Python Module Index


	i
	`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`