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...
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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...
Friday, 30 December 2016

The clockwisdom of SMARTS

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Image credit: Jonathan Cohen (CC-BY-NC) In earlier posts I discussed/investigated how stereochemistry is represented in SMILES. Here I...
Friday, 23 September 2016

Open Babel 2.4.0 released

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As announced by Geoff on the mailing list, Open Babel 2.4.0 is now available to download: I'm pleased to announce that Open Babel 2.4.0...
Sunday, 21 August 2016

My new thing - providing manuscript images as PDFs

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My latest oeuvre (on the topic of which fingerprint is best ) was published by J. Cheminf. a few weeks ago. For the first time, instead of p...
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