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some 2D/3D chemical space visualisation #100

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UnixJunkie opened this issue Oct 22, 2020 · 4 comments
Open

some 2D/3D chemical space visualisation #100

UnixJunkie opened this issue Oct 22, 2020 · 4 comments
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@UnixJunkie
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feature prio 02

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@UnixJunkie
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Should be able to handle thousands of molecules.
Implement something along the lines of the rubber band method from data warrior.
@UnixJunkie UnixJunkie self-assigned this Oct 22, 2020
@UnixJunkie
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maybe something GTM based

@UnixJunkie
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https://github.com/hagax8/ugtm

@UnixJunkie
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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.

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

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