So much to do, so little time

Trying to squeeze sense out of chemical data

Archive for the ‘toolkit’ tag

A New Toolkit on the Block

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A few days ago I was pointed to a new cheminformatics toolkit called Indigo, written in C++ with source code available under the GPLv3 license. Rich has previously commented on this. While it’s an initial release, it has a number of interesting components such as an Oracle cartridge, 2D depiction and scaffold detection and R-group generation. Unfortunately I wasn’t able to run the OS X binaries – I’ll give it a try on Linux. The future plans for the library also seem quite interesting including wrappers for other languages, chemical OCR etc. It’s also nice to see that they have a page describing the algorithms they implemented – some of them well known ones such as the Kabsch alignment method and others (fingerprints, depictions) that appear to be unique to the toolkit. Unfortunately, most of the descriptions are in Russian, so we’ll have to wait for English translations.

Written by Rajarshi Guha

October 31st, 2009 at 2:38 pm

Posted in cheminformatics

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CDL – A Cheminformatics Toolkit

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The Chemical Descriptors Library (CDL) has been around for a while, but hasn’t seemed to get much publicity. A paper describing the design and performance of the library just came out today. While the name suggests a library of descriptors, it’s actually a general C++ library for cheminformatics. The library appears to use the molecular graph as its core concept and uses the Boost Graph Library (BGL) to represent and manipulate molecular graphs. Some features include substructure searching using SMARTS, fingerprints, descriptors (CATS, a bunch of topological’s etc) and file format reading (SMILES and SDF as far as I can see).

It seems nice and is available under the Boost Software License. While it does a lot of the basic operations, it doesn’t appear as comprehensive as say OpenBabel or RDKit. However, it’s good to see the cheminformatics toolkit ecosystem growing.

An aside – I haven’t really done much C++ coding and what little I do is basically ‘C in C++’. But how do people get their heads around C++ templates? I tend to get a headache when trying to examine one. And I thought that writing Java was tedious – C++ with templates takes the cake!

Update - Their Sourceforge project page is here but I can’t seem to find a download link.  A software paper with no software!

Written by Rajarshi Guha

September 20th, 2008 at 2:20 pm

Posted in cheminformatics,software

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