Begin forwarded message:
> From: "Rajarshi Guha rguha^^indiana.edu" <
owner-chemistry@...>
> 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
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