icolos.core package

Subpackages

• icolos.core.composite_agents package
  • Submodules
  • icolos.core.composite_agents.base_agent module
  • icolos.core.composite_agents.scheduler module
  • icolos.core.composite_agents.workflow module
  • Module contents
• icolos.core.containers package
  • Submodules
  • icolos.core.containers.compound module
  • icolos.core.containers.generic module
  • icolos.core.containers.gmx_state module
  • icolos.core.containers.perturbation_map module
  • Module contents
• icolos.core.flow_control package
  • Submodules
  • icolos.core.flow_control.flow_control module
  • icolos.core.flow_control.iterator module
  • Module contents
• icolos.core.step_dispatch package
  • Submodules
  • icolos.core.step_dispatch.dispatcher module
  • Module contents
• icolos.core.step_utils package
  • Submodules
  • 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
  • Module contents
• icolos.core.workflow_steps package
  • Subpackages
    • icolos.core.workflow_steps.autodockvina package
      • Submodules
      • icolos.core.workflow_steps.autodockvina.docking module
      • icolos.core.workflow_steps.autodockvina.target_preparation module
      • Module contents
    • icolos.core.workflow_steps.calculation package
      • Submodules
      • 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
      • Module contents
    • icolos.core.workflow_steps.ccdc package
      • Submodules
      • icolos.core.workflow_steps.ccdc.docking module
      • Module contents
    • icolos.core.workflow_steps.confgen package
      • Submodules
      • 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
      • Module contents
    • icolos.core.workflow_steps.fpocket package
      • Submodules
      • icolos.core.workflow_steps.fpocket.base module
      • icolos.core.workflow_steps.fpocket.mdpocket module
      • Module contents
    • icolos.core.workflow_steps.gromacs package
      • Submodules
      • 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
      • Module contents
    • icolos.core.workflow_steps.io package
      • Submodules
      • 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
      • Module contents
    • icolos.core.workflow_steps.openff package
      • Submodules
      • icolos.core.workflow_steps.openff.openff2gmx module
      • Module contents
    • icolos.core.workflow_steps.pmx package
      • Submodules
      • 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
      • Module contents
    • icolos.core.workflow_steps.prediction package
      • Submodules
      • icolos.core.workflow_steps.prediction.model_building module
      • icolos.core.workflow_steps.prediction.predictor module
      • Module contents
    • icolos.core.workflow_steps.schrodinger package
      • Submodules
      • 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
      • Module contents
    • icolos.core.workflow_steps.structure_prediction package
      • Submodules
      • 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.core.workflow_steps.structure_prediction.rosetta_abinitio module
      • Module contents
  • Submodules
  • icolos.core.workflow_steps.step module
  • Module contents

Submodules

icolos.core.steps_utils module

icolos.core.steps_utils.initialize_step_from_dict(step_conf: dict) → StepBase

Map the configuration from JSON to an initialized step object

Parameters:

step_conf (dict) – dictionary containing configuration for the step

Raises:

ValueError – raised if provided step_type does not correspond to known step

Return StepBase:

Initialized step object with the provided config

Module contents