{"id":30873589,"url":"https://github.com/duboviy/pymolecule","last_synced_at":"2025-09-07T23:11:51.649Z","repository":{"id":74405243,"uuid":"89744350","full_name":"duboviy/pymolecule","owner":"duboviy","description":":atom: Molecular viewer [Work in 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src=\"https://raw.githubusercontent.com/duboviy/pymolecule/master/logo.png\" height=85 alt=\"logo\" title=\"logo\"\u003e pymolecule\u003c/h1\u003e\n\nMolecular viewer\n\u003ch1\u003e\u003cimg src=\"https://raw.githubusercontent.com/duboviy/pymolecule/master/glucose.png\" alt=\"glucose\" title=\"glucose\"\u003e\u003c/h1\u003e\n\n## Summary\n\nDraw atoms in different colors and place them in different places of space, thus obtaining a molecule.\nTo do this, you need to know the coordinates, that's why chemical expert system Open Babel is used, \nso you need to install it as a prerequisite package on your system to run successfully following scripts:\n\n```\napt-get install python-openbabel\n```\n\nUsing it, you can transform the SMILES formula to the list of atoms coordinates.\nSMILES can be found in Wikipedia articles about various substances.\n```\nFor example, glucose: OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O.\n\nAnd its coordinates:\n\nO3 3.08232699168 1.41136753836 1.97383867659\nC3 2.63605783234 0.116724346362 2.37092125466\nC3 2.87897272901 -0.854338624684 1.21070216538\nH 2.47296741411 -0.36351143938 0.319191621385\nO3 4.29331227545 -1.03408976253 1.03052197614\nC3 2.18198168708 -2.2062426467 1.4123437219\nH 2.52686439483 -2.70828022178 2.32628341407\nO3 0.757046712076 -2.07375697965 1.48816465135\nC3 2.4834103428 -3.09613160782 0.198042289604\nH 2.03158506981 -2.66605342385 -0.704362586236\nO3 1.84366255476 -4.36331585678 0.373985237387\nC3 3.99532722341 -3.24522583591 0.00523555683618\nH 4.41250004827 -3.77444425583 0.871020029013\nO3 4.29626886035 -4.03252960027 -1.15195954921\nC3 4.62954125722 -1.84273135567 -0.0947112115177\nH 5.71887138656 -1.95252927548 -0.108137148969\nO3 4.3079363412 -1.18316983652 -1.31789119536\nHO 2.91473185309 2.02688340774 2.71060639162\nH 1.56956736943 0.19992674022 2.5985040442\nH 3.17829013287 -0.18365904297 3.27321534863\nHO 0.532102901531 -1.64213847492 2.33074495499\nHO 0.907383263524 -4.15051515566 0.55676359202\nHO 3.89297302828 -3.59188323274 -1.91963488602\nHO 3.3506978517 -1.05986229308 -1.37211748251\n```\n\nYou can use module [render.py](render.py) to visualize Python code. \nIt is an entry point to run viewer app based on OpenGL library.\n\n## License\n\n**MIT** licensed library. See [LICENSE](LICENSE) for details.\n\n## Contributing\n\nIf you have suggestions for improving the pymolecule, please [open an issue or\npull request on GitHub](https://github.com/duboviy/pymolecule/).\n\n## Badges\n\n[![forthebadge](http://forthebadge.com/images/badges/fuck-it-ship-it.svg)](https://github.com/duboviy/pymolecule/)\n[![forthebadge](http://forthebadge.com/images/badges/built-with-love.svg)](https://github.com/duboviy/pymolecule/) [![forthebadge](http://forthebadge.com/images/badges/built-by-hipsters.svg)](https://github.com/duboviy/pymolecule/) [![forthebadge](http://forthebadge.com/images/badges/built-with-swag.svg)](https://github.com/duboviy/pymolecule/)\n\n[![forthebadge](http://forthebadge.com/images/badges/powered-by-electricity.svg)](https://github.com/duboviy/pymolecule/) [![forthebadge](http://forthebadge.com/images/badges/powered-by-oxygen.svg)](https://github.com/duboviy/pymolecule/) [![forthebadge](http://forthebadge.com/images/badges/powered-by-water.svg)](https://github.com/duboviy/pymolecule/) [![forthebadge](http://forthebadge.com/images/badges/powered-by-responsibility.svg)](https://github.com/duboviy/pymolecule/)\n\n[![Open Source Love](https://badges.frapsoft.com/os/v1/open-source.svg?v=102)](https://github.com/ellerbrock/open-source-badge/)\n\n[![forthebadge](http://forthebadge.com/images/badges/makes-people-smile.svg)](https://github.com/duboviy/pymolecule/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fduboviy%2Fpymolecule","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fduboviy%2Fpymolecule","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fduboviy%2Fpymolecule/lists"}