https://github.com/duboviy/pymolecule

:atom: Molecular viewer [Work in progress]
https://github.com/duboviy/pymolecule

atom atoms-in-molecules molecular-graphics molecular-structures molecule molecules openbabel pybel pyglet

Last synced: 9 months ago
JSON representation

:atom: Molecular viewer [Work in progress]

• Host: GitHub
• URL: https://github.com/duboviy/pymolecule
• Owner: duboviy
• License: mit
• Created: 2017-04-28T20:58:39.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2020-04-26T20:16:04.000Z (about 6 years ago)
• Last Synced: 2023-10-25T14:43:02.265Z (over 2 years ago)
• Topics: atom, atoms-in-molecules, molecular-graphics, molecular-structures, molecule, molecules, openbabel, pybel, pyglet
• Language: Python
• Homepage:
• Size: 41 KB
• Stars: 9
• Watchers: 2
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Codeowners: CODEOWNERS

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README

          


 pymolecule


Molecular viewer



## Summary

Draw atoms in different colors and place them in different places of space, thus obtaining a molecule.

To do this, you need to know the coordinates, that's why chemical expert system Open Babel is used, 

so you need to install it as a prerequisite package on your system to run successfully following scripts:

```

apt-get install python-openbabel

```

Using it, you can transform the SMILES formula to the list of atoms coordinates.

SMILES can be found in Wikipedia articles about various substances.

```

For example, glucose: OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O.

And its coordinates:

O3 3.08232699168 1.41136753836 1.97383867659

C3 2.63605783234 0.116724346362 2.37092125466

C3 2.87897272901 -0.854338624684 1.21070216538

H 2.47296741411 -0.36351143938 0.319191621385

O3 4.29331227545 -1.03408976253 1.03052197614

C3 2.18198168708 -2.2062426467 1.4123437219

H 2.52686439483 -2.70828022178 2.32628341407

O3 0.757046712076 -2.07375697965 1.48816465135

C3 2.4834103428 -3.09613160782 0.198042289604

H 2.03158506981 -2.66605342385 -0.704362586236

O3 1.84366255476 -4.36331585678 0.373985237387

C3 3.99532722341 -3.24522583591 0.00523555683618

H 4.41250004827 -3.77444425583 0.871020029013

O3 4.29626886035 -4.03252960027 -1.15195954921

C3 4.62954125722 -1.84273135567 -0.0947112115177

H 5.71887138656 -1.95252927548 -0.108137148969

O3 4.3079363412 -1.18316983652 -1.31789119536

HO 2.91473185309 2.02688340774 2.71060639162

H 1.56956736943 0.19992674022 2.5985040442

H 3.17829013287 -0.18365904297 3.27321534863

HO 0.532102901531 -1.64213847492 2.33074495499

HO 0.907383263524 -4.15051515566 0.55676359202

HO 3.89297302828 -3.59188323274 -1.91963488602

HO 3.3506978517 -1.05986229308 -1.37211748251

```

You can use module [render.py](render.py) to visualize Python code. 

It is an entry point to run viewer app based on OpenGL library.

## License

**MIT** licensed library. See [LICENSE](LICENSE) for details.

## Contributing

If you have suggestions for improving the pymolecule, please [open an issue or

pull request on GitHub](https://github.com/duboviy/pymolecule/).

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