Re: [Rdkit-discuss] mol file parsing, 3D or 2D

On 2018-01-17 10:25, Jason Biggs wrote: For the case in question, I find that if I read in a mol file containing 2D coordinates, and I skip the sanitization step altogether, then the 3D embedding algorithms fail. Well, yes, as I mentioned in the other thread: the only way you can get it to

Re: [Rdkit-discuss] mol file parsing, 3D or 2D

On Wed, Jan 17, 2018 at 10:12 AM, Dimitri Maziuk wrote: > On 2018-01-16 22:46, Greg Landrum wrote: > > It might be worth thinking about adding an option to the aromaticity >> perception code to maintain the original bond types and just set the >> "isAromatic" flag on the

Re: [Rdkit-discuss] mol file parsing, 3D or 2D

On 2018-01-16 22:46, Greg Landrum wrote: It might be worth thinking about adding an option to the aromaticity perception code to maintain the original bond types and just set the "isAromatic" flag on the bonds. This is how it's modeled in mmCIF chem. comp. It may or may not come from

Re: [Rdkit-discuss] mol file parsing, 3D or 2D

On Mon, Jan 15, 2018 at 11:59 PM, Jason Biggs wrote: > Thanks for the detailed reply > > >> >> The fact that this isn't happening for you indicates that you are reading >> the molecules in without sanitizing them - the mol file parser calls >> assignStereochemistry() by

Re: [Rdkit-discuss] mol file parsing, 3D or 2D

Thanks for the detailed reply > > The fact that this isn't happening for you indicates that you are reading > the molecules in without sanitizing them - the mol file parser calls > assignStereochemistry() by default if you sanitize. Are you sure that you > should be disabling sanitization? > > I

Re: [Rdkit-discuss] mol file parsing, 3D or 2D

Hi Jason, On Sun, Jan 14, 2018 at 8:23 PM, Jason Biggs wrote: > Two question about mol file conformer reading: > > Looking through the .mol files included for testing, and chose > "Code/GraphMol/Depictor/test_data/7UPJ_spread.mol" at random. > > When I read in this file