fix molecule sanitization in reader.py - #45
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
The
_sanitize_moleculefunction gets called, but the result is not used (#40 ). This leads to missing values for some of the properties (AtomHybridization gets set to unspecified).This does not affect model training because the training dataset does not use SMILES string, but passes molecule objects (which have been created from sanitized molfiles).
To avoid future discrepancies between training and inference, I moved the SMILES to mol conversion to chebi_utils. This gives us the chance to update the chebai and chebifier repositories as well which both have their own SMILES-processing functionality.
Todo