[Rdkit-discuss] 3D alignment in Python: align conformers of 2 molecules

I'm trying to align all conformers of 2 molecules (and keep the best ones) using the python api by following some of the tutorials: http://nbviewer.ipython.org/gist/greglandrum/4316435/Working%20in%203D.ipynb http://nbviewer.ipython.org/github/greglandrum/rdkit_blog/blob/master/notebooks/Using%2

Re: [Rdkit-discuss] 3D alignment in Python: align conformers of 2 molecules

Hi Thomas, I think there are a couple of problems with the code here: 1) you aren't storing the confirmation of the conformer of "mol" that produces the best alignment (cid in the above code) 2) you aren't keeping the best alignment since you repeatedly run the same molecule instances through the

Re: [Rdkit-discuss] 3D alignment in Python: align conformers of 2 molecules

Hi Greg, thanks for your quick reply. This helped to improve the alignment. How can I reproduce the alignment done in with the Open3DAlign Node in Python? Is it possible at all? Best Regards, Thomas From: greg.land...@gmail.com Date: Fri, 27 Jun 2014 05:10:42 +0200 Subject: Re: [Rdkit-discuss

Re: [Rdkit-discuss] 3D alignment in Python: align conformers of 2 molecules

On Fri, Jun 27, 2014 at 7:57 AM, Thomas Strunz wrote: > > thanks for your quick reply. This helped to improve the alignment. > > I'm glad to hear it! > How can I reproduce the alignment done in with the Open3DAlign Node in > Python? Is it possible at all? > But of course. :-) There's some exam