implicit_solvent_ddm.workflow_phases

Workflow phase functions for the Double Decoupling Method (DDM) workflow.

This module contains the individual phase functions that make up the DDM workflow, providing a clean separation of concerns and improved maintainability.

Functions

compute_free_energy_and_consolidate(job, ...)	Phase 7: Compute free energy and consolidate results.
decompose_system_and_generate_restraints(...)	Phase 3: Decompose system and generate restraints.
initilized_jobs(job, message)	Placeholder job for synchronization and logging.
run_endstate_simulations(job, config)	Phase 2: Run endstate simulations for complex, receptor, and ligand systems.
run_intermediate_simulations(job, config, ...)	Phase 5: Run intermediate state simulations.
run_post_analysis_intermediate_simulations(...)	Phase 6: Run Energy post-processing with sander imin=5 This phase: 1.
setup_intermediate_simulations(job, ...)	Phase 4: Setups the intermediate state simulations with alchemical transformations.
setup_workflow_components(job, config)	Phase 1: Setup workflow components and MD input files.
update_config(job, config, ...)	Update configuration with binding modes from endstate simulations.
update_config_endstate(job, config, message)	Update configuration with binding modes from endstate simulations.