Re: [Rdkit-discuss] acepentalene aromaticity perception

2020-01-09 Thread Peter S. Shenkin
Since the entire system is antiaromatic, why are any carbons at all shown as aromatic in the SMILES? -P. On Thu, Jan 9, 2020 at 3:56 PM Andrew Dalke wrote: > Hi all, > > Could someone explain the following, which uses the SMILES from > https://en.wikipedia.org/wiki/Acepentalene : > > >>> from

Re: [Rdkit-discuss] Exhaustive fragmentation of molecules

2020-01-09 Thread Peter St. John
I wrote some code to do something like this that you might be able to start from: https://github.com/pstjohn/bde/blob/master/bde/fragment.py Mine was mainly concerned with going to/from SMILES strings of the parent mol and resulting radicals On Wed, Jan 8, 2020 at 3:40 AM Puck van Gerwen wrote:

[Rdkit-discuss] acepentalene aromaticity perception

2020-01-09 Thread Andrew Dalke
Hi all, Could someone explain the following, which uses the SMILES from https://en.wikipedia.org/wiki/Acepentalene : >>> from rdkit import Chem >>> Chem.CanonSmiles("C1=CC2=CC=C3C2=C1C=C3") 'c1cc2ccc3ccc1-c=3-2' >>> import rdkit >>> rdkit.__version__ '2019.09.1' I don't understand the aromatic

Re: [Rdkit-discuss] Making Morgan Fingerprints more SMILES-like

2020-01-09 Thread Greg Landrum
Hi Christian, The topic of how to specify atom invariants came up recently on the list here: https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg09400.html Here's a gist that shows how to specify your own atom invariants based solely upon atomic number and, optionally,

[Rdkit-discuss] Making Morgan Fingerprints more SMILES-like

2020-01-09 Thread Kramer, Christian via Rdkit-discuss
Dear RDKit community, Happy new year! I am looking for a way to make the circular Morgen Fingerprints more SMILES like. The background is that with the default definition of atom invariants in the RDKit implementation, Morgan Fingerprints do not explicitly take into account aromaticity, and use