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Md decoys #15

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Md decoys #15

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34e4094
saving changes
ftclark3 Apr 9, 2025
fa23e34
fixed typo
ftclark3 Jul 8, 2025
fce6e82
added missing 'self' references
ftclark3 Jul 8, 2025
7483959
refactored; basic setup of decoy ensemble is working now
ftclark3 Jul 9, 2025
c9715d7
changed 'AWSEMEnsemble' class name to 'DecoyEnsemble'
ftclark3 Jul 9, 2025
641dfb9
stripped DecoyEnsemble down to the bare minimum
ftclark3 Jul 9, 2025
107d780
updated call to Structure in test_optimization
ftclark3 Jul 10, 2025
2bb3b83
refactored, passing most tests but failing some due to inaccurate ele…
ftclark3 Jul 10, 2025
d0b23f3
tests passing now (except for the dca tests requiring hmmer, which ha…
ftclark3 Jul 10, 2025
9fe70c2
tests still passing (except for that hmmer issue) and AWSEMIndicators…
ftclark3 Jul 10, 2025
d3386c9
got rid of unused classes
ftclark3 Jul 10, 2025
88834d3
updated documentation
ftclark3 Jul 10, 2025
2a88e03
refactored DecoyEnsemble to minimize memory usage and implemented avg…
ftclark3 Jul 11, 2025
790adce
got pdb.py from my amyloid_atlas branch, which allows prody for loadi…
ftclark3 Jul 11, 2025
6068d3c
undid unnecessary modification to structure processing in AWSEM
ftclark3 Jul 11, 2025
6d5586b
changed name of DecoyEnsemble.average to DecoyEnsemble.avg
ftclark3 Jul 11, 2025
1c1a5ef
fix wrong variable used
ftclark3 Jul 11, 2025
3b64349
reinitialize indicator function generator each time attribute is acce…
ftclark3 Jul 11, 2025
3a281d7
take absolute value of gamma (sqrt(gamma**2)) for approximate varianc…
ftclark3 Jul 11, 2025
26795fe
i guess our sign convention caused taking the absolute value of the g…
ftclark3 Jul 12, 2025
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