LICENSE
README.md
pyproject.toml
src/ABFE_Workflow.egg-info/PKG-INFO
src/ABFE_Workflow.egg-info/SOURCES.txt
src/ABFE_Workflow.egg-info/dependency_links.txt
src/ABFE_Workflow.egg-info/entry_points.txt
src/ABFE_Workflow.egg-info/requires.txt
src/ABFE_Workflow.egg-info/top_level.txt
src/abfe/__init__.py
src/abfe/_version.py
src/abfe/calculate_abfe.py
src/abfe/calculate_abfe_gmx.py
src/abfe/conf.py
src/abfe/orchestration/__init__.py
src/abfe/orchestration/build_approach_flow.py
src/abfe/orchestration/build_ligand_flow.py
src/abfe/orchestration/generate_conf.py
src/abfe/orchestration/generate_scheduler.py
src/abfe/orchestration/generate_snake.py
src/abfe/rules/__init__.py
src/abfe/rules/ligand_equilibration_workflow/Snakefile.smk
src/abfe/rules/ligand_equilibration_workflow/complex_equil_setup.smk
src/abfe/rules/ligand_equilibration_workflow/complex_equil_simulation.smk
src/abfe/rules/ligand_equilibration_workflow/ligand_equil_setup.smk
src/abfe/rules/ligand_equilibration_workflow/ligand_equil_simulation.smk
src/abfe/rules/ligand_fep_workflow/Snakefile.smk
src/abfe/rules/ligand_fep_workflow/calculate_result.smk
src/abfe/rules/ligand_fep_workflow/complex_fep_ana.smk
src/abfe/rules/ligand_fep_workflow/complex_fep_setup.smk
src/abfe/rules/ligand_fep_workflow/complex_fep_simulation.smk
src/abfe/rules/ligand_fep_workflow/ligand_fep_ana.smk
src/abfe/rules/ligand_fep_workflow/ligand_fep_setup.smk
src/abfe/rules/ligand_fep_workflow/ligand_fep_simulation.smk
src/abfe/rules/receptor_workflow/Snakefile.smk
src/abfe/rules/receptor_workflow/Snakefile_gmx.smk
src/abfe/rules/receptor_workflow/build_ligand_systems.smk
src/abfe/rules/receptor_workflow/post_commands.smk
src/abfe/rules/receptor_workflow/simulations.smk
src/abfe/scripts/__init__.py
src/abfe/scripts/abfe_slurm_status.py
src/abfe/scripts/final_receptor_results.py
src/abfe/scripts/free_energy/__init__.py
src/abfe/scripts/free_energy/alchemlyb_analysis.py
src/abfe/scripts/free_energy/calculate_ABFE_ligand_dG.py
src/abfe/scripts/free_energy/calculate_ABFE_transformation_dG.py
src/abfe/scripts/preparation/__init__.py
src/abfe/scripts/preparation/generate_ABFE_systems.py
src/abfe/scripts/preparation/generate_boresch_restraints.py
src/abfe/scripts/preparation/parametrize.py
src/abfe/scripts/preparation/topology_fixer.py
src/abfe/template/__init__.py
src/abfe/template/complex_equil_workflow/emin/emin.mdp
src/abfe/template/complex_equil_workflow/npt_equil1/npt_equil1.mdp
src/abfe/template/complex_equil_workflow/npt_equil2/npt_equil2.mdp
src/abfe/template/complex_equil_workflow/npt_prod/npt_prod.mdp
src/abfe/template/complex_equil_workflow/nvt_heat/nvt_heat.mdp
src/abfe/template/complex_fep_workflow/template/coul/emin/emin.mdp
src/abfe/template/complex_fep_workflow/template/coul/npt/npt.mdp
src/abfe/template/complex_fep_workflow/template/coul/npt-norest/npt-norest.mdp
src/abfe/template/complex_fep_workflow/template/coul/nvt/nvt.mdp
src/abfe/template/complex_fep_workflow/template/coul/prod/prod.mdp
src/abfe/template/complex_fep_workflow/template/restraints/emin/emin.mdp
src/abfe/template/complex_fep_workflow/template/restraints/npt/npt.mdp
src/abfe/template/complex_fep_workflow/template/restraints/npt-norest/npt-norest.mdp
src/abfe/template/complex_fep_workflow/template/restraints/nvt/nvt.mdp
src/abfe/template/complex_fep_workflow/template/restraints/prod/prod.mdp
src/abfe/template/complex_fep_workflow/template/vdw/emin/emin.mdp
src/abfe/template/complex_fep_workflow/template/vdw/npt/npt.mdp
src/abfe/template/complex_fep_workflow/template/vdw/npt-norest/npt-norest.mdp
src/abfe/template/complex_fep_workflow/template/vdw/nvt/nvt.mdp
src/abfe/template/complex_fep_workflow/template/vdw/prod/prod.mdp
src/abfe/template/gmx_submit_kernels/def_cpu_job.sh
src/abfe/template/gmx_submit_kernels/def_cpu_job_cont.sh
src/abfe/template/gmx_submit_kernels/def_gpu_job.sh
src/abfe/template/gmx_submit_kernels/def_gpu_job_cont.sh
src/abfe/template/ligand_equil_workflow/emin/emin.mdp
src/abfe/template/ligand_equil_workflow/npt_equil1/npt_equil1.mdp
src/abfe/template/ligand_equil_workflow/npt_equil2/npt_equil2.mdp
src/abfe/template/ligand_equil_workflow/nvt_heat/nvt_heat.mdp
src/abfe/template/ligand_fep_workflow/template/coul/emin/emin.mdp
src/abfe/template/ligand_fep_workflow/template/coul/npt/npt.mdp
src/abfe/template/ligand_fep_workflow/template/coul/npt-norest/npt-norest.mdp
src/abfe/template/ligand_fep_workflow/template/coul/nvt/nvt.mdp
src/abfe/template/ligand_fep_workflow/template/coul/prod/prod.mdp
src/abfe/template/ligand_fep_workflow/template/vdw/emin/emin.mdp
src/abfe/template/ligand_fep_workflow/template/vdw/npt/npt.mdp
src/abfe/template/ligand_fep_workflow/template/vdw/npt-norest/npt-norest.mdp
src/abfe/template/ligand_fep_workflow/template/vdw/nvt/nvt.mdp
src/abfe/template/ligand_fep_workflow/template/vdw/prod/prod.mdp
src/abfe/utils/DEBUG_submit_all_approachjobs.sh
src/abfe/utils/__init__.py
src/abfe/utils/build_dag_png.sh
src/abfe/utils/check_dag_completion.sh
src/abfe/utils/converter.py
src/abfe_cli/ABFECalculator.py
src/abfe_cli/ABFECalculatorGmx.py
src/abfe_cli/__init__.py