├── .coveragerc ├── .coveralls.yml ├── .dockerignore ├── .gitattributes ├── .github └── ISSUE_TEMPLATE.md ├── .gitignore ├── CONTRIBUTING.md ├── DEVELOPMENT.md ├── DockerMakefiles ├── .gitignore ├── DockerMake.yml ├── Environments.yml ├── Moldesign.yml ├── PySCF.yml ├── README.md ├── buildfiles │ ├── ambertools │ │ └── runsander.py │ ├── deploybase │ │ └── cleanapt │ ├── moldesign │ │ ├── moldesign.dockerignore │ │ └── moldesign.yml │ └── notebook │ │ └── run_notebook.sh └── requirements.txt ├── LICENSE ├── MANIFEST.in ├── NOTICES ├── README.md ├── codeship-services.yml ├── codeship-steps.yml ├── deployment ├── README.md ├── build-env.dockerfile ├── deploy-tokens.crypt ├── print-environment.sh ├── publish.sh ├── pull-cache.sh ├── pull-chemdocker.sh ├── push-and-tag.sh ├── push-coverage.sh ├── requirements.txt ├── run-ci-tests.sh ├── send-test-status.py ├── test-env.dockerfile ├── test-tokens.crypt └── test-version-number.sh ├── docs ├── .gitignore ├── Makefile ├── api │ ├── datastructures.rst │ ├── geometry.rst │ ├── molecule.rst │ ├── test.rst │ └── wfn.rst ├── autogen_api.sh ├── biomolecule.rst ├── conf.py ├── creating_and_converting.rst ├── dynamics.rst ├── features.rst ├── generate_package_api.py ├── geometry.rst ├── img │ ├── atompos.png │ ├── atoms.png │ ├── benz_min_traj.png │ ├── bonds.png │ ├── chains.png │ ├── data.png │ ├── ethyl_after.png │ ├── ethyl_init.png │ ├── ethyl_noadjust.png │ ├── geometrybuilder.png │ ├── howdoi_annotated.png │ ├── howdoi_method_autocomplete.png │ ├── howdoi_orbs.png │ ├── howdoi_pdb1.png │ ├── howdoi_pdb_assm.png │ ├── howdoi_purplewater.png │ ├── howdoi_subtle.png │ ├── howdoi_view1.png │ ├── molecule.png │ ├── properties.png │ ├── questiondoc.png │ ├── residues.png │ ├── shifttab_online.png │ ├── struc_benzene.png │ ├── tab_autocomplete.png │ └── wfn.png ├── index.rst ├── install.rst ├── integrators.rst ├── interactive.rst ├── properties.rst ├── quickstart.rst ├── requirements.txt ├── structure.rst ├── toplevel.rst └── visualization.rst ├── environment.yml ├── moldesign ├── HISTORY.md ├── README.md ├── __init__.py ├── __main__.py ├── _notebooks │ ├── .building │ │ ├── Dexter_alkane.ipynb │ │ ├── Guided tour.ipynb │ │ ├── Header.ipynb │ │ ├── Parallel.ipynb │ │ ├── The harmonic oscillator.ipynb │ │ ├── Units and gravity.ipynb │ │ └── buckyball.ipynb │ ├── .gitattributes │ ├── .gitignore │ ├── 3AID.cif │ ├── Example 1. Build and simulate DNA.ipynb │ ├── Example 2. UV-vis absorption spectra.ipynb │ ├── Example 3. Simulating a crystal structure.ipynb │ ├── Example 4. HIV Protease bound to an inhibitor.ipynb │ ├── Example 5. Enthalpic barriers.ipynb │ ├── Getting Started.ipynb │ ├── Tutorial 1. Making a molecule.ipynb │ ├── Tutorial 2. Biochemical basics.ipynb │ ├── Tutorial 3. Quantum Chemistry.ipynb │ ├── data │ │ ├── 1bna.pdb │ │ ├── 1yu8.pdb │ │ ├── 3AID.pdb │ │ ├── bipyridine.sdf │ │ ├── buckyball.pdb │ │ ├── butane.xyz │ │ ├── nuc.inpcrd │ │ ├── nuc.pdb │ │ ├── nuc.prmtop │ │ ├── octane.xyz │ │ └── solar.csv │ ├── img │ │ ├── Header.png │ │ ├── Molecules.png │ │ ├── Top.png │ │ ├── butadiene_orbs.png │ │ ├── dna.png │ │ ├── holliday.png │ │ └── protease.png │ └── nbscripts │ │ ├── gen_example_md.py │ │ ├── gen_toc.py │ │ └── strip_nb_output.py ├── _static_data │ ├── .gitignore │ ├── amber_ffs.yml │ ├── apply_copyright.sh │ ├── chemical_components.dat │ ├── chemical_components.dir │ ├── img │ │ └── banner.png │ ├── nist_atomic.yml │ ├── pint_atomic_units.txt │ ├── residue_templates.json │ └── scripts │ │ ├── generate_residue_data.py │ │ └── generate_residue_templates.py ├── _tests │ ├── .gitignore │ ├── README.md │ ├── __init__.py │ ├── benchmarks │ │ ├── README.md │ │ ├── gamess │ │ │ └── ethylene-cas2x2-SA3-321g │ │ │ │ └── input │ │ └── psi4 │ │ │ └── input.dat │ ├── conftest.py │ ├── data │ │ ├── 1KBU.cif.bz2 │ │ ├── 1KBU.pdb.bz2 │ │ ├── 1hpk.pdb │ │ ├── 1pyn.pdb.gz │ │ ├── 1yu8.pdb │ │ ├── 2jaj.pdb.gz │ │ ├── 2p8w.cif.bz2 │ │ ├── 3ac2.pdb.bz2 │ │ ├── 3aid.cif.bz2 │ │ ├── 3aid.pdb.gz │ │ ├── 3b5x.cif.bz2 │ │ ├── 3p3k.pdb.gz │ │ ├── 5b7a.pdb.bz2 │ │ ├── ACTG.cif │ │ ├── ACTG.pdb │ │ ├── bipyridine.mol2 │ │ ├── bipyridine.sdf │ │ ├── bipyridine.xyz │ │ └── propane.pdb │ ├── debug-job │ ├── helpers.py │ ├── molecule_fixtures.py │ ├── object_fixtures.py │ ├── test_alignments.py │ ├── test_ambertools_xface.py │ ├── test_atom_bond_computed_properties.py │ ├── test_atom_containers.py │ ├── test_atoms.py │ ├── test_biopython_xface.py │ ├── test_cli.py │ ├── test_config.py │ ├── test_constraints.py │ ├── test_copies.py │ ├── test_dna_primary_structure.py │ ├── test_gaussian_math.py │ ├── test_geometry.py │ ├── test_imports.py │ ├── test_io.py │ ├── test_mathutils.py │ ├── test_minimizers.py │ ├── test_molecules.py │ ├── test_objects.py │ ├── test_openbabel_xface.py │ ├── test_openmm_xface.py │ ├── test_pdb_processing.py │ ├── test_pdbfixer_xface.py │ ├── test_protein_primary_structure.py │ ├── test_qm_xfaces.py │ ├── test_qmmm.py │ ├── test_symmetry.py │ ├── test_tools.py │ ├── test_trajectory.py │ ├── test_units.py │ └── test_wfn.py ├── _version.py ├── compute │ ├── CHEMDOCKER_TAG │ ├── README.md │ ├── __init__.py │ ├── compute.py │ ├── configuration.py │ ├── packages.py │ └── remote_procedure_calls.py ├── data │ ├── __init__.py │ ├── atomic.py │ ├── biochemical.py │ ├── chemical_components.py │ ├── data.py │ └── ff.py ├── exceptions.py ├── external │ ├── README.md │ ├── __init__.py │ ├── licenses │ │ └── PYTHON │ ├── pathlib.py │ ├── pyquante2 │ │ ├── LICENSE │ │ ├── __init__.py │ │ ├── one.py │ │ └── utils.py │ └── transformations.py ├── fileio.py ├── forcefields │ ├── __init__.py │ ├── amber.py │ ├── errors.py │ ├── ffparams.py │ └── forcefieldbase.py ├── geom │ ├── README.md │ ├── __init__.py │ ├── alignment.py │ ├── constraints.py │ ├── coords.py │ ├── grads.py │ ├── monitor.py │ ├── setcoord.py │ ├── shake.py │ └── symmetry.py ├── helpers │ ├── README.md │ ├── __init__.py │ ├── helpers.py │ ├── logs.py │ ├── pdb.py │ └── qmmm.py ├── integrators │ ├── README.md │ ├── __init__.py │ ├── base.py │ ├── openmm.py │ └── verlet.py ├── interfaces │ ├── README.md │ ├── __init__.py │ ├── ambertools.py │ ├── biopython_interface.py │ ├── nbo_interface.py │ ├── openbabel.py │ ├── openmm.py │ ├── opsin_interface.py │ ├── parmed_interface.py │ ├── pdbfixer_interface.py │ ├── pyscf_interface.py │ ├── symmol_interface.py │ └── tleap_interface.py ├── mathutils │ ├── __init__.py │ ├── eigen.py │ ├── grids.py │ ├── spherical_harmonics.py │ └── vectormath.py ├── method.py ├── min │ ├── README.md │ ├── __init__.py │ ├── base.py │ ├── descent.py │ ├── scipy.py │ └── smart.py ├── models │ ├── README.md │ ├── __init__.py │ ├── amber.py │ ├── base.py │ ├── jsonmodel.py │ ├── models.py │ ├── nwchem.py │ ├── openbabel.py │ ├── openmm.py │ ├── pyscf.py │ ├── qmmm.py │ └── toys.py ├── molecules │ ├── README.md │ ├── __init__.py │ ├── atomcollections.py │ ├── atoms.py │ ├── biounits.py │ ├── bond_graph.py │ ├── bonds.py │ ├── chain.py │ ├── coord_arrays.py │ ├── molecule.py │ ├── primary_structure.py │ ├── properties.py │ ├── residue.py │ └── trajectory.py ├── orbitals │ ├── __init__.py │ ├── atomic_basis_fn.py │ ├── basis.py │ ├── cartesian.py │ ├── gaussians.py │ ├── orbitals.py │ ├── primitives.py │ ├── spherical.py │ └── wfn.py ├── parameters.py ├── tools │ ├── README.md │ ├── __init__.py │ ├── build.py │ └── topology.py ├── units │ ├── __init__.py │ ├── constants.py │ ├── quantity.py │ ├── tools.py │ └── unitsystem.py ├── utils │ ├── README.md │ ├── __init__.py │ ├── _deadfunctions.py.txt │ ├── apply_copyright.sh │ ├── callsigs.py │ ├── classes.py │ ├── databases.py │ ├── descriptors.py │ ├── docparsers │ │ ├── __init__.py │ │ ├── google.py │ │ └── sphinxlicense │ │ │ ├── AUTHORS │ │ │ └── LICENSE │ 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