Re: [Rdkit-discuss] About PCA

Dear Takayuki, I tested in a fairly recent svn checkout as well as on 2012.03.1, which is the version I also used for this example (the Stats.py has not changed since 2009). I ran it on a set of public serineprotease inhibitors (http://cheminformatics.org/datasets/bohm/bohm-test.3d.sdf, chosen

Re: [Rdkit-discuss] About PCA

Dear Greg and Niko. Thank you for your quick repry. To Greg, thanks for your recommendation. I tried PCA with matplotlib and it worked with no problem. Thanks. But Matplotlib returned view that was different from R. To Niko. I using RDKit, version RDKit_2012_06_1. And, when I tried PCA with the

[Rdkit-discuss] About PCA

Dear All. I want to do PCA with molecular fingerprint . So, I wrote following code. But, this code did not work . Does anyone have a suggestion? Thanks. Takayuki 1 from rdkit import Chem 2 from rdkit.Chem import AllChem 3 from rdkit.ML.Data import Stats 4 import numpy 5 import sys

Re: [Rdkit-discuss] About PCA

Hi Takayuki, I was able to run your code snippet without any errors (with different example molecules of course). Could possible explain in more detail what is not working for you? What version of RDKit are you using (from rdkit import rdBase;print rdBase.rdkitVersion) ? Niko On Jan 17, 2013,