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How can I compute energy from a protein PDB file?

I asked the above question.

Then I thought, Why don't I check how BioJava obtains bond information from a protein PDB file?

Surprisingly, BioJava's tutorial doesn't have any discussion on Bonds.

I checked BioJava's GitHub repo, but I failed to find any such information.

How does BioJava retrieve bond information from a PDB file?

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