[Rdkit-discuss] Does rdkit depend on pandas?

2017-06-06 Thread Michał Nowotka
Hi, I just upgraded rdkit from 2017.03.1 to 2017.03.2 using Conda. What I have noticed is that pandas are now installed during the installation of rdkit. Does rdkit depend on pandas now? Is it safe to remove it? If it works without pandas, maybe it makes sense to remove the dependency. Kind

Re: [Rdkit-discuss] Does rdkit depend on pandas?

2017-06-06 Thread Brian Kelley
No. The main reason that the conda recipe includes pandas is for testing the pandas extension. We could probably remove it from the run-time dependency however and let the user install it in addition. In any case, feel free to remove pandas from the conda installation. Cheers, Brian On Tue,

Re: [Rdkit-discuss] Clustering

2017-06-06 Thread Abhik Seal
Hello all , How about doing some dimension reduction using pca or Tsne and then run clustering using some selected top components like top 20 and I think then the clustering would be fast . Thanks Abhik On Mon, Jun 5, 2017 at 6:11 AM David Cosgrove wrote: > Hi, >

Re: [Rdkit-discuss] RDkit Molecule Fragmenter

2017-06-06 Thread Greg Landrum
On Tue, Jun 6, 2017 at 1:43 PM, Popov, Maxim (Ext) wrote: > > > I have discovered a very usefule tool in Knime, Molecule Fragmenter by > RDKit, but can’t find a corresponding class or function outside of Knime. > Can I use the Fragmenter without Knime? > > > Yep:

Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 116, Issue 14

2017-06-06 Thread Schwarze, Manuel
Hi Maxim, The KNIME node "RDKit Molecule Fragmenter" is indeed quite useful. Since what it does for you in KNIME is based on RDKit functionality, you can do the same also outside of KNIME. Usually, there is not a single method to call, rather a code block that performs multiple operations,

[Rdkit-discuss] RDkit Molecule Fragmenter

2017-06-06 Thread Popov, Maxim (Ext)
Dear All, I have discovered a very usefule tool in Knime, Molecule Fragmenter by RDKit, but can't find a corresponding class or function outside of Knime. Can I use the Fragmenter without Knime? Thanks! Maxim -- Check

Re: [Rdkit-discuss] RDkit Molecule Fragmenter

2017-06-06 Thread Jan Halborg Jensen
I was also searching for this functionality earlier For what it’s worth here’s some *very* simple code I hacked together to do fragmentation. The focus is aromatic heterocycles, but it could be more general by, for example '[c,n]-[*]’ -> ‘[R]-[*]’ and ring = Chem.MolFromSmarts(‘[R]’) instead