Chemical Space fails on Extended SMILES

Issues
#1

The algorithm that calculates “Chemical Space” fails when using extended smiles or molfiles that contain extended information.

An example extended smiles that would fail is: “CO©[H]N1C=CC=C1 |c:5,7,H:3.2|”

Regular SMILES does work, but will also fail if a null/undefined record is encountered. Both issues are a problem for users with irregular or sparse compound datasets.

Please see documentation at this URL for Chemxon’s extended smiles format: https://docs.chemaxon.com/display/docs/chemaxon-extended-smiles-and-smarts-cxsmiles-and-cxsmarts.md#:~:text=Chemaxon%20Extended%20SMILES%2FSMARTS%20is,or%20use%20them%20as%20comment.

#2

Hello! Thanks for your feedback.
Indeed at the moment chemical space doesn’t support extended smiles format. We will see what we can do about this issue.
As for empty values - could you provide more details about the error you are getting? Maybe a stacktrace from the console if possible. And version of Chem package you are using.
Thank you in advance!

#3

Hello Maria,

The issue with Chemical Space failing has to do with SMILES with unknown chirality. Please see the attached screen shot. It is my preference that if a SMILES cannot be included in the calculation of chemical space, that the operation would still proceed and any molecules that fail would be excluded and a warning popup would notify the user that “X chemicals failed to be included in the analysis: rows [123, 456]”. Would you please consider this suggestion. Thank you for the wonder tool.

I am using Chem Package 1.4.24.

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#4

Oh, I see. Yes, we faced the issue you described before. The only difference is that the reason molecules failed were some others than unknown chirality. This bug has been fixed in version 1.5.10 of Chem package. This version is already available on npm. But it requires Datagrok version 1.13.2 or higher. Which version of Datagrok are you using?
As for warning with total number and indexes of failed molecules - indeed it is agood idea. We will implement in the next Chem version.

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#5

I have Datagrok version 1.13.7. If Chem version 1.5.10 will fix this issue I would like for it to be installed. Let’s chat over email.

#6

Hi Tom, I’ve sent you an email with installation instructions.

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