Skip to content

Commit

Permalink
hbond analysis: fixed incorrect residue handling with trailing numbers (
Browse files Browse the repository at this point in the history
#1339)

* test for correct TIP3P resname in hbond analysis table (#801)

* Fixed incorrect handling of residue names with trailing numbers in HydrogenBondAnalysis (issue #801)

- fixes #801
- analysis.hbond.hbond_analysis.HydrogenBondAnalysis now correctly stores and parses
  donor and acceptor names and is not tripped up by resnames that end in numbers, such
  as TIP3
- store timeseries as _timeseries with donor and acceptor atom identifiers as
  tuples instead of strings (avoids the use of fragile lib.util.parse_residue())
- made timeseries a property that is generated on the fly so that old code does not break, but
  it is not cached (to avoid memory consumption for big trajectories) and so users should cache
  themselves if needed
- added tests
- rewrote parts of the docs and added notes on use of timeseries
- updated DEPRECATION warning for 1-based indices to 0.17.0 (should have been removed in
  0.16.0 but we forgot)

* hbond analysis doc fixes/improvements

- mostly numpy style (whenever possible):
  Apparently, napoleon does not like a single Notes and See Also section, need to
  use reST.
- named the 1-based indices "idx" in the docs.
- added example for analysis
  - describe convenience analysis functions
  - how to use pandas

* HydrogneBondAnalysis: internal clean up

Use atom.index instead of atom.index+1 internally and for debug output.

* Hbond analysis: fixed docs (stated wrong defaults for updating)

* hbond analysis: addressed review comments
  • Loading branch information
orbeckst authored and kain88-de committed May 14, 2017
1 parent 429795a commit 1f9a31f
Show file tree
Hide file tree
Showing 3 changed files with 554 additions and 269 deletions.
6 changes: 4 additions & 2 deletions package/CHANGELOG
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ The rules for this file:
------------------------------------------------------------------------------

mm/dd/17 utkbansal, kain88-de, xiki-tempula, kaplajon, wouterboomsma,
richardjgowers, Shtkddud123, QuantumEntangledAndy
richardjgowers, Shtkddud123, QuantumEntangledAndy, orbeckst

* 0.16.1

Expand All @@ -38,7 +38,9 @@ Fixes
(PR #1325)
* Fix PDBParser docs for conect (issue #1246)
* Fixed bug where amber topology files would fail to load if number of atoms was
exectly divisible by number of atoms per line (issue #1331)
exactly divisible by number of atoms per line (issue #1331)
* Fixed incorrect handling of residue names with trailing numbers in
HydrogenBondAnalysis (issue #801)
* Fixed AnalysisBase class provides numerical start,stop,step values (PR #1340)

Changes
Expand Down
Loading

0 comments on commit 1f9a31f

Please sign in to comment.