Re: [Rdkit-discuss] How to import RDkit into the ipython notebook

2013-12-24 Thread Mark Forster
A set of walkthrough notes for RDKit and iPython notebook installation on a Debian based Linux machine. Build RDkit from source. Instructions take from page http://www.rdkit.org/docs/Install.html#building-from-source [1] First Install these dependencies on Debian based Linux system.

Re: [Rdkit-discuss] Compound Neutralization

2013-12-24 Thread Gerebtzoff, Gregori
Hi Yingfeng, Let me remind you some chemistry basics: Chlorine atom has 17 electrons. In last orbit it has 7 electrons hence it requires 1 electron to complete octet. Hence it's valency is 1. Thus it's not a surprise that your smiles is generating an error. In order to check for get the charge