Sunday, 1 October 2017

Open Babel in a snap

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Maintainers of Linux distributions do an amazing job packaging applications for users, so that "apt/dnf install openbabel"  makes ...
2 comments:
Saturday, 23 September 2017

How many cheminformaticians does it take to read a SMILES string?

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A few days ago I posted the following poll question on Twitter: How many Hs are on the N in the molecule described by this SMILES string? ...
Monday, 28 August 2017

My ACS talk on Kekulization and aromatic SMILES

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Here are the slides for the talk I presented last week at the ACS meeting in Washington. It describes my understanding of the Daylight toolk...
Sunday, 23 July 2017

Faster toolkit, faster!

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After an extended hiatus, I've been back doing a bit of work on Open Babel, and specifically I've been working on improving performa...
Friday, 5 May 2017

Using WebLogo3 to create a sequence logo from Python

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A sequence logo is a way to display the variation at particular positions of multiple-aligned sequences. Here I used WebLogo 3 to do this. ...
Monday, 23 January 2017

Whiskas statistics and the pitfalls of mean rank

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In the fingerprint similarity paper I published last year, I made the following observation: "However the use of the mean rank is itse...
4 comments:
Saturday, 14 January 2017

Counting hydrogens in a SMILES string - The Rules

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Hydrogens are not usually listed explicitly in a SMILES string, but instead can be inferred from a set of rules. To be precise, when reading...