Md decoys#15

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cabb99:optimizationfrom

ftclark3:md_decoys

Commits on Apr 9, 2025

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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
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got pdb.py from my amyloid_atlas branch, which allows prody for loading the structures. this probably wasn't necessary
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undid unnecessary modification to structure processing in AWSEM
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changed name of DecoyEnsemble.average to DecoyEnsemble.avg
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fix wrong variable used
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reinitialize indicator function generator each time attribute is accessed
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take absolute value of gamma (sqrt(gamma**2)) for approximate variance calculation
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Commits on Jul 12, 2025

i guess our sign convention caused taking the absolute value of the gammas to make all energies negative. so now, we take the negative of the absolute values of the gammas to make all energies posi…
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