Hello,
I've been working with the mol_utils.py module and noticed that the code uses [Yb] and [Lu] as placeholders or connectors of fragments in SMILES strings. While this approach is unique, it might be more intuitive and consistent with common practices in cheminformatics to use the * wildcard as a placeholder.
Reasons for the suggestion:
- The
* wildcard is a widely recognized placeholder in SMILES notation.
- Using
[Yb] and [Lu] might lead to confusion as these are valid representations for the Ytterbium and Lutetium elements respectively.
- I've encountered some issues when processing the SMILES strings with other tools due to these placeholders.
Here's a simple example of how the replacement might look:
Original: F[Yb]
Suggested: F*
I believe making this change would enhance the module's compatibility and user-friendliness. I hope you'll consider this suggestion. Thank you for your great work on this project!
Best regards,
Madiha
Hello,
I've been working with the
mol_utils.pymodule and noticed that the code uses[Yb]and[Lu]as placeholders or connectors of fragments in SMILES strings. While this approach is unique, it might be more intuitive and consistent with common practices in cheminformatics to use the*wildcard as a placeholder.Reasons for the suggestion:
*wildcard is a widely recognized placeholder in SMILES notation.[Yb]and[Lu]might lead to confusion as these are valid representations for the Ytterbium and Lutetium elements respectively.Here's a simple example of how the replacement might look:
Original:
F[Yb]Suggested:
F*I believe making this change would enhance the module's compatibility and user-friendliness. I hope you'll consider this suggestion. Thank you for your great work on this project!
Best regards,
Madiha