core.workflow_steps.schrodinger.prepwizard.StepPrepwizard attribute) (icolos.core.workflow_steps.schrodinger.protein_interaction.StepProteinInteraction attribute) (icolos.core.workflow_steps.schrodinger.residue_scanning.StepResidueScanning attribute) (icolos.core.workflow_steps.step.StepBase attribute) (icolos.core.workflow_steps.structure_prediction.dssp.StepDSSP attribute) (icolos.core.workflow_steps.structure_prediction.pdb_fixer.StepPdbFixer attribute) (icolos.core.workflow_steps.structure_prediction.peptide_embedder.StepPeptideEmbedder attribute)

U

UCB (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) UNDERLINE (icolos.utils.general.citation_generator.ConsoleColours attribute) underscore_attrs_are_private (icolos.core.composite_agents.base_agent.BaseAgent.Config attribute) (icolos.core.composite_agents.scheduler.Scheduler.Config attribute) (icolos.core.composite_agents.workflow.WorkFlow.Config attribute) (icolos.core.step_utils.input_preparator.InputPreparator.Config attribute) (icolos.core.step_utils.step_writeout.WriteOutHandler.Config attribute) (icolos.core.workflow_steps.schrodinger.desmond_exec.StepDesmondExec.Config attribute) (icolos.core.workflow_steps.schrodinger.desmond_preprocessor.StepDesmondSetup.Config attribute) (icolos.core.workflow_steps.schrodinger.fep_plus_execution.StepFepPlusExec.Config attribute) (icolos.core.workflow_steps.schrodinger.glide.StepGlide.Config attribute) (icolos.core.workflow_steps.schrodinger.ligprep.StepLigprep.Config attribute) (icolos.core.workflow_steps.schrodinger.macromodel.StepMacromodel.Config attribute) (icolos.core.workflow_steps.schrodinger.prime.StepPrime.Config attribute) (icolos.core.workflow_steps.step.StepBase.Config attribute) (icolos.utils.execute_external.license_token_guard.SchrodingerLicenseTokenGuard.Config attribute)

UNIQUE_MOLS (icolos.utils.enums.step_enums.StepOpenFFEnum attribute) unroll_compounds() (icolos.core.step_utils.input_merger.InputMerger method) unroll_conformers() (icolos.core.containers.compound.Compound method) (in module icolos.core.containers.compound) unroll_enumerations() (in module icolos.core.containers.compound) update_all_relations() (icolos.core.containers.compound.Compound method) update_coordinates() (icolos.core.containers.compound.Conformer method) update_data() (icolos.core.containers.generic.GenericData method) use_tordist (icolos.core.step_utils.gold_config.ConfigFlags attribute)

V

validate() (icolos.config_containers.container.ConfContainer method) (icolos.config_containers.workflow_container.WorkflowContainer method) VALIDATION_LIB (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) value (icolos.core.composite_agents.base_agent.AgentEnvironmentParameters.WorkflowExportParameters attribute) VDW (icolos.utils.enums.program_parameters.KallistoEnum attribute) VEC (icolos.utils.enums.program_parameters.JazzyEnum attribute) VEC_OPT (icolos.utils.enums.program_parameters.JazzyEnum attribute) VEC_OPT_MMF94 (icolos.utils.enums.program_parameters.JazzyEnum attribute) VEC_OPT_MMF94S (icolos.utils.enums.program_parameters.JazzyEnum attribute) VEC_OPT_UFF (icolos.utils.enums.program_parameters.JazzyEnum attribute) VEC_STRENGHT_ONLY (icolos.utils.enums.program_parameters.JazzyEnum attribute) VERSION (icolos.utils.enums.composite_agents_enums.BaseAgentEnum attribute) version_match() (in module icolos.utils.entry_point_functions.parsing_functions) VINA (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_CALL (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_CENTER_X (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_CENTER_Y (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_CENTER_Z (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_CONFIGURATION (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_CPU (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_ENERGY_RANGE (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_EXHAUSTIVENESS (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_FLEX (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_HELP (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_HELP_ADVANCED (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_LIGAND (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_LOCAL_ONLY (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_NUM_MODES (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_OUT (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_RANDOMIZE_ONLY (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_RECEPTOR (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute)

VINA_SCORE_ONLY (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_SEED (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_SIZE_X (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_SIZE_Y (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_SIZE_Z (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_VERSION (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_VERSION_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_WEIGHT_GAUSS1 (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_WEIGHT_GAUSS2 (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_WEIGHT_HYDROGEN (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_WEIGHT_HYDROPHOBIC (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_WEIGHT_REPULSION (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VINA_WEIGHT_ROT (icolos.utils.enums.program_parameters.AutoDockVinaEnum attribute) VIRTUAL_LIB (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) VIS (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_BASE64 (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_FIG_SIZE (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_FLATTEN_MOLECULE (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_HELP (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_HIGHLIGHT_ATOMS (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_IGNORE_SA (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_IGNORE_SDC (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_IGNORE_SDX (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_OPT (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_OPT_MMF94 (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_OPT_MMF94S (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_OPT_UFF (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_SA_THRESHOLD (icolos.utils.enums.program_parameters.JazzyEnum attribute) VIS_SDC_THRESHOLD (icolos.utils.enums.program_parameters.JazzyEnum attribute) visualise_perturbation_map() (icolos.core.containers.perturbation_map.PerturbationMap method) vmap_output (icolos.core.containers.perturbation_map.PerturbationMap attribute)

W

WAIT_FLAG (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) wait_interval_seconds (icolos.utils.execute_external.license_token_guard.TokenGuardParameters attribute) wait_limit_seconds (icolos.utils.execute_external.license_token_guard.TokenGuardParameters attribute) WARMUP (icolos.utils.enums.step_enums.StepActiveLearningEnum attribute) WARNING (icolos.utils.enums.logging_enums.LoggingConfigEnum attribute) water (icolos.core.containers.gmx_state.GromacsState attribute) (icolos.core.workflow_steps.pmx.assemble_systems.StepPMXAssembleSystems attribute) (icolos.core.workflow_steps.pmx.atomMapping.StepPMXatomMapping attribute) (icolos.core.workflow_steps.pmx.base.StepPMXBase attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) WATER (icolos.utils.enums.program_parameters.StepPMXEnum attribute) WATER_AND_IONS (icolos.utils.enums.step_enums.StepGromacsEnum attribute) WATER_POSRE (icolos.utils.enums.step_enums.StepGromacsEnum attribute) WBO (icolos.utils.enums.program_parameters.XTBOutputEnum attribute) WEIGHT (icolos.utils.enums.step_enums.StepBoltzmannWeightingEnum attribute) WEIGHT_INPUT (icolos.utils.enums.step_enums.StepBoltzmannWeightingEnum attribute) WEIGHT_OUTPUT_PREFIX (icolos.utils.enums.step_enums.StepBoltzmannWeightingEnum attribute) WEIGHT_PROPERTIES (icolos.utils.enums.step_enums.StepBoltzmannWeightingEnum attribute) work_dir (icolos.core.composite_agents.workflow.WorkflowData attribute) (icolos.core.flow_control.flow_control.BaseStepConfig attribute) (icolos.core.flow_control.iterator.IterSettingsParameters attribute) (icolos.core.step_utils.input_preparator.StepInputParameters attribute) (icolos.core.workflow_steps.calculation.base.StepCalculationBase attribute) (icolos.core.workflow_steps.calculation.boltzmann_weighting.StepBoltzmannWeighting attribute) (icolos.core.workflow_steps.calculation.clustering.StepClustering attribute) (icolos.core.workflow_steps.calculation.cosmo.StepCosmo attribute) (icolos.core.workflow_steps.calculation.cresset_ec.StepCressetEC attribute) (icolos.core.workflow_steps.calculation.esp_sim.StepEspSim attribute) (icolos.core.workflow_steps.calculation.feature_counter.StepFeatureCounter attribute) (icolos.core.workflow_steps.calculation.rms_filter.StepRMSFilter attribute) (icolos.core.workflow_steps.calculation.rmsd.StepRMSD attribute) (icolos.core.workflow_steps.calculation.shaep.StepShaep attribute) (icolos.core.workflow_steps.calculation.turbomole.StepTurbomole attribute) (icolos.core.workflow_steps.confgen.base.StepConfgenBase attribute) (icolos.core.workflow_steps.confgen.crest.StepCREST attribute) (icolos.core.workflow_steps.confgen.omega.StepOmega attribute) (icolos.core.workflow_steps.confgen.xtb.StepXTB attribute) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket attribute) (icolos.core.workflow_steps.gromacs.base.StepGromacsBase attribute) (icolos.core.workflow_steps.gromacs.cluster.StepGMXCluster attribute) (icolos.core.workflow_steps.gromacs.clusters_ts.StepClusterTS attribute) (icolos.core.workflow_steps.gromacs.do_dssp.StepGMXDoDSSP attribute) (icolos.core.workflow_steps.gromacs.editconf.StepGMXEditConf attribute) (icolos.core.workflow_steps.gromacs.genion.StepGMXGenion attribute) (icolos.core.workflow_steps.gromacs.mmpbsa.StepGMXmmpbsa attribute) (icolos.core.workflow_steps.gromacs.rsmd.StepGMXrmsd attribute) (icolos.core.workflow_steps.gromacs.select.StepGMXselect attribute) (icolos.core.workflow_steps.gromacs.solvate.StepGMXSolvate attribute) (icolos.core.workflow_steps.gromacs.trajcat.StepGMXTrjcat attribute) (icolos.core.workflow_steps.gromacs.trjconv.StepGMXTrjconv attribute) (icolos.core.workflow_steps.io.base.StepIOBase attribute) (icolos.core.workflow_steps.io.data_manipulation.StepDataManipulation attribute) (icolos.core.workflow_steps.io.embedder.StepEmbedding attribute) (icolos.core.workflow_steps.io.initialize_compound.StepInitializeCompound attribute) (icolos.core.workflow_steps.openff.openff2gmx.StepOFF2gmx attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) (icolos.core.workflow_steps.prediction.model_building.StepModelBuilder attribute) (icolos.core.workflow_steps.prediction.predictor.StepPredictor attribute) (icolos.core.workflow_steps.schrodinger.fep_analysis.StepFepPlusAnalysis attribute) (icolos.core.workflow_steps.schrodinger.fep_base.StepFEPBase attribute) (icolos.core.workflow_steps.schrodinger.fep_plus_execution.StepFepPlusExec attribute) (icolos.core.workflow_steps.schrodinger.ligprep.StepLigprep attribute) (icolos.core.workflow_steps.schrodinger.macromodel.StepMacromodel attribute) (icolos.core.workflow_steps.schrodinger.prepwizard.StepPrepwizard attribute) (icolos.core.workflow_steps.schrodinger.protein_interaction.StepProteinInteraction attribute) (icolos.core.workflow_steps.schrodinger.residue_scanning.StepResidueScanning attribute) (icolos.core.workflow_steps.step.StepBase attribute) (icolos.core.workflow_steps.structure_prediction.dssp.StepDSSP attribute) (icolos.core.workflow_steps.structure_prediction.pdb_fixer.StepPdbFixer attribute) (icolos.core.workflow_steps.structure_prediction.peptide_embedder.StepPeptideEmbedder attribute) WorkFlow (class in icolos.core.composite_agents.workflow) workflow (icolos.core.step_utils.input_preparator.InputPreparator attribute) (icolos.scripts.icolos_workflow.IcolosWorkflow attribute) WORKFLOW (icolos.utils.enums.composite_agents_enums.WorkflowEnum attribute) WorkFlow.Config (class in icolos.core.composite_agents.workflow) workflow_data (icolos.core.composite_agents.workflow.WorkFlow attribute) (icolos.core.step_utils.step_writeout.WriteOutHandler attribute) WORKFLOW_SCHEMA (icolos.utils.enums.general_utils_enums.JSONSchemasEnum attribute) WorkflowContainer (class in icolos.config_containers.workflow_container) WorkflowData (class in icolos.core.composite_agents.workflow) WorkflowEnum (class in icolos.utils.enums.composite_agents_enums) WorkflowHeaderParameters (class in icolos.core.composite_agents.workflow) workflows (icolos.core.step_dispatch.dispatcher.StepDispatcher attribute) write() (icolos.core.containers.compound.Conformer method) (icolos.core.containers.generic.GenericData method) (icolos.core.step_utils.step_writeout.WriteOutHandler method) write_conformers() (icolos.core.workflow_steps.step.StepBase method) write_cpt() (icolos.core.containers.gmx_state.GromacsState method) write_edr() (icolos.core.containers.gmx_state.GromacsState method) write_generic_by_extension() (icolos.core.workflow_steps.step.StepBase method)

write_generic_by_name() (icolos.core.workflow_steps.step.StepBase method) write_input_files() (icolos.core.workflow_steps.gromacs.base.StepGromacsBase method) write_log() (icolos.core.containers.gmx_state.GromacsState method) write_molecule_to_sdf() (in module icolos.utils.general.molecules) write_ndx() (icolos.core.containers.gmx_state.GromacsState method) write_out_all_files() (icolos.core.containers.generic.GenericContainer method) write_props() (icolos.core.containers.gmx_state.GromacsState method) write_structure() (icolos.core.containers.gmx_state.GromacsState method) write_topol() (icolos.core.containers.gmx_state.GromacsState method) write_tpr() (icolos.core.containers.gmx_state.GromacsState method) write_trajectory() (icolos.core.containers.gmx_state.GromacsState method) writeout (icolos.core.flow_control.flow_control.BaseStepConfig attribute) (icolos.core.workflow_steps.calculation.base.StepCalculationBase attribute) (icolos.core.workflow_steps.calculation.boltzmann_weighting.StepBoltzmannWeighting attribute) (icolos.core.workflow_steps.calculation.clustering.StepClustering attribute) (icolos.core.workflow_steps.calculation.cosmo.StepCosmo attribute) (icolos.core.workflow_steps.calculation.cresset_ec.StepCressetEC attribute) (icolos.core.workflow_steps.calculation.esp_sim.StepEspSim attribute) (icolos.core.workflow_steps.calculation.feature_counter.StepFeatureCounter attribute) (icolos.core.workflow_steps.calculation.rms_filter.StepRMSFilter attribute) (icolos.core.workflow_steps.calculation.rmsd.StepRMSD attribute) (icolos.core.workflow_steps.calculation.shaep.StepShaep attribute) (icolos.core.workflow_steps.calculation.turbomole.StepTurbomole attribute) (icolos.core.workflow_steps.confgen.base.StepConfgenBase attribute) (icolos.core.workflow_steps.confgen.crest.StepCREST attribute) (icolos.core.workflow_steps.confgen.omega.StepOmega attribute) (icolos.core.workflow_steps.confgen.xtb.StepXTB attribute) (icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket attribute) (icolos.core.workflow_steps.gromacs.base.StepGromacsBase attribute) (icolos.core.workflow_steps.gromacs.cluster.StepGMXCluster attribute) (icolos.core.workflow_steps.gromacs.clusters_ts.StepClusterTS attribute) (icolos.core.workflow_steps.gromacs.do_dssp.StepGMXDoDSSP attribute) (icolos.core.workflow_steps.gromacs.editconf.StepGMXEditConf attribute) (icolos.core.workflow_steps.gromacs.genion.StepGMXGenion attribute) (icolos.core.workflow_steps.gromacs.mmpbsa.StepGMXmmpbsa attribute) (icolos.core.workflow_steps.gromacs.rsmd.StepGMXrmsd attribute) (icolos.core.workflow_steps.gromacs.select.StepGMXselect attribute) (icolos.core.workflow_steps.gromacs.solvate.StepGMXSolvate attribute) (icolos.core.workflow_steps.gromacs.trajcat.StepGMXTrjcat attribute) (icolos.core.workflow_steps.gromacs.trjconv.StepGMXTrjconv attribute) (icolos.core.workflow_steps.io.base.StepIOBase attribute) (icolos.core.workflow_steps.io.data_manipulation.StepDataManipulation attribute) (icolos.core.workflow_steps.io.embedder.StepEmbedding attribute) (icolos.core.workflow_steps.io.initialize_compound.StepInitializeCompound attribute) (icolos.core.workflow_steps.openff.openff2gmx.StepOFF2gmx attribute) (icolos.core.workflow_steps.pmx.box_water_ions.StepPMXBoxWaterIons attribute) (icolos.core.workflow_steps.pmx.doublebox.StepPMXdoublebox attribute) (icolos.core.workflow_steps.pmx.genlib.StepPMXgenlib attribute) (icolos.core.workflow_steps.pmx.gentop.StepPMXgentop attribute) (icolos.core.workflow_steps.pmx.ligandHybrid.StepPMXligandHybrid attribute) (icolos.core.workflow_steps.pmx.mutate.StepPMXmutate attribute) (icolos.core.workflow_steps.pmx.prepare_simulations.StepPMXPrepareSimulations attribute) (icolos.core.workflow_steps.pmx.prepare_transitions.StepPMXPrepareTransitions attribute) (icolos.core.workflow_steps.prediction.model_building.StepModelBuilder attribute) (icolos.core.workflow_steps.prediction.predictor.StepPredictor attribute) (icolos.core.workflow_steps.schrodinger.fep_analysis.StepFepPlusAnalysis attribute) (icolos.core.workflow_steps.schrodinger.fep_base.StepFEPBase attribute) (icolos.core.workflow_steps.schrodinger.fep_plus_execution.StepFepPlusExec attribute) (icolos.core.workflow_steps.schrodinger.ligprep.StepLigprep attribute) (icolos.core.workflow_steps.schrodinger.macromodel.StepMacromodel attribute) (icolos.core.workflow_steps.schrodinger.prepwizard.StepPrepwizard attribute) (icolos.core.workflow_steps.schrodinger.protein_interaction.StepProteinInteraction attribute) (icolos.core.workflow_steps.schrodinger.residue_scanning.StepResidueScanning attribute) (icolos.core.workflow_steps.step.StepBase attribute) (icolos.core.workflow_steps.structure_prediction.dssp.StepDSSP attribute) (icolos.core.workflow_steps.structure_prediction.pdb_fixer.StepPdbFixer attribute) (icolos.core.workflow_steps.structure_prediction.peptide_embedder.StepPeptideEmbedder attribute) WRITEOUT (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_AGGREGATION (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_AGGREGATION_HIGHESTISBEST (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_AGGREGATION_KEY (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_AGGREGATION_MODE (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_AGGREGATION_MODE_ALL (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_AGGREGATION_MODE_BESTPERCOMPOUND (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_AGGREGATION_MODE_BESTPERENUMERATION (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_CATEGORY (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_CATEGORY_CONFORMERS (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_CATEGORY_ENUMERATIONS (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_CATEGORY_EXTRADATA (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_KEY (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_SELECTED_TAGS (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_SELECTED_TAGS_HIGHESTISBEST (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_COMP_SELECTED_TAGS_KEY (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_CONFIG (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION_AUTOMATIC (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION_BASE_NAME (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION_DIR (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION_FORMAT (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION_MERGE (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION_MODE (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION_RESOURCE (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION_TYPE (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION_TYPE_FILE (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION_TYPE_REINVENT (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION_TYPE_REST (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION_TYPE_STDERR (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_DESTINATION_TYPE_STDOUT (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_GENERIC (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_GENERIC_KEY (icolos.utils.enums.step_enums.StepBaseEnum attribute) WRITEOUT_GMX (icolos.utils.enums.step_enums.StepBaseEnum attribute) WriteOutEnum (class in icolos.utils.enums.write_out_enums) WriteOutHandler (class in icolos.core.step_utils.step_writeout) WriteOutHandler.Config (class in icolos.core.step_utils.step_writeout)

X

XRAY_SPLIT (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) XRAY_STRUCTURES (icolos.utils.enums.step_enums.StepFepPlusEnum attribute) XTB (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_ACC (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_CHRG (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_CYCLES (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_ETEMP (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_GBSA (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_GFN (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_HELP (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_HELP_IDENTIFICATION_STRING (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_ITERATION (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_MOPAC (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_OPT (icolos.utils.enums.program_parameters.XTBEnum attribute)

XTB_ORCA (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_P (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_PERIODIC (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_QMDFF (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_TM (icolos.utils.enums.program_parameters.XTBEnum attribute) XTB_UHF (icolos.utils.enums.program_parameters.XTBEnum attribute) XTBEnum (class in icolos.utils.enums.program_parameters) XTBExecutor (class in icolos.utils.execute_external.xtb) XTBOPT_LOG (icolos.utils.enums.program_parameters.XTBOutputEnum attribute) XTBOPT_SDF (icolos.utils.enums.program_parameters.XTBOutputEnum attribute) XTBOutputEnum (class in icolos.utils.enums.program_parameters) XTBRESTART (icolos.utils.enums.program_parameters.XTBOutputEnum attribute) XTBTOPO_MOL2 (icolos.utils.enums.program_parameters.CrestOutputEnum attribute) XTBTOPO_SDF (icolos.utils.enums.program_parameters.XTBOutputEnum attribute)