Re: [Rdkit-discuss] Shape Tanimoto distance question

Hi Leon, You can convert the tanimoto distance to similarity, but the formula is: Similarity = 1 - Distance Best, -greg On Tue, Jun 29, 2021 at 3:21 AM topgunhaides wrote: > Hi guys, > > A quick question: > > RDKit computes the "Shape Tanimoto distance" by calling the > "ShapeTanimotoDist". >

[Rdkit-discuss] Shape Tanimoto distance question

Hi guys, A quick question: RDKit computes the "Shape Tanimoto distance" by calling the "ShapeTanimotoDist". I assume that similarities and distances can be interconverted using the following equation? Shape Tanimoto similarity = 1 / (1 + Shape Tanimoto distance) Correct? Thank you! Best, Leon

Re: [Rdkit-discuss] N-fmoc deprotection smarts error

Hi Matt, Thank you for this. You are indeed right that I got caught by the visualization and didn't check my smiles yesterday. I thought the red was indicating an obvious valence error on the oxygen there and that molecule just made no sense. I appreciate the swift answer. Thank you, Fio On Sun,

Re: [Rdkit-discuss] RDKit molecule standardization/normalization protocol

HI JP, you are welcome, thanks a lot for reporting the problem with a reproducible! No need to bother filing a GitHub issue, I have already done that and also submitted a fix: https://github.com/rdkit/rdkit/pull/4282 Reionizing is good to make sure that charges are shuffled around if needed and l

Re: [Rdkit-discuss] RDKit molecule standardization/normalization protocol

Hi Paolo! Nice to hear from you -- and thanks for the lightning-fix+working example. Very helpful as usual. (I don't imagine you need me to open a github issue on this, but I'd be happy to if you think that is helpful/want to keep a record). Any thoughts on whether it is useful to reionize after