Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

2015-02-23 Thread Dimitri Maziuk
On 02/23/2015 06:12 AM, Markus Sitzmann wrote: > And I am not saying it is perfect, it just provides another > implementation to double-check things in question. It has the CACTVS > chemoinformatic toolkit as chemistry backend which I think is > well-tested. > On Mon, Feb 23, 2015 at 10:54 AM, JP

Re: [Rdkit-discuss] Clustering functions in Java API

2015-02-23 Thread Greg Landrum
On Mon, Feb 23, 2015 at 4:24 PM, Patrick Walters wrote: > I agree that there are plenty of implementations of clustering, machine > learning, etc. It would be better for the RDKit developers to focus on > cheminformatics. This being said, there are some opportunities for domain > specific perf

Re: [Rdkit-discuss] Clustering functions in Java API

2015-02-23 Thread Patrick Walters
I agree that there are plenty of implementations of clustering, machine learning, etc. It would be better for the RDKit developers to focus on cheminformatics. This being said, there are some opportunities for domain specific performance enhancement. One of the slow steps in many clustering alg

Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

2015-02-23 Thread Markus Sitzmann
Well, the http://cactus.nci.nih.gov/chemical/structure/ site is my baby which I had to leave behind 1 1/2 years ago (I am not with NIH anymore). Igor who replied in this thread was also involved in some parts of it. Traffic on this cactus service is between 5 to 10 million requests per month - so I

Re: [Rdkit-discuss] Clustering functions in Java API

2015-02-23 Thread Maciek Wójcikowski
Hello, If interested in clustering in python I can recommend, as usual, sklearn: http://scikit-learn.org/stable/modules/clustering.html It's pretty much all you should need. Have fun! Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2015-02-23 11:43 GMT+01:00 Anthony B

Re: [Rdkit-discuss] Clustering functions in Java API

2015-02-23 Thread Anthony Bradley
Hi Anthony, On Sun, Feb 22, 2015 at 11:03 AM, Anthony Bradley mailto:anthony.brad...@worc.ox.ac.uk>> wrote: Hi all, I am currently working with RDKit from the Java API (well jython actually). As has been discussed most of the documentation for this is found by trawling: Code/JavaWrappers/gmwra

Re: [Rdkit-discuss] Clustering functions in Java API

2015-02-23 Thread Greg Landrum
Hi Anthony, On Sun, Feb 22, 2015 at 11:03 AM, Anthony Bradley < anthony.brad...@worc.ox.ac.uk> wrote: > Hi all, > > I am currently working with RDKit from the Java API (well jython actually). > > As has been discussed most of the documentation for this is found by > trawling: > > Code/JavaWrapper

Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

2015-02-23 Thread JP
Ok so I got out my test set of 6,940,083 molecules. First, I generated the inchi using 2014_09_2. I then checked out (and built) the master (with Greg's latest commits) from github and regenerated the inchis for all these molecules. 3,257 molecules (of 6,940,083) gave me a different inchis betwe