Fix for cases where tokenization failed #54
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Co-authored-by: Alex Rogozhnikov <arogozhnikov@users.noreply.github.com>
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Description
When tokenization failed (e.g., given a malformed SMILES string like
Zn), we did not properly addNoneto structure contexts, resulting in a mismatch betweenentity_dataandstructure_contextdata when we zip them together afterwards. This fixes the issue and adds new logic to assignchain_idonly based on non-null structural contexts. This is because the ranking code expects contiguous numbering ofchain_id.Test plan
Tested examples that crashed previously with malformed SMILES strings; these do not crash as they did before and instead produce output with malformed SMILES omitted.