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