[Rdkit-discuss] unexpected "attempt to add self-bond" error

2010-12-24 Thread Andrew Dalke
Here's a fun one. I was writing up an article about how to generate a SMILES with an arbitrary atom ordering by using a lot of dot disconnects. I had to work around what I think is a problem with RDKit's SMILES parser Here's a minimal example of the failure >>> mol = Chem.MolFromSmiles("C1.C12

Re: [Rdkit-discuss] unexpected "attempt to add self-bond" error

2010-12-26 Thread Greg Landrum
Hi Andrew, On Sat, Dec 25, 2010 at 4:24 AM, Andrew Dalke wrote: > Here's a fun one. > > I was writing up an article about how to generate a SMILES with an arbitrary > atom ordering by using a lot of dot disconnects. Heh, I was wondering if you were going to take that one up. Knowing how much yo

Re: [Rdkit-discuss] unexpected "attempt to add self-bond" error

2010-12-28 Thread Andrew Dalke
On Dec 27, 2010, at 5:41 AM, Greg Landrum wrote: > Heh, I was wondering if you were going to take that one up. Knowing > how much you enjoy (ab)using dot diconnects it seemed likely. :-) And take it up I did. Here's the essay I just wrote about the technique. http://dalkescientific.com/writings/d