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delete bonds from the topology after it is created by PDBFile#106

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ftclark3 wants to merge 1 commit into
cabb99:masterfrom
ftclark3:patch-26
Open

delete bonds from the topology after it is created by PDBFile#106
ftclark3 wants to merge 1 commit into
cabb99:masterfrom
ftclark3:patch-26

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@ftclark3

@ftclark3 ftclark3 commented Jun 5, 2026

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Description

We need to verify that this doesn't break anything, but in the long run this should reduce the chances of unexpected behavior and enable using standard 3 letter codes in -openmmawsem.pdb files

Todos

  • Simplify topology processing: it will only have the Bonds that we explicitly add

Questions

  • Need to verify that nothing relies on the Bonds created by PDBFile

Status

  • Ready to go

We need to verify that this doesn't break anything, but in the long run this should reduce the chances of unexpected behavior and enable using standard 3 letter codes in -openmmawsem.pdb files
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