├── .git_archival.txt ├── .gitattributes ├── .github ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── ci.yaml │ └── docs.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── devtools ├── envs │ └── base.yaml └── scripts │ └── extract-code-blocks.py ├── docs ├── development.md ├── guide-atm.md ├── guide-fe.md ├── guide-md.md ├── guide-septop.md ├── index.md ├── javascripts │ └── mathjax.js ├── migration.md └── scripts │ └── gen_ref_pages.py ├── examples ├── eralpha │ ├── config-atm-rest.yaml │ ├── config-atm.yaml │ ├── config-septop-rest.yaml │ ├── config-septop.yaml │ ├── edges-atm.yaml │ ├── edges-septop.yaml │ ├── forcefield │ │ ├── 2d │ │ │ ├── vacuum.mol2 │ │ │ └── vacuum.parm7 │ │ ├── 2e │ │ │ ├── vacuum.mol2 │ │ │ └── vacuum.parm7 │ │ ├── 3a │ │ │ ├── vacuum.mol2 │ │ │ └── vacuum.parm7 │ │ └── 3b │ │ │ ├── vacuum.mol2 │ │ │ └── vacuum.parm7 │ └── proteins │ │ └── eralpha │ │ └── protein.pdb └── temoa │ ├── config-atm.yaml │ ├── edges-atm.yaml │ ├── forcefield │ ├── g1 │ │ ├── vacuum.mol2 │ │ └── vacuum.parm7 │ └── g4 │ │ ├── vacuum.mol2 │ │ └── vacuum.parm7 │ └── proteins │ └── temoa │ ├── protein.mol2 │ └── protein.parm7 ├── femto ├── __init__.py ├── fe │ ├── __init__.py │ ├── _cli.py │ ├── atm │ │ ├── __init__.py │ │ ├── _analyze.py │ │ ├── _cli.py │ │ ├── _config.py │ │ ├── _equilibrate.py │ │ ├── _runner.py │ │ ├── _sample.py │ │ ├── _setup.py │ │ └── _utils.py │ ├── config.py │ ├── corrections.py │ ├── ddg.py │ ├── fep.py │ ├── inputs.py │ ├── py.typed │ ├── reference.py │ ├── septop │ │ ├── __init__.py │ │ ├── _analyze.py │ │ ├── _cli.py │ │ ├── _config.py │ │ ├── _equilibrate.py │ │ ├── _runner.py │ │ ├── _sample.py │ │ ├── _setup.py │ │ └── _utils.py │ ├── tests │ │ ├── __init__.py │ │ ├── atm │ │ │ ├── __init__.py │ │ │ ├── conftest.py │ │ │ ├── test_analyze.py │ │ │ ├── test_cli.py │ │ │ ├── test_config.py │ │ │ ├── test_equilibrate.py │ │ │ ├── test_runner.py │ │ │ ├── test_sample.py │ │ │ ├── test_setup.py │ │ │ └── test_utils.py │ │ ├── conftest.py │ │ ├── data │ │ │ ├── cdk2 │ │ │ │ ├── 1h1q.sdf │ │ │ │ ├── 1h1q.xml │ │ │ │ ├── 1oiu.sdf │ │ │ │ ├── 1oiu.xml │ │ │ │ └── cdk2.pdb │ │ │ └── temoa │ │ │ │ ├── g1.mol2 │ │ │ │ ├── g1.xml │ │ │ │ ├── g4.mol2 │ │ │ │ ├── g4.xml │ │ │ │ ├── temoa.sdf │ │ │ │ └── temoa.xml │ │ ├── septop │ │ │ ├── __init__.py │ │ │ ├── conftest.py │ │ │ ├── test_analyze.py │ │ │ ├── test_cli.py │ │ │ ├── test_config.py │ │ │ ├── test_equilibrate.py │ │ │ ├── test_runner.py │ │ │ ├── test_sample.py │ │ │ ├── test_setup.py │ │ │ └── test_utils.py │ │ ├── systems.py │ │ ├── test_cli.py │ │ ├── test_core.py │ │ ├── test_corrections.py │ │ ├── test_ddg.py │ │ ├── test_fep.py │ │ ├── test_inputs.py │ │ ├── test_reference.py │ │ ├── test_uwham.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── test_cli.py │ │ │ └── test_queue.py │ ├── utils │ │ ├── __init__.py │ │ ├── cli.py │ │ └── queue.py │ └── uwham.py └── md │ ├── __init__.py │ ├── anneal.py │ ├── config.py │ ├── constants.py │ ├── hremd.py │ ├── prepare.py │ ├── py.typed │ ├── reporting │ ├── __init__.py │ ├── _reporting.py │ └── openmm.py │ ├── rest.py │ ├── restraints.py │ ├── simulate.py │ ├── tests │ ├── __init__.py │ ├── conftest.py │ ├── data │ │ ├── 1h1q.parm7 │ │ └── 1h1q.rst7 │ ├── mocking.py │ ├── reporting │ │ ├── __init__.py │ │ ├── test_openmm.py │ │ └── test_reporting.py │ ├── test_anneal.py │ ├── test_config.py │ ├── test_hremd.py │ ├── test_prepare.py │ ├── test_rest.py │ ├── test_restraints.py │ ├── test_simulate.py │ └── utils │ │ ├── __init__.py │ │ ├── test_geometry.py │ │ ├── test_models.py │ │ ├── test_mpi.py │ │ └── test_openmm.py │ └── utils │ ├── __init__.py │ ├── amber.py │ ├── geometry.py │ ├── logging.py │ ├── models.py │ ├── mpi.py │ └── openmm.py ├── mkdocs.yml └── pyproject.toml /.git_archival.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Psivant/femto/HEAD/.git_archival.txt 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