Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
26 of 82 committers (31.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.9%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
WebGL accelerated JavaScript molecular graphics library
Basic Info
- Host: GitHub
- Owner: 3dmol
- License: other
- Language: Jupyter Notebook
- Default Branch: master
- Homepage: https://3dmol.org/
- Size: 1.01 GB
Statistics
- Stars: 888
- Watchers: 29
- Forks: 211
- Open Issues: 37
- Releases: 47
Topics
Metadata Files
README.md
3Dmol.js
3Dmol.js is an object-oriented, WebGL accelerated JavaScript library for online molecular visualization.
Since 3Dmol.js is licensed under the permissive BSD open-source license, you are free to use it in any project, as long the code is properly acknowledged and cited.
With 3Dmol.js, you can add beautifully rendered molecular visualizations to your web applications. Features include: * support for pdb, sdf, mol2, xyz, cif, cdjson, mmtf, prmtop, gro, pqr, cube, and vasp formats * parallelized molecular surface computation * sphere, stick, line, cross, cartoon, and surface styles * atom property based selection and styling * labels * clickable interactivity with molecular data * geometric shapes including spheres and arrows
See the documentation to learn how to use 3Dmol.js as a hosted viewer, embeddable viewer, or as a component of a larger application.
Examples
HTML
```html
```JavaScript
We support the use of both PDB queries as well as PDB files.
First you simply create the viewer with a div's id.
javascript
var viewer = $3Dmol.createViewer($("#div"));
Then you can download a protein data bank model (here pdb:1MO8) and display it with the styling of your choosing.
```javascript $3Dmol.download("pdb:1MO8",viewer,{multimodel:true, frames:true},function(){ viewer.setStyle({}, {cartoon:{color:"spectrum"}}); viewer.render(); });
```
Surfaces
We also support the use of surfaces that are asynchronously loaded and support different color schemes
javascript
viewer.addSurface($3Dmol.SurfaceType.VDW, {
opacity:0.85,
voldata: new $3Dmol.VolumeData(volumedata, "cube"),
volscheme: new $3Dmol.Gradient.ROYGB(range[1],range[0])
},{});
Shapes
The use of different shapes and styles is supported.
javascript
viewer.addCylinder({start:{x:0.0,y:2.0,z:0.0},
end:{x:0.0,y:10.0,z:0.0},
radius:0.5,
fromCap:false,
toCap:true,
color:'teal'});
viewer.addCylinder({start:{x:15.0,y:0.0,z:0.0},
end:{x:20.0,y:0.0,z:0.0},
radius:1.0,
color:'black',
fromCap:false,
toCap:false});
Documentation
Please check out our documentation at 3dmol.js. We have tutorials, as well as the stable release of the platform.
Contact
Please address any questions or concerns to dkoes@pitt.edu. You may also submit an issue on github.
Citing
If you use 3Dmol.js, please cite our Bioinformatics paper.
Funding
3DMol.js is funded through R35GM140753 (and previously R01GM108340) from the National Institute of General Medical Sciences. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of General Medical Sciences or the National Institutes of Health.
Owner
- Name: 3Dmol.js
- Login: 3dmol
- Kind: organization
- Email: dkoes+3dmol@pitt.edu
- Website: http://3dmol.org
- Repositories: 5
- Profile: https://github.com/3dmol
A modern, object-oriented JavaScript library for visualizing molecular data
GitHub Events
Total
- Create event: 4
- Release event: 3
- Issues event: 38
- Watch event: 74
- Issue comment event: 67
- Push event: 35
- Pull request review event: 1
- Pull request event: 8
- Fork event: 16
Last Year
- Create event: 4
- Release event: 3
- Issues event: 38
- Watch event: 74
- Issue comment event: 67
- Push event: 35
- Pull request review event: 1
- Pull request event: 8
- Fork event: 16
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| David Koes | d****s@p****u | 1,049 |
| Alec Helbling | s****1@p****t | 170 |
| Nick Rego | n****2@q****u | 155 |
| Adithya Krishna | a****h@r****m | 100 |
| nbr2 | n****2@g****m | 95 |
| helblazer811 | a****1@g****m | 94 |
| jaxmatrix | j****8@g****m | 88 |
| Ryan D. Guild | r****7@p****u | 81 |
| Manohar-94 | k****3@g****m | 80 |
| mattragoza | m****2@p****u | 79 |
| Jing Li | j****2@p****u | 51 |
| jlc206 | j****6@p****u | 43 |
| jus1in | j****0@g****m | 40 |
| tjakubiec218 | t****8@y****m | 31 |
| Luthaf | l****f@l****r | 24 |
| K7S3 | k****i@r****n | 23 |
| David Koes | d****s@b****u | 21 |
| BassemHermina | b****n@g****m | 21 |
| Nick Rego | n****2@j****) | 18 |
| Daniel Bryan | d****n@g****m | 17 |
| Zirui Huang | 4****7@q****m | 15 |
| Prajwal Kulkarni | p****6@g****m | 14 |
| dependabot[bot] | 4****] | 13 |
| Daniel Caspi | d****n@e****t | 13 |
| Jai Shukla | j****y@l****n | 12 |
| David Koes | d****s@f****l | 11 |
| Arthur | a****t@y****m | 10 |
| helblazer811 | a****1@g****m | 9 |
| Justin McCandless | j****s@g****m | 8 |
| Nicolas CARPi | 3****i | 8 |
| and 52 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 181
- Total pull requests: 86
- Average time to close issues: 11 months
- Average time to close pull requests: 3 months
- Total issue authors: 96
- Total pull request authors: 20
- Average comments per issue: 4.37
- Average comments per pull request: 1.81
- Merged pull requests: 47
- Bot issues: 0
- Bot pull requests: 11
Past Year
- Issues: 27
- Pull requests: 4
- Average time to close issues: about 2 months
- Average time to close pull requests: 1 day
- Issue authors: 15
- Pull request authors: 3
- Average comments per issue: 2.67
- Average comments per pull request: 0.5
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- JavierSanchez-Utges (26)
- dkoes (15)
- RyanGuild (8)
- adithyaakrishna (6)
- dxdc (6)
- NicolasCARPi (5)
- sdr0598 (4)
- coltonbh (3)
- prajwalkulkarni (3)
- duerrsimon (3)
- data2code (2)
- deliciouslyevil (2)
- ajasja (2)
- shubihu (2)
- elliothershberg (2)
Pull Request Authors
- adithyaakrishna (33)
- prajwalkulkarni (22)
- dependabot[bot] (16)
- donbyron02 (5)
- NicolasCARPi (4)
- Rasic2 (4)
- Luthaf (3)
- dxdc (3)
- RyanGuild (2)
- asford (2)
- cmishra (2)
- dkoes (2)
- andfaulkner (1)
- choephix (1)
- tjakubiec218 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 3
-
Total downloads:
- npm 22,797 last-month
- Total docker downloads: 635,012
-
Total dependent packages: 17
(may contain duplicates) -
Total dependent repositories: 75
(may contain duplicates) - Total versions: 57
- Total maintainers: 2
npmjs.org: 3dmol
JavaScript/TypeScript molecular visualization library
- Homepage: http://3dmol.org
- License: BSD-3-Clause
-
Latest release: 2.5.2
published 7 months ago
Rankings
Maintainers (2)
conda-forge.org: py3dmol
- Homepage: https://github.com/3dmol/3Dmol.js/tree/master/py3Dmol
- License: MIT
-
Latest release: 1.8.1
published over 3 years ago
Rankings
repo1.maven.org: org.webjars.npm:3dmol
WebJar for 3dmol
- Homepage: https://www.webjars.org
- Documentation: https://appdoc.app/artifact/org.webjars.npm/3dmol/
- License: BSD 3-Clause
-
Latest release: 1.5.1
published almost 6 years ago
Rankings
Dependencies
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- 1213 dependencies
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- @babel/core ^7.18.6 development
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- @babel/plugin-transform-typescript ^7.18.8 development
- @babel/polyfill ^7.12.1 development
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- babel-preset-minify ^0.5.2 development
- del ^6.0.0 development
- eslint ^7.32.0 development
- file-loader ^6.2.0 development
- glcheck 3dmol/glcheck#master development
- glob-parent ^5.1.2 development
- gulp ^4.0.2 development
- gulp-clean ^0.4.0 development
- gulp-cli ^2.3.0 development
- gulp-concat ^2.6.1 development
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- gulp-shell ^0.8.0 development
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- gulp-uglify ^3.0.2 development
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- jest ^27.5.1 development
- jsdoc ^3.6.10 development
- jsdom ^19.0.0 development
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- typescript ^3 development
- url-loader ^4.1.1 development
- webpack ^5 development
- webpack-cli ^4.10.0 development
- webpack-dev-server 4.9.3 development
- ini ^2.0.0
- jquery ^3.6.0
- netcdfjs ^1.0.0
- pako ^2.0.4
- upng-js ^2.1.0
- yargs-parser ^20.2.9
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