Monday, 3 June 2019

Building a PubChem query

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Evan Bolton was visiting recently and I got to watch over his shoulder as he built up a PubChem query on the website step-by-step. I helpful...
Sunday, 17 February 2019

Transitive reduction of large graphs

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There are a number of graph algorithms with not-so-obvious names, and " transitive reduction " is one of those. When I first neede...
Sunday, 25 November 2018

SMARTS for dummies

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One of Roger's observations came to mind recently when I was looking at some SMARTS patterns in Open Babel that were causing some proble...
6 comments:
Tuesday, 2 October 2018

DeepSMILES - a SMILES-like syntax for use in machine-learning

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At the last ICCS , Andrew Dalke and I got talking. We had both been around the poster session, and had heard first-hand the problems of ...
Friday, 20 July 2018

Streamlining the handling of aromaticity

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I've done a bit of work over the last year or two stripping back some accumulated cruft in Open Babel. One question that's been on m...
Tuesday, 10 July 2018

Clarifying the Cahn-Ingold-Prelog rules

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What happens when four software developers get together and compare their implementations of the CIP rules? This is the background to a rece...
Thursday, 14 June 2018

Cheminformatics for deep learners: Canonical SMILES and why you should avoid them

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I've already gotten the " valid SMILES " issue off my chest, but there's something else that's been bugging me about d...
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