LICENSE
README.rst
pyproject.toml
src/bindflow/__init__.py
src/bindflow/_gmx_check.py
src/bindflow/_version.py
src/bindflow/cli.py
src/bindflow/home.py
src/bindflow/runners.py
src/bindflow.egg-info/PKG-INFO
src/bindflow.egg-info/SOURCES.txt
src/bindflow.egg-info/dependency_links.txt
src/bindflow.egg-info/entry_points.txt
src/bindflow.egg-info/requires.txt
src/bindflow.egg-info/top_level.txt
src/bindflow/data/ci_systems/WP6.tar.gz
src/bindflow/data/ci_systems/config-fep.yml
src/bindflow/data/ci_systems/config-mmpbsa.yml
src/bindflow/data/gmx_ff/Slipids_2020.ff.tar.gz
src/bindflow/data/gmx_ff/amber99sb-star-ildn.ff.tar.gz
src/bindflow/data/gmx_water_models/water_models.yml
src/bindflow/data/gmx_water_models/amber/ffnonbonded.itp
src/bindflow/data/gmx_water_models/amber/ions.itp
src/bindflow/data/gmx_water_models/amber/spc.itp
src/bindflow/data/gmx_water_models/amber/spce.itp
src/bindflow/data/gmx_water_models/amber/tip3p.itp
src/bindflow/data/gmx_water_models/amber/tip4p.itp
src/bindflow/data/gmx_water_models/amber/tip4pew.itp
src/bindflow/data/gmx_water_models/amber/tip5p.itp
src/bindflow/data/gmx_water_models/amber/watermodels.dat
src/bindflow/data/gmx_water_models/charmm/ffnonbonded.itp
src/bindflow/data/gmx_water_models/charmm/ions.itp
src/bindflow/data/gmx_water_models/charmm/spc.itp
src/bindflow/data/gmx_water_models/charmm/spce.itp
src/bindflow/data/gmx_water_models/charmm/tip3p.itp
src/bindflow/data/gmx_water_models/charmm/tip4p.itp
src/bindflow/data/gmx_water_models/charmm/tip5p.itp
src/bindflow/data/gmx_water_models/charmm/tips3p.itp
src/bindflow/data/gmx_water_models/charmm/watermodels.dat
src/bindflow/data/gmx_water_models/configurations/spc216.gro
src/bindflow/data/gmx_water_models/configurations/tip4p.gro
src/bindflow/data/gmx_water_models/configurations/tip5p.gro
src/bindflow/data/gmx_water_models/oplsaa/ffnonbonded.itp
src/bindflow/data/gmx_water_models/oplsaa/ions.itp
src/bindflow/data/gmx_water_models/oplsaa/spc.itp
src/bindflow/data/gmx_water_models/oplsaa/spce.itp
src/bindflow/data/gmx_water_models/oplsaa/tip3p.itp
src/bindflow/data/gmx_water_models/oplsaa/tip4p.itp
src/bindflow/data/gmx_water_models/oplsaa/tip4pew.itp
src/bindflow/data/gmx_water_models/oplsaa/tip5p.itp
src/bindflow/data/gmx_water_models/oplsaa/tip5pe.itp
src/bindflow/data/gmx_water_models/oplsaa/watermodels.dat
src/bindflow/free_energy/__init__.py
src/bindflow/free_energy/fep_analysis.py
src/bindflow/free_energy/gather_results.py
src/bindflow/free_energy/mmxbsa_analysis.py
src/bindflow/mdp/__init__.py
src/bindflow/mdp/_path_handler.py
src/bindflow/mdp/mdp.py
src/bindflow/mdp/templates/__init__.py
src/bindflow/mdp/templates/complex/membrane/equi/00_min.mdp
src/bindflow/mdp/templates/complex/membrane/equi/01_nvt.mdp
src/bindflow/mdp/templates/complex/membrane/equi/02_nvt.mdp
src/bindflow/mdp/templates/complex/membrane/equi/03_npt.mdp
src/bindflow/mdp/templates/complex/membrane/equi/04_npt.mdp
src/bindflow/mdp/templates/complex/membrane/equi/05_npt.mdp
src/bindflow/mdp/templates/complex/membrane/equi/06_npt.mdp
src/bindflow/mdp/templates/complex/membrane/equi/prod.mdp
src/bindflow/mdp/templates/complex/membrane/fep/bonded/00_min.mdp
src/bindflow/mdp/templates/complex/membrane/fep/bonded/01_nvt.mdp
src/bindflow/mdp/templates/complex/membrane/fep/bonded/02_npt.mdp
src/bindflow/mdp/templates/complex/membrane/fep/bonded/03_npt_norest.mdp
src/bindflow/mdp/templates/complex/membrane/fep/bonded/prod.mdp
src/bindflow/mdp/templates/complex/membrane/fep/coul/00_min.mdp
src/bindflow/mdp/templates/complex/membrane/fep/coul/01_nvt.mdp
src/bindflow/mdp/templates/complex/membrane/fep/coul/02_npt.mdp
src/bindflow/mdp/templates/complex/membrane/fep/coul/03_npt_norest.mdp
src/bindflow/mdp/templates/complex/membrane/fep/coul/prod.mdp
src/bindflow/mdp/templates/complex/membrane/fep/vdw/00_min.mdp
src/bindflow/mdp/templates/complex/membrane/fep/vdw/01_nvt.mdp
src/bindflow/mdp/templates/complex/membrane/fep/vdw/02_npt.mdp
src/bindflow/mdp/templates/complex/membrane/fep/vdw/03_npt_norest.mdp
src/bindflow/mdp/templates/complex/membrane/fep/vdw/prod.mdp
src/bindflow/mdp/templates/complex/membrane/mmpbsa/prod.mdp
src/bindflow/mdp/templates/complex/soluble/equi/00_min.mdp
src/bindflow/mdp/templates/complex/soluble/equi/01_nvt.mdp
src/bindflow/mdp/templates/complex/soluble/equi/02_nvt.mdp
src/bindflow/mdp/templates/complex/soluble/equi/03_npt.mdp
src/bindflow/mdp/templates/complex/soluble/equi/04_npt.mdp
src/bindflow/mdp/templates/complex/soluble/equi/prod.mdp
src/bindflow/mdp/templates/complex/soluble/fep/bonded/00_min.mdp
src/bindflow/mdp/templates/complex/soluble/fep/bonded/01_nvt.mdp
src/bindflow/mdp/templates/complex/soluble/fep/bonded/02_npt.mdp
src/bindflow/mdp/templates/complex/soluble/fep/bonded/03_npt_norest.mdp
src/bindflow/mdp/templates/complex/soluble/fep/bonded/prod.mdp
src/bindflow/mdp/templates/complex/soluble/fep/coul/00_min.mdp
src/bindflow/mdp/templates/complex/soluble/fep/coul/01_nvt.mdp
src/bindflow/mdp/templates/complex/soluble/fep/coul/02_npt.mdp
src/bindflow/mdp/templates/complex/soluble/fep/coul/03_npt_norest.mdp
src/bindflow/mdp/templates/complex/soluble/fep/coul/prod.mdp
src/bindflow/mdp/templates/complex/soluble/fep/vdw/00_min.mdp
src/bindflow/mdp/templates/complex/soluble/fep/vdw/01_nvt.mdp
src/bindflow/mdp/templates/complex/soluble/fep/vdw/02_npt.mdp
src/bindflow/mdp/templates/complex/soluble/fep/vdw/03_npt_norest.mdp
src/bindflow/mdp/templates/complex/soluble/fep/vdw/prod.mdp
src/bindflow/mdp/templates/complex/soluble/mmpbsa/prod.mdp
src/bindflow/mdp/templates/ligand/equi/00_min.mdp
src/bindflow/mdp/templates/ligand/equi/01_nvt.mdp
src/bindflow/mdp/templates/ligand/equi/02_nvt.mdp
src/bindflow/mdp/templates/ligand/equi/03_npt.mdp
src/bindflow/mdp/templates/ligand/equi/prod.mdp
src/bindflow/mdp/templates/ligand/fep/coul/00_min.mdp
src/bindflow/mdp/templates/ligand/fep/coul/01_nvt.mdp
src/bindflow/mdp/templates/ligand/fep/coul/02_npt.mdp
src/bindflow/mdp/templates/ligand/fep/coul/03_npt_norest.mdp
src/bindflow/mdp/templates/ligand/fep/coul/prod.mdp
src/bindflow/mdp/templates/ligand/fep/vdw/00_min.mdp
src/bindflow/mdp/templates/ligand/fep/vdw/01_nvt.mdp
src/bindflow/mdp/templates/ligand/fep/vdw/02_npt.mdp
src/bindflow/mdp/templates/ligand/fep/vdw/03_npt_norest.mdp
src/bindflow/mdp/templates/ligand/fep/vdw/prod.mdp
src/bindflow/mmpbsa_in/__init__.py
src/bindflow/mmpbsa_in/input_loader.py
src/bindflow/mmpbsa_in/templates/gb.in
src/bindflow/mmpbsa_in/templates/pb.in
src/bindflow/mmpbsa_in/templates/pb_gb.in
src/bindflow/orchestration/__init__.py
src/bindflow/orchestration/flow_builder.py
src/bindflow/orchestration/generate_scheduler.py
src/bindflow/preparation/__init__.py
src/bindflow/preparation/boresch.py
src/bindflow/preparation/solvent.py
src/bindflow/preparation/system_builder.py
src/bindflow/rules/__init__.py
src/bindflow/rules/equi/Snakefile
src/bindflow/rules/equi/boresch.smk
src/bindflow/rules/equi/complex/membrane/setup.smk
src/bindflow/rules/equi/complex/membrane/simulation.smk
src/bindflow/rules/equi/complex/soluble/setup.smk
src/bindflow/rules/equi/complex/soluble/simulation.smk
src/bindflow/rules/equi/ligand/setup.smk
src/bindflow/rules/equi/ligand/simulation.smk
src/bindflow/rules/fep/Snakefile
src/bindflow/rules/fep/calculate_result.smk
src/bindflow/rules/fep/gather_receptor_results.smk
src/bindflow/rules/fep/complex/ana.smk
src/bindflow/rules/fep/complex/membrane/setup.smk
src/bindflow/rules/fep/complex/membrane/simulation.smk
src/bindflow/rules/fep/complex/soluble/setup.smk
src/bindflow/rules/fep/complex/soluble/simulation.smk
src/bindflow/rules/fep/ligand/ana.smk
src/bindflow/rules/fep/ligand/setup.smk
src/bindflow/rules/fep/ligand/simulation.smk
src/bindflow/rules/mmpbsa/Snakefile
src/bindflow/rules/mmpbsa/ana.smk
src/bindflow/rules/mmpbsa/gather_receptor_results.smk
src/bindflow/rules/mmpbsa/setup.smk
src/bindflow/rules/mmpbsa/simulation.smk
src/bindflow/rules/super_flow/Snakefile
src/bindflow/rules/super_flow/build_ligand_systems.smk
src/bindflow/utils/cluster.py
src/bindflow/utils/tools.py
test/test_fep.py
test/test_mmpbsa.py
test/test_small.py