updates for chain-wise calculations and fixes multichain processing#14

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ftclark3 wants to merge 31 commits intocabb99:mainfrom

ftclark3:amyloid_atlas

Commits on Apr 15, 2025

adding support for multiple chains but need to make some more changes and test
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Commits on Apr 16, 2025

stopped resetting resnums for the _cleaned.pdb because we're now telling openmm to keepIds when writing it
ftclark3
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added start_mask to the mask computation for electrostatics and the mask attribute of the AWSEM class
ftclark3
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Commits on Apr 18, 2025

fixed multichain sequence separation mask computation
ftclark3
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Commits on Apr 19, 2025

added local density test for multichain structures. need to add frustration tests in the future
ftclark3
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Commits on Apr 22, 2025

think everything is working now, but should still add some tests. Also, watch out for the changes made to the constraints on the pairs for which configurational frustration is evaluated. Now, a pai…
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Commits on Apr 23, 2025

Commits on Apr 24, 2025

Commits on Apr 27, 2025

improved error handling
ftclark3
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Commits on Apr 29, 2025

added tcl script write constraint to nearest neighbors for highly frustrated contacts (in addition to minimally frustrated contacts, which was already implemented)
ftclark3
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Commits on Apr 30, 2025

Commits on May 9, 2025

Commits on May 16, 2025

logging state of the code that worked correctly (as far as I can tell) but needs to be refactored
ftclark3
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Commits on May 17, 2025

Commits on May 21, 2025

added option to approximate density affects of fibril above and below chain in amyloid
ftclark3
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