├── .dockerignore ├── .gitattributes ├── .gitignore ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── NOTICE ├── README.md ├── RELEASES.md ├── codeship-services.yml ├── codeship-steps.yml ├── deployment ├── jupyter_unsecure.json └── run_notebook.sh ├── docker-compose.yml ├── img ├── protein.png ├── selector.png └── smallmol.png ├── js ├── .babelrc ├── .eslintrc ├── .gitignore ├── README.md ├── package.json ├── src │ ├── .gitattributes │ ├── 3dmol │ │ └── LICENSE │ ├── base_widget.js │ ├── d3 │ │ └── LICENSE │ ├── embed.js │ ├── example.js │ ├── extension.js │ ├── index.js │ ├── molviz2d.js │ ├── molviz3d.js │ ├── nbmolviz.css │ ├── nbmolviz_2d_component.jsx │ ├── nbmolviz_2d_model.js │ ├── nbmolviz_2d_view.js │ ├── nbmolviz_3d_component.jsx │ ├── nbmolviz_3d_model.js │ ├── nbmolviz_3d_view.js │ └── utils │ │ └── widget_utils.js └── webpack.config.js ├── nbmolviz ├── .gitignore ├── __init__.py ├── __main__.py ├── _version.py ├── base │ ├── __init__.py │ ├── base_widget.py │ └── mdt2json.py ├── colormaps.py ├── install.py ├── mdtconfig │ ├── __init__.py │ ├── compute.py │ ├── docker.py │ ├── images.py │ ├── interfaces.py │ └── visualization.py ├── methods │ ├── README.md │ ├── __init__.py │ ├── atomgroups.py │ ├── atoms.py │ ├── method.py │ ├── molecules.py │ └── trajectory.py ├── uielements │ ├── README.md │ ├── __init__.py │ ├── components.py │ ├── configurator.py │ ├── logwidget.py │ └── plotting.py ├── utils.py ├── viewers │ ├── README.md │ ├── __init__.py │ ├── common.py │ ├── geometry_viewer.py │ ├── graph_viewer.py │ ├── orbital_viewer.py │ ├── trajectory_viewer.py │ └── viewercontainer.py ├── widget_utils.py └── widgets │ ├── __init__.py │ ├── components.py │ ├── geombuilder.py │ ├── parameterization.py │ ├── selection.py │ └── symmetry.py ├── notebooks └── strip_nb_output.py ├── requirements.txt ├── set_filters.sh ├── setup.cfg ├── setup.py ├── tests ├── .dockerignore ├── Dockerfile ├── galileo │ ├── README.md │ ├── bin │ │ └── galileo │ ├── collector │ │ └── test_notebooks.js │ ├── nightwatch_config │ │ ├── customCommands │ │ │ ├── assertKernelIdle.js │ │ │ ├── assertTrueInBrowser.js │ │ │ ├── checkCellExecutedWithoutErrors.js │ │ │ ├── clearNbOutputs.js │ │ │ ├── elementScreenshot.js │ │ │ ├── executeCell.js │ │ │ ├── log.js │ │ │ ├── openNotebook.js │ │ │ ├── restartKernel.js │ │ │ ├── tagCellOutputsWithId.js │ │ │ ├── utils.js │ │ │ ├── waitForIdleKernel.js │ │ │ └── waitForTrue.js │ │ ├── globals.js │ │ └── nightwatch.js │ └── package.json ├── nb │ ├── .gitattributes │ ├── .gitignore │ ├── test_animations.ipynb │ ├── test_compute_widgets.ipynb │ ├── test_draw_protein.ipynb │ ├── test_draw_small_molecule.ipynb │ ├── test_geometry_builder_widget.ipynb │ ├── test_parameterization.ipynb │ ├── test_selection_widget.ipynb │ ├── test_symmetry_widget.ipynb │ └── test_volumetric.ipynb └── py │ ├── README.md │ ├── requirements.txt │ └── test_nbmolviz.py └── versioneer.py /.dockerignore: 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