[Rdkit-discuss] Preserving hydrogens necessary for imine cis/trans stereochemistry?

Is there a recommended way in RDKit to preserve hydrogens necessary for representing cis/trans stereochemistry of imines? For example, given the attached SDF I need to maintain explicit hydrogens in the output SMILES string to maintain the imine cis/trans stereo-chemistry. mol =

Re: [Rdkit-discuss] How to match any halogen of a structure with any halogen of a substructure?

Dear All, In case it helps, there is a wealth of functional groups already in RDKit available here: https://github.com/rdkit/rdkit/blob/master/Data/Functional_Group_Hierarchy.txt For instance, the functional group halogen pattern we use is a bit more complicated:

Re: [Rdkit-discuss] Preserving hydrogens necessary for imine cis/trans stereochemistry?

There isn't currently any easy way to do this. One workaround that could make the manual stuff a bit less painful would be find those Hs, convert them into Ds, call RemoveHs(), and then convert the Ds back into Hs. It seems like it does make sense to modify the RemoveHs() function:

Re: [Rdkit-discuss] How to match any halogen of a structure with any halogen of a substructure?

Hi Alexis, Try aromatic form instead of Kekule notation. Best, Michal On 17 May 2017 at 12:55, Alexis Parenty wrote: > Hi everyone, > > I am looking for substructure match between a smarts and a smiles, but I > want any heteroatom from the smarts to match any

[Rdkit-discuss] How to match any halogen of a structure with any halogen of a substructure?

Hi everyone, I am looking for substructure match between a smarts and a smiles, but I want any heteroatom from the smarts to match any heteroatom from a smiles: [image: Inline images 1] The following does not return what I would expect: smarts1 = "

Re: [Rdkit-discuss] How to match any halogen of a structure with any halogen of a substructure?

Hi Michal, thanks for your response. I think I made a typo somewhere in my previous code since it now works fine, even without the the kekule notation... Sorry about the confusion... Best, Alexis On 17 May 2017 at 13:59, Michal Krompiec wrote: > Hi Alexis, > Try