Fix hydrogen handling in scaffolds with explicit attachment points #70
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mrwnmsr
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Dec 18, 2023
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When a scaffold is provided during decoding, we assume the model is free to attach further atoms to any atom in the scaffold, unless it contains explicit attachment points, in which case we only allow attaching to those atoms. However, the handling of these attachment points had a bug regarding explicit hydrogens, which would cause the scaffold molecule to be malformed and decoding to fail. This PR fixes this issue by carefully updating the hydrogen count where appropriate.