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Updated PSA module #438

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Merged
merged 19 commits into from
Sep 21, 2015
Merged

Updated PSA module #438

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5a2f6ba
PSA updated: new metrics, Hausdorff/nearest neigh analysis and plotti…
sseyler Sep 16, 2015
bc13c02
Fixed psa.py conflicts (numpy --> np)
sseyler Sep 16, 2015
3bb5ec6
Added enhancements to PSA in CHANGELOG
sseyler Sep 17, 2015
3af46b2
Added new DIMS AdK trajectory to test data
sseyler Sep 17, 2015
a68bf3a
Added DCD2 (DIMS AdK transition) to datafiles
sseyler Sep 17, 2015
4a5caf6
Minor tweaks to nearest neighbor plotting method
sseyler Sep 18, 2015
3492ae6
Added basic tests for PSA
sseyler Sep 18, 2015
8a23524
Revert "Added DCD2 (DIMS AdK transition) to datafiles"
sseyler Sep 19, 2015
673fbeb
PSA.HP/PSA.NN now properties, fixed NN plot method
sseyler Sep 19, 2015
e029273
Added back DCD2 to datafiles
sseyler Sep 19, 2015
9cc3e4d
Added seaborn to 'extras_require' in setup.py, try/except for seaborn…
sseyler Sep 19, 2015
c913236
Updated CHANGELOG for PSA tests and new AdK DIMS DCD test file
sseyler Sep 19, 2015
e2b99d8
'PSA' now 'PSAnalysis' (less namespace confusion); added import for p…
sseyler Sep 19, 2015
6583416
Added note about PSA --> PSAnalysis in CHANGELOG
sseyler Sep 19, 2015
b0374da
Instances of PSA --> PSAnalysis
sseyler Sep 19, 2015
2c3ad5a
Made 'get_psa_pairs' a property
sseyler Sep 21, 2015
83b6d98
Updated documentation for psa_pairs, nearest_neighbors, hausdorff_pai…
sseyler Sep 21, 2015
0ef949c
psa_pairs, nearest_neighbors, hausdorff_pairs are properties whose co…
sseyler Sep 21, 2015
2ae4ae6
Added note directives to docs for getter methods (where analyses must…
sseyler Sep 21, 2015
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12 changes: 12 additions & 0 deletions package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,18 @@ Enhancements
* `Atom` and `AtomGroup` now expose occupancy value as `occupancy` and
`occupancies` properties (Issue #396)
* XYZReader now supports frame indexing (Issue #428)
* `PSA` changed to `PSAnalysis` to reduce namespace clutter
* `PSAnalysis` now includes Hausdorff pairs analysis and associated nearest
neighbor
plotting method
* New class `PSAPair` added to MDAnalysis.analysis.psa for handling
Hausdorff pairs analysis
* `PSAnalysis` can now generate annotated heat maps
* Added three new distance functions to MDAnalysis.analysis.psa
* Additional getters added to `Path` and `PSAnalysis`
* MSD matrix function now globally available in MDAnalysis.analysis.psa
* Function for obtaining coordinate axes from numpy trajectories now
globally available in MDAnalysis.analysis.psa

Changes
* An AtomGroup with 0 atoms now yields an `IndexError` on call to
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