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Merged
orbeckst merged 2 commits into from
Mar 31, 2017
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analysis.gnm: optimizations and doc/code cleanup #1272

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analysis.gnm: optimizations and doc/code cleanup
orbeckst Mar 23, 2017
6145479
analysis.gnm: implemented review comments (#1272)
orbeckst Mar 31, 2017
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12 changes: 11 additions & 1 deletion package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,9 @@ Enhancements
* Groups (atomgroup, residuegroup, and segmentgroup) have more operators,
included set operators (Issue #726)
* Universes built with Merge now use the MemoryReader (Issue #1251)
* speed improvement for analysis.gnm.closeContactGNMAnalysis(...,
weights="size") by about 5x (partially Issue #1191)


Fixes
* Trajectory slicing made completely Pythonic (Issue #918 PR #1195)
Expand Down Expand Up @@ -153,13 +156,20 @@ Changes
* Remove deprecated PrimitivePDB* classes
* Remove deprecated `delta` keyword for ChainReader
* Remove deprecated permissive_pdb_reader flag

* Removed superfluous and confusing keywords `start` and `end` for resid
selection in analysis.helanal.helanal_main() and
analysis.helanal.helanal_trajectory()
* weights="size" parameter in analysis.gnm.closeContactGNMAnalysis to
replace MassWeight=True

Deprecations (Issue #599)
* Use of rms_fit_trj deprecated in favor of AlignTraj class (Issue #845)
* Moved analysis.x3dna to the analysis.legacy module (Issue #906)
* The keyword argument *quiet* is deprecated in favor of *verbose*
throughout the library (Issue #903)
* MassWeight=True parameter in analysis.gnm.closeContactGNMAnalysis
deprecated in favor of weights="size".


05/15/16 jandom, abhinavgupta94, orbeckst, kain88-de, hainm, jbarnoud,
dotsdl, richardjgowers, BartBruininks, jdetle
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