[Rdkit-discuss] Double Bond Stereochemistry in the RDKit

2018-12-03 Thread Kovas Palunas 
Hi All,

I’m looking for a bit more clarity regarding double bond stereochem in RDKit.  
Currently, my understanding is that there are 3 ways to currently store this 
information:


  1.  STEREOE/STEREOZ tags + stereo atoms on either side of bond set by CIP 
ranks, as computed when calling MolFromSmiles to make a new molecule or 
AssignStereochemistry on an existing molecule
  2.  Manually set STEREOCIS/STEREOTRANS tags + manually set stereo atoms
  3.  ENDUPRIGHT/etc. single bond directionality tags, which are set when 
reading a molecule from smiles/inchi/mol file

Is one of these methods the “ground truth” that is looked for by RDKit 
functions that care about this info, like the substructure matching code or the 
SMILES writing code?

I am currently working on code that mutates molecules using a predetermined 
list of changes to be made to the molecule.  I’d like to be able to include 
bond stereochemistry changing/creation/destruction here, and was thinking of 
doing so using the STEREOCIS/STEREOTRANS tags (and also providing the reference 
stereo atoms).  Before I do this I want to make sure that molecules with these 
tags will be handled correctly by other RDKit functions downstream.  Would 
these tags be a good choice here?  Are there any caveats I should keep in mind 
as I work with this information?

Thanks!

- Kovas

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[Rdkit-discuss] Bond tags in SVGs

2018-12-03 Thread Lukas Pravda 
Hi all,

 

I was wondering if there is a way how you can tag  elements (bonds) in 
the svg created by rdkit.

 

i.e. transform something like this: 





 

Into:





 

Or similar. I’ve found possibility of tagging atoms in the SVG using 
Draw.rdMolDraw2D.MolDraw2DSVG.drawOptions() method that exposes property 
includeAtomTags. This then renders following additional elements into the SVG:

rdkit:atom idx="4" label="O-" x="153.479" y="82.8259" />

 

But I have not seen anything like this for bonds (latest release of RDKIT and 
python). Thanks, in advance for any hints. I was wondering about using 
highlightBondLists and then based on the svg infer the bond annotation, but 
that seems to be a bit of an overkill.

 

Cheers,

Lukas

 

 

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