Temp decoy#24

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ftclark3 wants to merge 79 commits into

cabb99:mainfrom

ftclark3:temp_decoy

Commits on Apr 9, 2025

saving changes
ftclark3
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Commits on Jul 8, 2025

Commits on Jul 9, 2025

Commits on Jul 11, 2025

refactored DecoyEnsemble to minimize memory usage and implemented avg/std classes
ftclark3
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got pdb.py from my amyloid_atlas branch, which allows prody for loading the structures. this probably wasn't necessary
ftclark3
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undid unnecessary modification to structure processing in AWSEM
ftclark3
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changed name of DecoyEnsemble.average to DecoyEnsemble.avg
ftclark3
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fix wrong variable used
ftclark3
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reinitialize indicator function generator each time attribute is accessed
ftclark3
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take absolute value of gamma (sqrt(gamma**2)) for approximate variance calculation
ftclark3
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Commits on Jul 13, 2025

updated parallel tempering writer to write total energy and other energies from the same frame as the sequence
ftclark3
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Commits on Jul 14, 2025

Commits on Jul 27, 2025

partial implementation of covariance matrix potts model; still need to do a lot more work
ftclark3
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Commits on Jul 28, 2025

temporary md decoys thing for single temperature only
ftclark3
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Commits on Jul 31, 2025

updated indicator function saving
Finley Clark
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fixed handling of standard deviation calculation
ftclark3
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fixing std calculation
ftclark3
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Commits on Aug 2, 2025

Commits on Aug 6, 2025

frustration-inspired calculation for group meeting
ftclark3
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Commits on Aug 23, 2025

saving in the state where we can at least calculate the total energy by the looping method. now need to figure out how to get analytical mean and variance from the looping method
ftclark3
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Commits on Sep 17, 2025

Commits on Oct 27, 2025

improved comments
ftclark3
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Commits on Nov 7, 2025

merging fixed Gamma.py from carlos_main
ftclark3
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Commits on Nov 8, 2025

Commits on Nov 9, 2025

Commits on Nov 16, 2025

small optimization edits; should come back to this soon
Finley Clark
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bringing up to date
Finley Clark
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cleaning up tiny unmerged diff (just a newline)
Finley Clark
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Commits on Nov 26, 2025

Commits on Dec 5, 2025

changed name of AWSEMParameters class to Parameters
ftclark3
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Commits on Dec 6, 2025

Commits on Dec 8, 2025

Commits on Dec 10, 2025

Commits on Dec 11, 2025

Commits on Dec 12, 2025

refactored attributes and properties of _AWSEMBase
ftclark3
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Commits on Dec 22, 2025

saving changes
ftclark3
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