├── .gitattributes ├── .gitignore ├── .travis.yml ├── CITATION.rst ├── LICENSE ├── MANIFEST.in ├── README.rst ├── conda-recipe └── meta.yaml ├── docs ├── Makefile ├── _templates │ └── autosummary │ │ └── module.rst ├── api │ ├── gaudi.cli.rst │ ├── gaudi.genes.rst │ ├── gaudi.objectives.rst │ └── gaudi.rst ├── conf.py ├── data │ ├── gaudimm-logo-whitebg.jpg │ ├── gaudimm-logo.jpg │ ├── gaudinspect_linux.jpg │ ├── gaudinspect_win.png │ ├── gaudiview-browse.png │ └── gaudiview.jpg ├── developers.rst ├── faq.rst ├── index.rst ├── input.rst ├── installation.rst ├── output.rst ├── primer.rst ├── requirements.txt ├── tutorial-firstrun.rst ├── tutorial-visualization.rst └── usage.rst ├── environment.yml ├── examples ├── batch_rmsd.py ├── batch_run.py ├── full_gaudi_input.yaml └── interactive_debugging.py ├── gaudi ├── __init__.py ├── _cpdrift.py ├── _version.py ├── algorithms.py ├── base.py ├── box.py ├── cli │ ├── __init__.py │ ├── gaudi_cli.py │ ├── gaudi_run.py │ └── gaudi_view.py ├── exceptions.py ├── genes │ ├── __init__.py │ ├── molecule.py │ ├── mutamers.py │ ├── normalmodes.py │ ├── rotamers.py │ ├── search.py │ ├── torsion.py │ └── trajectory.py ├── objectives │ ├── __init__.py │ ├── angle.py │ ├── contacts.py │ ├── coordination.py │ ├── distance.py │ ├── dsx.py │ ├── energy.py │ ├── gold.py │ ├── hbonds.py │ ├── inertia.py │ ├── ligscore.py │ ├── nwchem.py │ ├── smina.py │ ├── solvation.py │ ├── vina.py │ └── volume.py ├── parallel.py ├── parse.py ├── plugin.py └── similarity.py ├── resources ├── logo.png └── logo.xcf ├── setup.cfg ├── setup.py ├── tests ├── _gold.sh ├── conftest.py ├── data │ ├── 1amb.dcd │ ├── 1amb.pdb │ ├── 3pk2_full_ligand.mol2 │ ├── 3pk2_full_ligand.pdb │ ├── 3pk2_ligand.mol2 │ ├── 3pk2_ligand.pdb │ ├── 3pk2_ligand_rotated.pdb │ ├── 3pk2_ligand_with_metal.mol2 │ ├── 3pk2_metal.mol2 │ ├── 3pk2_metals.mol2 │ ├── 3pk2_metals.pdb │ ├── 3pk2_protein.pdb │ ├── 3pk2_waters.pdb │ ├── 4c3w.mol2 │ ├── 4c3w_ligand.mol2 │ ├── 4c3w_metal.mol2 │ ├── 4c3w_protein.mol2 │ ├── 4c3w_protein.pdb │ ├── 5dfr_minimized.pdb │ ├── 5er1_ligand.mol2 │ ├── 5er1_protein.mol2 │ └── butane.pdb ├── run_test.py ├── test_fixtures.py ├── test_genes_molecule.py ├── test_genes_normalmodes.py ├── test_genes_rotamers.py ├── test_genes_search.py ├── test_genes_torsion.py ├── test_genes_trajectory.py ├── test_objectives_contacts.py ├── test_objectives_coordination.py ├── test_objectives_dsx.py ├── test_objectives_energy.py ├── test_objectives_gold.py ├── test_objectives_nwchem.py ├── test_objectives_smina.py ├── test_objectives_vina.py ├── test_similarity.py └── test_validators.py └── versioneer.py /.gitattributes: -------------------------------------------------------------------------------- 1 | gaudi/_version.py export-subst 2 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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