{"id":13498861,"url":"https://github.com/nglviewer/nglview","last_synced_at":"2025-05-14T01:06:02.385Z","repository":{"id":38208605,"uuid":"45852176","full_name":"nglviewer/nglview","owner":"nglviewer","description":"Jupyter widget to interactively view molecular structures and trajectories","archived":false,"fork":false,"pushed_at":"2025-01-24T00:43:29.000Z","size":327237,"stargazers_count":863,"open_issues_count":37,"forks_count":134,"subscribers_count":20,"default_branch":"master","last_synced_at":"2025-05-12T01:07:19.670Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://nglviewer.org/nglview/latest/","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nglviewer.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-11-09T16:48:57.000Z","updated_at":"2025-05-10T20:53:29.000Z","dependencies_parsed_at":"2023-01-27T08:46:07.475Z","dependency_job_id":"62f6cc4c-a72b-426a-996b-b4da0bdf4fbc","html_url":"https://github.com/nglviewer/nglview","commit_stats":{"total_commits":1358,"total_committers":49,"mean_commits":"27.714285714285715","dds":0.4285714285714286,"last_synced_commit":"249467b55ad1c141ae665508d5055ec75fffde47"},"previous_names":["arose/nglview"],"tags_count":90,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nglviewer%2Fnglview","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nglviewer%2Fnglview/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nglviewer%2Fnglview/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nglviewer%2Fnglview/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nglviewer","download_url":"https://codeload.github.com/nglviewer/nglview/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253656409,"owners_count":21943081,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-07-31T21:00:45.774Z","updated_at":"2025-05-14T01:05:57.376Z","avatar_url":"https://github.com/nglviewer.png","language":"Jupyter Notebook","funding_links":[],"categories":["Jupyter Notebook","Interactive Widgets","Interactive Widgets \u0026 Visualization","شیمی"],"sub_categories":["Interactive Jupyter Widget Ecosystem","کار با زمان و تقویم"],"readme":"[Citation](#cite) | [Installation](#installation) | [Example](#example) | [Usage](#usage) | [Command line](#command-line) | [API doc](#api-doc) | [Interface classes](docs/interface_classes.md) | [Website](#website) | [Acknowledgment](#acknowledgment)\n\n![Build Status](https://github.com/nglviewer/nglview/actions/workflows/test.yml/badge.svg)\n![Build Extension Status](https://github.com/nglviewer/nglview/actions/workflows/build-extension.yml/badge.svg)\n\n## Try nglview online: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/hainm/nglview-binder/master?urlpath=lab/tree/nglview/notebooks)\n\n\nAn [IPython/Jupyter](http://jupyter.org/) widget to interactively view molecular structures and trajectories. Utilizes the embeddable [NGL Viewer](https://github.com/nglviewer/ngl) for rendering. Support for showing data from the file-system, [RCSB PDB](http:www.rcsb.org), [simpletraj](https://github.com/arose/simpletraj) and from objects of analysis libraries [mdtraj](http://mdtraj.org/), [pytraj](http://amber-md.github.io/pytraj/latest/index.html), [mdanalysis](http://www.mdanalysis.org/), [ParmEd](http://parmed.github.io/ParmEd/), [rdkit](https://github.com/rdkit/rdkit), [ase](https://wiki.fysik.dtu.dk/ase/), [HTMD](https://www.htmd.org), [biopython](https://github.com/biopython/biopython.github.io/), [cctbx](https://cci.lbl.gov/cctbx_docs/iotbx/), [pyrosetta](http://pyrosetta.org), [schrodinger's Structure](http://content.schrodinger.com/Docs/r2015-4/python_api/api/schrodinger.structure.Structure-class.html)\n\nShould work with Python 3. If you experience problems, please file an [issue](https://github.com/nglviewer/nglview/issues).\n\nAsk question about usage? Please post [here](https://github.com/nglviewer/nglview/discussions)\n\n![membrane](examples/images/membrane.gif)\n\nTable of contents\n=================\n\n* [Installation](#installation)\n* [Example](#example)\n* [Showcase from users](#showcase-from-users)\n* [Usage](#usage)\n* [Contributing](#contributing)\n* [Command line](#command-line)\n* [API doc](#api-doc)\n* [Interface classes](docs/interface_classes.md)\n* [Changelog](CHANGELOG.md)\n* [FAQ](#faq)\n* [Website](#website)\n* [Acknowledgment](#acknowledgment)\n* [Cite](#cite)\n* [License](#license)\n\n\nInstallation\n============\n\nReleased version\n----------------\n\n- Available on `conda-forge` channel\n\n    ```bash\n    conda install nglview -c conda-forge\n    ```\n\n- Available on [PyPI](https://pypi.python.org/pypi/nglview/)\n\n```bash\n   pip install nglview\n```\n\nJupyterlab: `nglview` works best with jupyterlab \u003e= 3.0 and no further steps needed.\nKnown to work versions\n\n|nglview|lab|notebook|ipywidgets|Known issue(s)|VSCode\n|--|--|--|--|--|--|\n|3.1.0|4.0.10|7.0.6|8.1.1|[HTML embed doesn't work](https://github.com/jupyter-widgets/ipywidgets/issues/3878)|No|\n|3.0.8|4.0.10|7.0.6|8.1.1|[show_pdbid doesn't work](https://github.com/nglviewer/nglview/issues/1082)|Yes|\n\n## Notes\n\nIf you are using `notebook` v5.0, you need to increase the `iopub_data_rate_limit`\nto [visualize big structure (e.g: solvated system)](https://github.com/arose/nglview/issues/633)\n\n```\njupyter notebook --NotebookApp.iopub_data_rate_limit=10000000\n```\n\nDevelopment version\n-------------------\n\nRequirement: `ipywidgets \u003e= 7.0`, `notebook \u003e= 4.2`\n\nThe development version can be installed directly from github:\n\n### notebook user\n\n```bash\n    git clone https://github.com/arose/nglview\n    cd nglview\n    python setup.py install\n\n    # if you edit files in ./js folder, make sure to rebuild the code\n    cd js\n    npm install\n\n    # probably need to activate widgetsnbextension\n    # python -m ipykernel install --sys-prefix\n    # jupyter nbextension enable --py --sys-prefix widgetsnbextension\n    # jupyter nbextension enable --py --sys-prefix nglview\n\n    # tested with ipywidgets 5.2.2, notebook 4.2.1\n```\n\nExample\n=======\n\n- Notebooks: please see our [Jupyter notebook examples](examples/README.md)\n- Simple demo for trajectory (take time to load): [biomembrane](http://amber-md.github.io/pytraj/latest/ngl_player.html)\n\nShowcase from users\n===================\n- Please check [user examples](examples/user_examples.md). Feel free to contribute.\n- Also check [a series of excelent tutorials about/using nglview from volkamerlab](https://projects.volkamerlab.org/teachopencadd/search.html?q=nglview)\n\nUsage\n=====\n\nOpen a notebook\n\n    jupyter notebook\n\nand issue\n\n```Python\nimport nglview\nview = nglview.show_pdbid(\"3pqr\")  # load \"3pqr\" from RCSB PDB and display viewer widget\nview\n```\n\nA number of convenience functions are available to quickly display data from\nthe file-system, [RCSB PDB](http:www.rcsb.org), [simpletraj](https://github.com/arose/simpletraj) and from objects of analysis libraries [mdtraj](http://mdtraj.org/), [pytraj](http://amber-md.github.io/pytraj/latest/index.html), [mdanalysis](http://www.mdanalysis.org/), [ParmEd](http://parmed.github.io/ParmEd/), [rdkit](https://github.com/rdkit/rdkit), [HTMD](https://github.com/Acellera/htmd), [biopython](https://github.com/biopython/biopython.github.io/).\n\n| Function                                 | Description                                           |\n|------------------------------------------|-------------------------------------------------------|\n| `show_file(path)`                        | Shows any NGL supported file formats (pdb, gro, mol2, sdf, dx, ..) in `path`       |\n| `show_pdbid(pdbid)`                      | Shows `pdbid` fetched from RCSB PDB                   |\n| `show_simpletraj(struc_path, traj_path)` | Shows structure \u0026 trajectory loaded with `simpletraj` |\n| `show_mdtraj(traj)`                      | Shows `MDTraj` trajectory `traj`                      |\n| `show_pytraj(traj)`                      | Shows `PyTraj` trajectory `traj`                      |\n| `show_parmed(structure)`                 | Shows `ParmEd` structure                              |\n| `show_mdanalysis(univ)`                  | Shows `MDAnalysis` Universe or AtomGroup `univ`       |\n| `show_rdkit(mol)`                        | Shows `rdkit` rdkit.Chem.rdchem.Mol                   |\n| `show_ase(atoms)`                        | Shows `ase` Atoms                                     |\n| `show_asetraj(traj)`                     | Shows `ase` trajectory `traj`                         |\n| `show_pymatgen(struct)`                  | Shows `pymatgen` Structure                            |\n| `show_htmd(mol)`                         | Shows `HTMD` Molecules                                |\n| `show_biopython(mol)`                    | Shows `Biopython` structural entities                 |\n| `show_iotbx(mol)`                        | Shows `cctbx's iotbx` structure                       |\n| `show_rosetta(pose)`                     | Shows `pyrosetta's Pose`                              |\n| `show_iodata(obj)`                       | Shows `iodata's IOData`                               |\n| `show_psi4(obj)`                         | Shows `psi4's Molecule`                               |\n| `show_qcelemental`                       | Shows `QCelementary's Molecule`                       |\n| `show_openbabel`                         | Shows `openbabel's OMol`                              |\n| `show_prody`                             | Shows `prody's Ensemble or AtomGroup`                 |\n\n\nAPI\n===\n\nRepresentations\n---------------\n\n```python\nview.add_representation('cartoon', selection='protein')\n\n# or shorter\nview.add_cartoon(selection=\"protein\")\nview.add_surface(selection=\"protein\", opacity=0.3)\n\n# specify color\nview.add_cartoon(selection=\"protein\", color='blue')\n\n# specify residue\nview.add_licorice('ALA, GLU')\n\n# clear representations\nview.clear_representations()\n\n# update parameters for ALL cartoons of component 0 (default)\nview.update_cartoon(opacity=0.4, component=0)\n\n# remove ALL cartoons of component 0 (default)\nview.remove_cartoon(opacity=0.4, component=0)\n\n# Not using default representation\nview = nv.show_file('your.pdb', default=False)\nview.center()\nview.add_rope()\n```\n\nRepresentations can also be changed by overwriting the `representations` property\nof the widget instance `view`. The available `type` and `params` are described\nin the NGL Viewer [documentation](http://nglviewer.org/ngl/api/index.html).\n\n```Python\nview.representations = [\n    {\"type\": \"cartoon\", \"params\": {\n        \"sele\": \"protein\", \"color\": \"residueindex\"\n    }},\n    {\"type\": \"ball+stick\", \"params\": {\n        \"sele\": \"hetero\"\n    }}\n]\n```\n\nThe widget constructor also accepts a `representation` argument:\n\n```Python\ninitial_repr = [\n    {\"type\": \"cartoon\", \"params\": {\n        \"sele\": \"protein\", \"color\": \"sstruc\"\n    }}\n]\n\nview = nglview.NGLWidget(struc, representation=initial_repr)\nview\n```\n\n\nProperties\n----------\n\n```Python\n# set the frame number\nview.frame = 100\n```\n\n```Python\n# parameters for the NGL stage object\nview.stage.set_parameters(**{\n    # \"percentages, \"dist\" is distance to camera in Angstrom\n    \"clipNear\": 0, \"clipFar\": 100, \"clipDist\": 10,\n    # percentages, start of fog and where on full effect\n    \"fogNear\": 0, \"fogFar\": 100,\n    # background color\n    \"backgroundColor\": \"black\",\n})\n\n# note: NGLView accepts both origin camel NGL keywords (e.g. \"clipNear\")\n# and snake keywords (e.g \"clip_near\")\n```\n\n```python\n# parameters to control the `delay` between snapshots\n# change `step` to play forward (positive value) or backward (negative value)\n# note: experimental code\nview.player.parameters = dict(delay=0.04, step=-1)\n```\n\n```python\n# update camera type\nview.camera = 'orthographic'\n```\n\n```python\n# change background color\nview.background = 'black'\n```\nTrajectory\n----------\n\n```python\n# adding new trajectory\nview.add_trajectory(traj)\n# traj could be a `pytraj.Trajectory`, `mdtraj.Trajectory`, `MDAnalysis.Universe`,\n# `parmed.Structure`, `htmd.Molecule` or derived class of `nglview.Trajectory`\n\n# change representation\nview[0].add_cartoon(...) # equal to view.add_cartoon(component=0)\nview[1].add_licorice(...) # equal to view.add_licorice(component=1)\n```\n\nAdd extra component\n-------------------\n\n```python\n# Density volumes (MRC/MAP/CCP4, DX/DXBIN, CUBE)\n# Or adding derived class of `nglview.Structure`\nview.add_component('my.ccp4')\n\n# add component from url\nview.add_component('rcsb://1tsu.pdb')\n# NOTE: Trajectory is a special case of component.\n```\n\nMouse\n-----\n```python\n# coot mouse style (https://en.wikipedia.org/wiki/Coot_(software))\nview.stage.set_parameters(mouse_preset='coot')\n```\n\nInteraction controls\n--------------------\n- [Mouse](https://github.com/arose/ngl/blob/master/docs/usage/interaction-controls.md#mouse)\n- [Keyboard](https://github.com/arose/ngl/blob/master/docs/usage/interaction-controls.md#keyboard)\n\n\nMovie making\n------------\n\nRequire: moviepy (`pip install moviepy`)\n\n```python\nfrom nglview.contrib.movie import MovieMaker\nmovie = MovieMaker(view, output='my.gif', in_memory=True)\nmovie.make()\n```\n\nEmbed widget\n------------\n[embed](docs/embed.md)\n\nAPI doc\n=======\n- [Latest version](http://nglviewer.github.io/nglview/latest/api.html)\n- [All releases versions](http://nglviewer.github.io/nglview/release/index.html)\n- [Development version](http://nglviewer.github.io/nglview/dev/api.html)\n\nCommand line\n============\n\n```bash\n\n# open a notebook and import nglview\nnglview\n\n# Require installing pytraj (PR for other backends is welcome)\n# open notebook, load `my.pdb` to pytraj's trajectory then display `view`\nnglview my.pdb\n\n# load density data\nnglview my.ccp4\n\n# open notebook, create trajectory with given topology `my.parm7` and trajecotry file `traj.nc`,\n# then display `view`\nnglview my.parm7 -c traj.nc\n\n# load all trajectories with filename ending with 'nc'\n# make sure to use quote \" \"\nnglview my.parm7 -c \"*.nc\"\n\n# open notebook, copy content from `myscript.py`\nnglview myscript.py\n\n# create a remote notebook\n# just follow its instruction\nnglview my.pdb --remote\nnglview my.parm7 -c traj.nc --remote\nnglview mynotebook.ipynb --remote\n\n# demo (don't need pytraj)\nnglview demo\n\n# specify web browser\nnglview my.pdb --browser=google-chrome\n```\n\nFAQ\n===\n\n[Q\u0026A](docs/FAQ.md)\n\nWebsite\n=======\n\n- http://nglviewer.github.io/nglview/latest\n- http://nglviewer.github.io/nglview/dev\n\nTalks\n=====\n[Talks about NGL and nglview](./talks.md)\n\nContributing\n============\n\n[Join us here](./CONTRIBUTING.md)\n\nProjects integrating NGLView\n============================\n\n(Feel free to make a PR to add/remove your project here. Thanks.)\n\n- [AMBER](http://ambermd.org/) -  A package of programs for molecular dynamics simulations of proteins and nucleic acids\n- [mbuild](https://github.com/iModels/mbuild) - A hierarchical, component based molecule builder\n- [deepchem](https://github.com/deepchem/deepchem) - Deep-learning models for Drug Discovery and Quantum Chemistry\n- [htmd](https://github.com/Acellera/htmd) - High throughput molecular dynamics simulations\n- [Moleidoscope](https://github.com/kbsezginel/Moleidoscope) - Molecular kaleidoscope\n- [ssbio](https://github.com/nmih/ssbio) - Tools for enabling structural systems biology\n- [hublib](https://github.com/martin-hunt/hublib) - hublib is a Python library for the [HUBzero](https://hubzero.org/) science gateway platform.\n- [molPX](https://github.com/markovmodel/molPX): ipython API to visualize MD-trajectories along projected trajectories\n- [nanoribbon](https://github.com/oschuett/nanoribbon)\n- [ase](https://github.com/rosswhitfield/ase): Atomic Simulation Environment\n- [pida](https://github.com/jharman25/pida): Software for analyzing multiple protein-protein interaction docking solutions,\n- [pytim](https://github.com/Marcello-Sega/pytim)\n- [MobleyLab/drug-computing](https://github.com/MobleyLab/drug-computing) Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course.\n- [pyiron](https://pyiron.github.io/): an integrated development environment for implementing, testing, and running simulations in computational materials science.\n- [BioSimSpace](https://biosimspace.org/): An interoperable framework for biomolecular simulation\n- [pyrod](https://github.com/schallerdavid/pyrod): PyRod - Tracing water molecules in molecular dynamics simulations\n- [kugupu](https://github.com/kugupu/kugupu): kugupu - a molecular network generator to study charge transport pathways in amorphous materials\n- [pnab](https://github.com/alenaizan/pnab): proto-Nucleic Acid Builder\n- [opencadd](https://github.com/volkamerlab/opencadd): A Python library for structural cheminformatics\n- [teachopencadd](https://github.com/volkamerlab/teachopencadd): TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data\n- [query.libretexts.org](https://query.libretexts.org/Sandboxes/jupyterteam@ucdavis.edu): query.libretexts.org\n- [datamol](https://github.com/datamol-org/datamol):  A python library to work with molecules.\n- [dynophores](https://github.com/dominiquesydow/dynophores): Dynamic pharmacophore modeling of molecular interactions\n- [pychemcurv](https://github.com/gVallverdu/pychemcurv): Discrete and local curvature applied to chemistry and chemical reactivity\n- [AutoSolvate](https://github.com/Liu-group/AutoSolvate): Automated workflow for generating quantum chemistry calculation of explicitly solvated molecules\n- [plipify](https://github.com/volkamerlab/plipify): PLIPify: Protein-Ligand Interaction Frequencies across Multiple Structures\n- [Melodia](https://github.com/rwmontalvao/Melodia): Differential Geometry of Proteins Backbones\n- [pyrosetta_viewer3d](https://github.com/RosettaCommons/pyrosetta_viewer3d): Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab\n- [py4vasp](https://vasp.at/py4vasp): Python interface for VASP\n- [eminus](https://github.com/wangenau/eminus): A plane wave density functional theory code.\n- [MolSysMT](https://github.com/uibcdf/MolSysMT): Molecular Systems Multi-Tool\n\nAcknowledgment\n==============\n- Funding: Hai Nguyen is supported by NIH Grant GM103297, \"The Center for HIV RNA Studies\" (2015 to 02-2017).\n- Many thanks to `nglview` [contributors](https://github.com/arose/nglview/graphs/contributors)\n\nCite\n====\nIf you would like to acknowledge our work, feel free to cite:\n\nHai Nguyen, David A Case, Alexander S Rose; NGLview - Interactive molecular graphics for Jupyter notebooks, Bioinformatics, , btx789, https://doi.org/10.1093/bioinformatics/btx789\n\nLicense\n=======\n\nGenerally MIT, see the LICENSE file for details.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnglviewer%2Fnglview","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnglviewer%2Fnglview","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnglviewer%2Fnglview/lists"}