Re: [Rdkit-discuss] drawing code take 2

2016-09-08 Thread Dimitri Maziuk
On 09/08/2016 10:25 AM, Greg Landrum wrote: > Dimitri, > Why do you want 2D drawings that include H atoms? I have an NMR spectroscopist doing peak assignments, proton spectra are the most commonly used kind for metabolites & such. As you're well aware, atom nomenclature is an "interesting" issue

Re: [Rdkit-discuss] drawing code take 2

2016-09-08 Thread Greg Landrum
Dimitri, This is yet another demonstration of why chemists don't normally do 2D depictions of molecules that include Hs: things are just too crowded. Even quite good 2D coordinate generators like MarvinSketch have problems with this: [image: Inline image 1] Why do you want 2D drawings that inclu

[Rdkit-discuss] drawing code take 2

2016-09-07 Thread Dimitri Maziuk
:( Here's one where AddHs() really breaks things. It is an unpleasant molecule to draw. So it looks like the issue is that - for CID 112084 call to AddHs() changed the layout (arguably not for the better), whereas - for CID 260719 it didn't change the layout/shorten the bonds when it really shoul