Performing chemical reactions using the Open Babel C++ API

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Performing chemical reactions using the Open Babel C++ API

Hans De Winter
All,

a client of us is looking for a tool to perform compound library  
enumerations by defining the building blocks and some general reaction  
schemes. The client has access to Pipeline Pilot in which this kind of  
stuff can be done, but for the particular project in mind it would be  
very convenient if this could be done using the Open Babel C++ API  
since it would make integration with other technologies easier.

Therefore, does anyone know whether library enumeration using user-
definable reaction schemes can be done with the OB C++ API, and if so,  
are there any drawbacks and stability problems to be taken care of?

Many thanks in advance,

Hans
---
Silicos NV
www.silicos.com


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Re: Performing chemical reactions using the Open Babel C++ API

David García Aristegui
Maybe Smilib could help...

"SmiLib [1] is a platform independent command line and graphical user
inferface software tool designed to rapidly create combinatorial libraries
in SMILES format(...). A combinatorial library is a set of molecules
created by virtual reactions of so-called building blocks with scaffold
molecules. Scaffolds are represented by Markush structures of molecules
that contain R-groups – sites of variability. Those scaffolds undergo
virtual reactions with building blocks – small Markush molecules
themselves – yielding newly synthesized reaction products(...)

Compatibility
SmiLib has shown to produce molecules in SMILES format that are compliant
with ChemDraw Ultra [5], Daylight SMILES Depict Service [6], Molecular
Operating Environment [7], CORINA 3D Structure Generator [8], the Open
Babel Package [9] and the Chemistry Development Kit [10](...)"

http://gecco.org.chemie.uni-frankfurt.de/smilib/SmiLib_v2.0.pdf

Best regards

> All,
>
> a client of us is looking for a tool to perform compound library
> enumerations by defining the building blocks and some general reaction
> schemes. The client has access to Pipeline Pilot in which this kind of
> stuff can be done, but for the particular project in mind it would be
> very convenient if this could be done using the Open Babel C++ API
> since it would make integration with other technologies easier.
>
> Therefore, does anyone know whether library enumeration using user-
> definable reaction schemes can be done with the OB C++ API, and if so,
> are there any drawbacks and stability problems to be taken care of?
>
> Many thanks in advance,
>
> Hans
> ---
> Silicos NV
> www.silicos.com
>
>
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://p.sf.net/sfu/dev2dev-palm
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>



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Re: Performing chemical reactions using the Open Babel C++ API

Craig James-2
In reply to this post by Hans De Winter
Hans,

> a client of us is looking for a tool to perform compound library
> enumerations by defining the building blocks and some general reaction
> schemes. The client has access to Pipeline Pilot in which this kind of
> stuff can be done, but for the particular project in mind it would be
> very convenient if this could be done using the Open Babel C++ API
> since it would make integration with other technologies easier.
>
> Therefore, does anyone know whether library enumeration using user-
> definable reaction schemes can be done with the OB C++ API, and if so,
> are there any drawbacks and stability problems to be taken care of?

The simple answer to this question is: No.

OpenBabel doesn't do reactions in the same way that Pipeline Pilot or Daylight can.  For trivial R-group substitution (which I don't consider to be a "reaction"), you can certainly use SMILES; in fact the OpenSMILES specification even has a simple example:

     http://opensmiles.org/spec/open-smiles-3-input.html#3.8

But if you want to do anything beyond monkeying with strings (trivial R-group substitution), you need a real reaction toolkit.  OpenBabel needs one, but it's a huge job and nobody has even started thinking about it.

Craig

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