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Adds sequence optimization #8

Merged
merged 135 commits into from
Sep 11, 2024
Merged

Adds sequence optimization #8

merged 135 commits into from
Sep 11, 2024

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cabb99
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@cabb99 cabb99 commented Sep 11, 2024 •
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Description

Adds methods for sequence optimization based on the MonteCarlo method, using the sequence as a base function.

  • New Gamma class for handling gamma parameters for AWSEM function.
  • Optimizations for energy calculations and explorations of the free energy landscape in sequence space.

Status

  • Ready for review

cabb99 and others added 30 commits April 18, 2024 20:11
@cabb99
Adds the Gamma class to handle multiple parameters
24e4fc8
@cabb99
Adds sample gamma arrays
cd7680c
@cabb99
Corrects Gamma reading of AWSEM files
3154663
changed valid_indices=range(len(_AA)) default argument to valid_indic…
07a9f8f 
…es=np.arange(len(_AA))
@ftclark3
Merge branch 'cabb99:main' into main
aeb85ad
Merge branch 'main' of https://github.com/cabb99/Frustratometer
98c1f14 
pulling merged fork to local
@cabb99
Adds simpler handling for gammas
3977dd3
@cabb99
Adds methods to calculate AB
dee0f9f
Merge remote-tracking branch 'refs/remotes/origin/main'
56cbd7e 
sync with remote to test frustratometer code against server
Merge branch 'main' of https://github.com/cabb99/Frustratometer
b55c00e
@cabb99
Update README.md
2b57b39 
Changes CI badge location. (Displays failing even if fails are passing)
@cabb99
Update README.md
d16d396 
Adds easter egg
@cabb99
Update README.md
3569c0f
@cabb99
Merge pull request #5 from cabb99/cabb99-readme
5ffc293 
Edits readme
added tests for sequence0 and sequence12
860ec9c
added commented lines to tests/test_awsem_frustratometer.py which use…
747fa60 
…r can uncomment to modify tests if desired
fixed Frustratometer.frustration(kind='configurational') call to Frus…
22789ee 
…tratometer.configurational_frustration()
Merge remote-tracking branch 'ftclark3/main'
1f9f33f 
getting up to date
removed .rar file generated by frustratometer server (decompressed fi…
5be2d18 
…les already present in tests/data)
added additional tests for sequences of varying heterogeneity and energy
ea1d061
building on on previous commit
9d79197
building on on previous commit
755863f
building on on previous commit
cbbb4c3
finished test updates -- increased tolerance so that low heterogeneit…
9786f86 
…y sequences pass
removed sequence parameter from frustratometer.Frustratometer.vmd() t…
902550c 
…o prevent accidental misuse
added sequence argument back to vmd function but raise warning if seq…
a8aaef2 
…uence passed to vmd is different from self.sequence
raise tolerance for sequence0 configurational frustration again
4452b65
Merge remote-tracking branch 'origin/main'
e4751f5 
bringing in carlos's stuff before push my commits back
@cabb99
Merge pull request #6 from ftclark3/main
c750ff7 
Fixing configurational call
@cabb99
Merge branch 'main' of https://github.com/cabb99/DCA_Frustratometer i…
8c28161 
…nto ML
cabb99 and others added 29 commits August 15, 2024 13:16
@cabb99
Adds function to compute energies in parallel
1f91b98
@cabb99
Fixes edge case scenario when ni*nj==mi*mj but mi!=mj
2163fa3
@cabb99
Changes test to new nersion of diff
fee3f27
@cabb99
Changes integer return to float return
9090d6a
@cabb99
Adds term to compute energy of selection
53e9505
@cabb99
Require numpy<2 (for prody)
cdde686
@cabb99
Adds sample energies for annealing
e5c5d1f
@cabb99
Fixes error on yaml syntax
c8a053a
@cabb99
Fixes numpy<2 requirement
043dfb7
@ftclark3
Merge branch 'cabb99:main' into main
25df349
Merge remote-tracking branch 'ftclark3/main'
47c8ad4 
latest updates from carlos and hana's modifications
added option to write frustratogram to image file and exit instead of…
87d5505 
… making movie or opening vmd and leaving it there
@cabb99
Adds utility function for naming time
44300ed
@cabb99
Minor formatting
761eb11
@cabb99
Install pydca with the constraint that numpy<2
92748fd
@cabb99
Adds nice time formatting to the benchmarks
54da893
@cabb99
Removes parallelism from build_mean_inner_product_matrix
a426b60
@cabb99
Adds energy term benchmarks
106793b
@cabb99
Removes extra tests
48a9388
@cabb99
Merge pull request #11 from ftclark3/main
53f2be1 
write frustratogram image instead of movie
@cabb99
Removes 3.12 test
b266b0e
fixed numbification
2574762
@cabb99
Merge pull request #12 from ftclark3/ML
860ff0d 
fixed numbification
@cabb99
Updates diff_mean_inner_product_2_by_2
be01535
@cabb99
Merge branch 'ML' of https://github.com/cabb99/DCA_Frustratometer int…
c3961ae 
…o ML
@cabb99
Merges with main
3c274ae
@cabb99
Merge pull request #10 from cabb99/ML
48ae297 
Sequence optimization
@cabb99
Merges changes
9619814
@cabb99
Merge branch 'HanaJaafari-main'
f2b61ef
@HanaJaafari HanaJaafari merged commit 4ce0ed1 into HanaJaafari:main Sep 11, 2024
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3 participants
@cabb99 @HanaJaafari @ftclark3