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Greg Landrum
377 followers -
Cheminformatician, developer, hiker, climber, cook
Cheminformatician, developer, hiker, climber, cook

377 followers
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Using custom fingerprints in PostgreSQL
A question recently came up on the mailing list about how to use custom fingerprints with the RDKit PostgreSQL cartridge without having to edit the cartridge code itself. Since the answer isn't trivial but may be useful to others, I'm doing a blog post with...

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A great-looking option for doing easy parallel/distributed computation in python
A few years ago I blogged about using an early version of Blaze to do some interesting data manipulations. Since then I've been paying attention to the progress of the various pieces of the Blaze ecosystem and experimenting with them. I have some really int...

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Avoiding unnecessary work and constructing molecules more quickly
I have previously talked/posted about ways to construct RDKit molecules more quickly. This post revisits that topic. By default the RDKit does a lot of work when constructing a molecule. The idea here is to set things up so that we only have to do that work...

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A question: RDKit performance on Windows
This one is a request for advice/expertise on performance tuning/compiler flag tweaking on Windows. The short story is that when the RDKit is built using Visual Studio on Windows it ends up being substantially slower than when it's built with g++ and run us...

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From earlier: not much in the way of clouds, but the Pilatus was making one.
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New RDKit blog post

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Tuning substructure queries II
Quite a while ago I did a blog post describing a method to exert more control over the way substructure queries match. The approach described in that post was integrated into the RDKit for the 2015.09 release; since then it's been expanded a bit. This post ...

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Tuning substructure queries II
Quite a while ago I did a blog post describing a method to exert more control over the way substructure queries match. The approach described in that post was integrated into the RDKit for the 2015.09 release; since then it's been expanded a bit. This post ...

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Using ipywidgets and py3Dmol to browse conformations in jupyter
Disclaimer:  This is unfortunately one where you need a backend server to do have a live widget, so I'm using standard blogger and screenshots. I've been looking at a lot of conformational manifolds lately. I used to do this with the RDKit's PyMol integrati...

This is great: I can sit on the balcony and enjoy a good G&T and still follow the progress of the Switzerland game via the cheers coming from the cafe next door
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