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

389 followers
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Using the new fingerprint bit rendering code
Motivation ¶ A frequent desire when working with chemical fingerprints is to see what the indvidual bits actually "mean". For most of the fingerprinting algorithms in the RDKit this question only means something in the context of a molecule, so there have b...
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Introducing the SubstructLibrary
This introduces another of the new features in the 2017.09 release of the RDKit: the SubstructLibrary - a class to make it straightforward to do substructure searches across sets of compounds. In [1]: from rdkit import Chem from rdkit.Chem import Draw from ...
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Revisting the MaxMinPicker
This is a guest post from Tim Dudgeon.   This post has a bit of history. It is primarily inspired by Roger Sayle's talk at the recent UGM in Berlin . If you have attended these great events you will know that Roger's talk is one of the highlights. In a way ...
Revisting the MaxMinPicker
Revisting the MaxMinPicker
rdkit.blogspot.com
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Using Feature Maps
This post provides a short demonstration of how to use the RDKit's feature map implementation to score aligned 3D conformations against each other based on the overlap of their pharmacophoric features.
The idea of the feature map is not a new one and there ...
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Chemical Topic Modeling with the RDKit and KNIME
We recently published a paper on the application of topic modeling, a method developed in the text mining community, to chemical data: http://pubs.acs.org/doi/abs/10.1021/acs.jcim.7b00249. Here I'm going to show how to use this approach inside of KNIME. I'm...
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Chemical Topic Modeling with the RDKit and KNIME
We recently published a paper on the application of topic modeling, a method developed in the text mining community, to chemical data: http://pubs.acs.org/doi/abs/10.1021/acs.jcim.7b00249. Here I'm going to show how to use this approach inside of KNIME. I'm...
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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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