Folders and files
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Molecular viewer
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 to visualize Python code. It is an entry point to run viewer app based on OpenGL library.
MIT licensed library. See LICENSE for details.
If you have suggestions for improving the pymolecule, please open an issue or pull request on GitHub.
Molecular viewer [Work in progress]
