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luost26 / 3D-Generative-SBDD

💊 A 3D Generative Model for Structure-Based Drug Design (NeurIPS 2021)
MIT License
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How to determine if the generated atoms/bonds are aromatic or not? #2

Closed mengliu1998 closed 2 years ago

mengliu1998 commented 2 years ago

Hi @luost26,

Thank you for this interesting work. I have a question about the bond inference process.

After sampling, we have the generated atom types and their positions, and our goal is to infer the bonds among these atoms. In this line, it seems that we can decide if an added bond should be aromatic or not. For this line, I am confused about what is the indicator for test data used in generation. From my understanding, what we have after sampling are generated atom types and their positions. How can we determine if the generated atoms/bonds should be aromatic or not?

Thank you in advance. Any discussions from others are also warmly welcome.

luost26 commented 2 years ago

Hi,

Thank you for your interest in our project. The indicators predicted by the network are not used in the final version. It's a legacy of previous experiments.

mengliu1998 commented 2 years ago

Got it. Thank you for the clarification.