some 2D/3D chemical space visualisation

Open UnixJunkie opened this issue 5 years ago • 4 comments

Should be able to handle thousands of molecules. Implement something along the lines of the rubber band method from data warrior.

Oct 22 '20 01:10 UnixJunkie

maybe something GTM based

Dec 02 '22 03:12 UnixJunkie

https://github.com/hagax8/ugtm

Dec 02 '22 03:12 UnixJunkie

would be really fun to implement something new and simple. Like a 2D map obtained by some simulated annealing. Particles are placed randomly at start. Then, molecules' fingerprint distances would be some kind of force to move them around. The distance could be mixed with abdolute difference in IC50.

Dec 02 '22 03:12 UnixJunkie

or based on this https://jcheminf.biomedcentral.com/articles/10.1186/s13321-022-00664-x Visualizing chemical space networks with RDKit and NetworkX

Jan 04 '23 05:01 UnixJunkie