Re: [Jmol-developers] 3D structure generator

[Miguel <mt...@mt...>]

Carl,

Over the past few months I have asked several people about algorithms for
generating 3d structures from 2d structures.

Basically, what I have been told is that the algorithms are all published.
They mostly involve geometry ... angles and distances. And the problem is
that there are no open-source implementations.

So, I think it is well worth it to do some research ... literature search
for these algorithms.

> Question: can I assume an in-memory connectivity graph of the molecule
> has already been built, or would I be parsing some compact form like
> Smiles and building the graph.
Yes, you can assume a connected graph built by CDK. I think there is even
some graph searching capability built into CDK.



Miguel