[OpenBabel-Devel] Fwd: CCL: Open Source 3D coordinate generation tool

[Geoffrey H. <ge...@pi...>]

Begin forwarded message:

> From: "Rajarshi Guha rguha^^indiana.edu" <own...@cc...>
> Date: August 20, 2007 3:12:19 PM EDT
> Subject: CCL: Open Source 3D coordinate generation tool
>
>
> Sent to CCL by: Rajarshi Guha [rguha===indiana.edu]
> Hi,
>   we have released a 3D coordinate generation tool called smi23d  
> which will convert a SMILES string to a  3D structure. The program  
> consists of two separate components: smi2sdf which converts a  
> SMILES string to a 'rough' set of 3D coordinates using the  
> stochastic proximity embedding (SPE) algorithm. Given the initial  
> rough coordinates, the program called mengine then optimizes them  
> using the MMFF94 forcefield to give a reasonable low energy structure.
>
> Note: these programs will only generate a single 3D structure.
>
> The code is written in C and is currently in the form of two  
> standalone programs. In the future we plan to convert it to a  
> library to ease inclusion within other systems. The software is  
> released under the Apache 2.0 license.
>
> The program and instructions of compiling and usage can be obtained
>> from http://www.chembiogrid.org/cheminfo/smi23d/
>
> At this point we have not performed significant benchmarking,  
> mainly due to lack of access to other programs. However we welcome  
> any comparisons with other programs and would be happy to help out  
> in such efforts.
>
> We have used smi3d to convert about 99% of PubChem to 3D, the  
> results of which are stored in a database which can be accessed at  
> http://www.chembiogrid.org/cheminfo/p3d/.
>
> -------------------------------------------------------------------
> Rajarshi Guha  <rguha###indiana.edu>
> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04  06F7 1BB9 E634 9B87 56EE