[Rdkit-discuss] Replacing H's with F's

2015-01-30 Thread Matthew Lardy
Hi all, I am having an issue using the Smarts based Reaction transformations in RDKit. This is a weird transformation, but I wanted to replace any or all of the protons on an aromatic ring with an F. The original transformation that I tried was: c(F)c But that didn't work. So then I tried

[Rdkit-discuss] Molecular descriptors / Fragments

2015-01-30 Thread Soren Wacker
Hi, I installed RDKit python -c 'from rdkit import rdBase; print rdBase.rdkitVersion' 2014.09.2 with conda. Before, I used molecular descriptors as explained here: http://www.rdkit.org/Python_Docs/rdkit.Chem.Descriptors-module.html For example, Descriptors.fr_Al_COO However, in the

Re: [Rdkit-discuss] Replacing H's with F's

2015-01-30 Thread Greg Landrum
Hi Matthew, On Fri, Jan 30, 2015 at 11:06 PM, Matthew Lardy mla...@gmail.com wrote: I am having an issue using the Smarts based Reaction transformations in RDKit. This is a weird transformation, but I wanted to replace any or all of the protons on an aromatic ring with an F. The original

Re: [Rdkit-discuss] Molecular descriptors / Fragments

2015-01-30 Thread Greg Landrum
Hi Soren, The functions should definitely still be there. In [1]: from rdkit import rdBase In [2]: rdBase.rdkitVersion Out[2]: '2014.09.2' In [3]: from rdkit import Chem In [4]: from rdkit.Chem import Descriptors In [5]: m = Chem.MolFromSmiles('c1c1NCOC') In [6]: Descriptors.fr_Al_COO(m)