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Add extended similarity comparison functionality #1051

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merged 75 commits into from
Sep 22, 2023
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2ccb3fe
Protect against null data set
drroe Sep 12, 2023
a5dd741
Add brute force trajectory refinement script
drroe Sep 12, 2023
61d74c8
Add libnpy files. https://github.com/llohse/libnpy
drroe Sep 13, 2023
648bea6
Start ability to read numpy array
drroe Sep 13, 2023
381d244
Read the data. Not in a data set yet.
drroe Sep 13, 2023
e6e109a
Convert to COORDS array. Right now this is purely for comparing against
drroe Sep 13, 2023
d57507c
Add note about libnpy to README
drroe Sep 13, 2023
200ce7a
Not yet set up for fortran ordering
drroe Sep 14, 2023
b56813d
Start crdtransform action
drroe Sep 14, 2023
c00fc4e
Enable crdtransform
drroe Sep 14, 2023
f0e5ef4
Add initial rms calc when doing by brute force. Add crdtransform test.
drroe Sep 14, 2023
b2e90ec
State not needed
drroe Sep 14, 2023
1cb3a1d
Fix bug in keep action that prevented it from working with crdaction
drroe Sep 14, 2023
4970dd9
Add normcoords
drroe Sep 14, 2023
6f754ec
Update dependencies
drroe Sep 14, 2023
c3e85af
Add mask to rms when doing refine. Add norm test.
drroe Sep 14, 2023
d75051b
Add test saves
drroe Sep 15, 2023
790139e
Use overall min/max for normalization
drroe Sep 18, 2023
06cb60c
Update for normalizing with overall min and max
drroe Sep 18, 2023
b764461
Change test name
drroe Sep 18, 2023
fc16488
Actually test the brute-force refinement
drroe Sep 18, 2023
6664ab8
Put each test in a separate function
drroe Sep 18, 2023
6ce1973
Start trim outliers functionality
drroe Sep 18, 2023
469ffde
Start ExtendedSimilarity class
drroe Sep 18, 2023
f108be6
Start comparison for COORDS set
drroe Sep 18, 2023
9a6825e
Add MSD
drroe Sep 18, 2023
d830b5f
Dont do the direct coords comparison in extended similarity yet. Start
drroe Sep 18, 2023
f71fadf
Test trim. Not working yet
drroe Sep 18, 2023
1c2a55d
Fix normalization and summation
drroe Sep 18, 2023
5eb6319
Redirect to a separate file for easier testing
drroe Sep 19, 2023
aa0904b
Try to simplify passing in options
drroe Sep 19, 2023
fe16115
Add coincidence threshold and weight factor options
drroe Sep 19, 2023
10bf8c8
Move options setup to outside the loop
drroe Sep 19, 2023
47b0281
More checks. Do confidence threshold
drroe Sep 19, 2023
f7d6f11
Use function pointers for weight array routines
drroe Sep 19, 2023
dd10908
Start implementing index arrays
drroe Sep 19, 2023
c59b896
DO counts
drroe Sep 19, 2023
be259f6
Start processing indexed arrays
drroe Sep 19, 2023
1aeafd0
Add absolute version of function
drroe Sep 19, 2023
26df2d8
Dissimilarity array
drroe Sep 19, 2023
55bb080
Sum arrays
drroe Sep 19, 2023
7e1b792
Add documentation, make format easier to compare
drroe Sep 20, 2023
94ea073
Place counters into their own class
drroe Sep 20, 2023
90a05f2
Add ability to choose metric
drroe Sep 20, 2023
ec9e354
Try to implement bub
drroe Sep 20, 2023
ed91909
Make all counters double to avoid any issues with type conversions.
drroe Sep 20, 2023
ee8b72d
Do the rest of the metrics
drroe Sep 20, 2023
129c14e
Hide some debug info
drroe Sep 20, 2023
4e29aeb
Hide some debug info
drroe Sep 20, 2023
8b6472c
Sort indices
drroe Sep 20, 2023
9078de3
Start creating output COORDS set if needed
drroe Sep 20, 2023
9255fcf
Ensure new output coords are set up
drroe Sep 20, 2023
e8e65d0
Start handling cases where the length of input coord set will be
drroe Sep 20, 2023
149ae3f
Do allocation if length will not be modified
drroe Sep 20, 2023
189479f
Test using new output coords
drroe Sep 20, 2023
5997a53
Populate trim output set
drroe Sep 20, 2023
2edb9fa
Add trimcoords test save
drroe Sep 20, 2023
62d0060
Fold Opts into ExtendedSimiliarity
drroe Sep 21, 2023
f324aa2
Start code for medioid.
drroe Sep 21, 2023
253dd4c
Add criterion option
drroe Sep 21, 2023
2082e2e
Start the sim to medoid code
drroe Sep 21, 2023
de67e79
Actually remove frames for medoid trim
drroe Sep 21, 2023
f69110e
Add trim coords medoid test
drroe Sep 22, 2023
2da6663
Test create new coords set for trim
drroe Sep 22, 2023
bbb5fa2
Improve docs, remove old code
drroe Sep 22, 2023
64f31a7
Hide some debug info
drroe Sep 22, 2023
2d66207
Add separate extended comparison command class
drroe Sep 22, 2023
80285bf
Clean up messages, hide more debug
drroe Sep 22, 2023
58d1dd6
Enable extended comparison command, improve help
drroe Sep 22, 2023
ec7d52d
Add out keyword
drroe Sep 22, 2023
e2250ee
Move SetDim so user args are not overwritten
drroe Sep 22, 2023
02351a6
Add ability to set all atoms into a single molecule for pseudo
drroe Sep 22, 2023
d743920
No longer hidden
drroe Sep 22, 2023
a9192af
Update manual.
drroe Sep 22, 2023
cbdf381
Revision bump for crdtransform and extendedcomp
drroe Sep 22, 2023
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2 changes: 2 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -251,3 +251,5 @@ External code/libraries bundled with CPPTRAJ
* CPPTRAJ uses code for the [permuted congruent pseudo-random number generator](https://www.pcg-random.org/index.html) PCG32 by Melissa O'Neill and the [Xoshiro 128++ pseudo-random number generator](http://prng.di.unimi.it) by David Blackman and Sebastino Vigna.

* The code for quaternion RMSD calculation was adapted from code in [qcprot.c](https://theobald.brandeis.edu/qcp/qcprot.c) originally written by Douglas L. Theobald and Pu Lio (Brandeis University).

* The code for reading numpy arrays in `src/libnpy` is from [libnpy](https://github.com/llohse/libnpy) written by Leon Merten Lohse et al. (Universität Göttingen).
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