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Using the Avogadro library from python
As we get closer to Avogadro 1.0, the python bindings are becoming more and more powerful. For example, take this small script (65 lines) which allows large files to be read in a separate thread. Once...
View ArticleSourceForge's Community Choise Awards
I'm pleased with Avogadro's nomination for SourceForge's Community Choise Awards. First of all, thanks to all people who have voted to get us nominated. Secondly, thanks to those who have already voted...
View ArticleMolsketch
The last 2 months Nicola Zonta and I have been working on improving Molsketch. While development is still at an early stage and bugs may be present, great progress has been made. Nicola released a...
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Avogadro 0.9.8
Avogadro 0.9.8 was released yesterday and the windows installer including the python bindings and dependencies is available from sourceforge. There are no big new features but several bugs are fixed...
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Symmetry classes: How to get them and what to do with them
For a long time, I've wanted to make a series of blog posts about my stereochemistry adventures. This is post will mainly be about symmetry but we'll get to it's relationship to stereochemistry at the...
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Article 19
As promised, here are some molecules with stereogenic units that are considered "hard" to detect. As can be seen from the image, the previous definition of atoms having four different neighbours (by...
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More para-stereocenters, permutation groups and the automorphism group
Rich Apodaca recently blogged about this stereochemistry related series of posts. He correctly pointed out that the automorphism group lies at the heart of the Razinger paper on stereoismer generation....
View ArticleMolsketch: Reaction & Mechanism arrows
Here is a short screencast showing some of the new features in Molsketch. First, there are the reaction and mechanism arrows. While there are only two major types of arrows, double clicking an arrow in...
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The automorphism group & bliss
In the previous post, an algorithm for computing the automorphism group was given. Although it drastically reduced the number of permutations to be checked, it was still much to slow for use in...
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Avogadro's packmol plugin
When running molecular dynamics (MD) simulations, one often needs to create an initial input structure. It is important that none of the atoms are too close to prevent the coordinates from "blowing...
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Article 14
It has been 6 months since my last post on stereochemistry. At the end of the post, the automorphisms for inositol were listed. These will now be used to enumerate all possible stereoisomers for a...
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Detecting stereogenic units: An alternative method
In case you already saw part of this post: I accidentally pressed publish before finishing. Sorry... The detection of stereogenic units in a molecule isn't always a trivial task. This is illustrated by...
View ArticleCheminformatics & Javascript: Part 1
Richard Apodaca already made several posts on this topic on his blog. After experimenting with javascript for the past few weeks, I agree with him that javascript could have a role in future web...
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Cheminformatics & Javascript: Part 2 (Ring perception)
In the second post of the javascript series ring perception will be used as an example to illustrate some of the difficulties to overcome when developing a javascript cheminformatics library. Readers...
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The SMILES stereochemistry enigma
Warning: The octahedral (OH) classes in this post are not correct. Please consult the OpenSMILES/OpenSMARTS specifications for the corrected version. Almost every cheminformatics system implementing...
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CMake, CTest and CDash: Creating portable c++ software
CMake is a powerful build system for C++ applications (and other languages) used by many software projects including KDE. The main difference between CMake and other build systems is that it generates...
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Unique Subgraphs in PubChem's Compound Database
Andrew Dalke already investigated the unique subgraphs up to a size of 7 in the PubChem's compound database. However, only the first 1,724 files were used and pubchem currently has 2,295. Since I...
View ArticleFingerprint Inverted Index and Fast Multiple Set Intersection
Andrew Dalke's post In search of an inverted index library explains what an inverted index is and how it can be used for fingerprint screening. This post will summarise what fingerprints are and how to...
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Fingerprint Searching Using Various Indexing Methods
The previous post already contained some details about fingerprints and database screening for substructure search. Another common search using fingerprints is a similarity search. Various similarity...
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Fingerprint Efficiency for Substructure Searching
A post on the cheminformatics and whatnot blog compared the fingerprint efficiency between OpenBabel's FP2 and Indigo's fingerprint. Clearly FP2 is far less efficient for substructure search screening....
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