rdkit.blogspot.com

RDKit

RDKit experiments and tutorials. Saturday, August 15, 2015. This is inspired by a question from a colleague this week. I'm going to present a method to exert a bit more control over substructure queries without having to do a massive amount of work. 201509.1.dev1 Sat Aug 15 17:54:55 2015. Our starting point is a query against ChEMBL for molecules that contain a phenyl ring with a substituent. Postgresql:/ localhost/chembl 20 select. But that would be something of a pain for more complex queries. Let's wr...

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RDKit experiments and tutorials. Saturday, August 15, 2015. This is inspired by a question from a colleague this week. I'm going to present a method to exert a bit more control over substructure queries without having to do a massive amount of work. 201509.1.dev1 Sat Aug 15 17:54:55 2015. Our starting point is a query against ChEMBL for molecules that contain a phenyl ring with a substituent. Postgresql:/ localhost/chembl 20 select. But that would be something of a pain for more complex queries. Let's wr...

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RDKit | rdkit.blogspot.com Reviews

https://rdkit.blogspot.com

RDKit experiments and tutorials. Saturday, August 15, 2015. This is inspired by a question from a colleague this week. I'm going to present a method to exert a bit more control over substructure queries without having to do a massive amount of work. 201509.1.dev1 Sat Aug 15 17:54:55 2015. Our starting point is a query against ChEMBL for molecules that contain a phenyl ring with a substituent. Postgresql:/ localhost/chembl 20 select. But that would be something of a pain for more complex queries. Let's wr...

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rdkit.blogspot.com

1

RDKit: Impact of the threshold on similarity search times

http://www.rdkit.blogspot.com/2015/08/impact-of-threshold-on-similarity.html

RDKit experiments and tutorials. Saturday, August 8, 2015. Impact of the threshold on similarity search times. Added timing information for chemfp with the larger ZINC set. A ChEMBL blog post. Included the (to me) somewhat surprising result that similarity search times while using the RDKit cartridge did not show much of a dependency on the similarity threshold being used. I wanted to investigate this a bit more closely. And now look at timing results for a number of threshold values:. A larger test: ZINC.

2

RDKit: March 2014

http://www.rdkit.blogspot.com/2014_03_01_archive.html

RDKit experiments and tutorials. Saturday, March 15, 2014. Impact of bit collisions on learning performance. In an earlier post. I looked at the minimal impact bit collisions in the RDKit's Morgan fingerprints has on calculated similarity between molecules. This time I'm going to look at the impact on the performance of machine-learning algorithms. I will use Datasets II from our model fusion. In some detail in an earlier post. Sun Mar 16 04:58:46 2014. Read in the results:. The same behavior is observed...

3

RDKit: August 2014

http://www.rdkit.blogspot.com/2014_08_01_archive.html

RDKit experiments and tutorials. Thursday, August 28, 2014. MMPA on ChEMBL hERG data using Pandas. The idea here is to try out using Pandas to visualize and work with the output of Jameed Hussain's MMPA code in the IPython notebook. The code is available in the RDKit Contrib dir. Jameed gave a couple tutorials on use of the tools at the 2013 UGM. The notebooks from his tutorials are here. Start by finding the hERG data in ChEMBL. Look at all the activity units available. Create the data set. Now generate...

4

RDKit: May 2015

http://www.rdkit.blogspot.com/2015_05_01_archive.html

RDKit experiments and tutorials. Friday, May 29, 2015. Generating a reference dataset of chemical "scaffolds". A set of scaffolds from CheMBL papers ¶. Andrew Dalke has been working. Sometimes I love my job! During the conversation we came up with a way to fake having access to our actual queries. This post is about that. I did a post. A while ago on the composition of the molecule sets we called "Datasets 2" in the model fusion. On to the work ¶. Start with the preliminaries ¶. Define a function to find...

5

RDKit: December 2014

http://www.rdkit.blogspot.com/2014_12_01_archive.html

RDKit experiments and tutorials. Monday, December 8, 2014. Package provides an interesting way of working with datasets from within Python. Inspired by this blog post. Heres a quick exploration of using Blaze Expressions. Populating the interactive namespace from numpy and matplotlib. Some technical details before getting started. This is the first post Ive done using Python 3.4. Im using the anaconda. Distribution and its excellent conda package manager to handle installing packages. Open Source Malaria...

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rdkit.blogspot.com

RDKit

RDKit experiments and tutorials. Saturday, August 15, 2015. This is inspired by a question from a colleague this week. I'm going to present a method to exert a bit more control over substructure queries without having to do a massive amount of work. 201509.1.dev1 Sat Aug 15 17:54:55 2015. Our starting point is a query against ChEMBL for molecules that contain a phenyl ring with a substituent. Postgresql:/ localhost/chembl 20 select. But that would be something of a pain for more complex queries. Let's wr...

rdkit.org

RDKit

RDKit: Open-Source Cheminformatics Software. Registration is now open for the 4th RDKit UGM, to take place from 2-4 September 2015 in Zurich Switzerland. More details here. And on the registration page. Git source code repository. Searchable archive of rdkit-discuss. Searchable archive of rdkit-devel. PDF version of the documentation. Downloadable version of the full HTML documentation. Materials from the 2012 UGM. Materials from the 2013 UGM. Materials from the 2014 UGM. Contributed by Gianluca Sforna.

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