Christian Kramer

Results 9 comments of Christian Kramer

bond.IsInRing() does not correctly identify ring bond

Hi Ichiru. I am not sure whether I understand you correctly. However, I do not think that if startAtom and endAtom are in a ring this is a sufficient criterion...

multiple smarts in --cut-smarts

Andrew commented on this request on the RDKit-discuss mailing list as: """ I took a look at the code. It expects that there is only a single SMARTS, so there's...

multiple smarts in --cut-smarts

At the RDKit UGM Hackathon 2019, this question came up again. Participants wanted to use the RECAP rules for cutting. Creating a single SMARTS to match all 11 rules might...

Failure with mmpdb fragment for some specific smiles

Hi Cheng, thanks for pointing out this issue. mmpdb does have functionality to skip erroneous SMILES, but this one seems to be another problem - the SMILES is complicated, but...

mmpdb transform --min-constant-size N - AttributeError: 'Fragmentation' object has no attribute 'num_variable_heavies'

Dear Niaev, thank you for the bug report. I will look into it, I just cannot promise when exactly. Best regards, Christian

Failure with mmpdb fragment for some specific smiles

Hi Pablo, I currently do not personally develop mmpdb any more. This is in the hands of @adalke and Jerome Hert. Maybe they can comment? Bests, Christian

Unexpected generated molecule with double cuts MMPDB

Hi Alice, I am not sure whether I understand your issue: The 3rd and the 5th SMILES string in your question are exactly the same - if you start with...

Unexpected generated molecule with double cuts MMPDB

Hi Alice, can you share the command you use to get the new compounds created and the full output if you run it with the --explain or --save-details option? Thanks,...

Obtain list of matched pairs with common core from an ID.

Hi Mike, this is not a standard use case that we implemented, so you need a workaround. You can generate a list of all matched pairs if you index to...