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Replace distance search with capped_distance in water bridge analysis #2480

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merged 6 commits into from
Feb 9, 2020
Merged

Replace distance search with capped_distance in water bridge analysis #2480

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e38ae9c
Replace distance search with capped_distance
Jan 29, 2020
15bbdfe
Add heavy test
Jan 30, 2020
fb55e7b
update water update
Jan 30, 2020
21ae01b
Update CHANGELOG
Feb 9, 2020
5f4915c
Update CHANGELOG
Feb 9, 2020
8ec5951
Merge branch 'develop' into develop
xiki-tempula Feb 9, 2020
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27 changes: 14 additions & 13 deletions package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ The rules for this file:
------------------------------------------------------------------------------
mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira,
PicoCentauri, davidercruz, jbarnoud, RMeli, IAlibay, mtiberti, CCook96,
Yuan-Yu
Yuan-Yu, xiki-tempula

* 0.21.0

Expand All @@ -33,7 +33,7 @@ Fixes
* Removes the MassWeight option from gnm (PR #2479).
* AtomGroup.guess_bonds now uses periodic boundary information when available
(Issue #2350)
* Chainreader and continuous option work correctly when readers work for more
* Chainreader and continuous option work correctly when readers work for more
than one format (Issue #2353)
* PDBQTParser now gives icode TopologyAttrs (Issue #2361)
* GROReader and GROWriter now can handle boxes with box vectors >1000nm
Expand All @@ -45,9 +45,9 @@ Fixes
* The expected frames are made available when a trajectory slice is sliced itself
with an incomplete slice and/or with a negative step (Issue #2413)
* TXYZ parser uses strings for the atom types like other parsers (Issue #2435)
* ITPParser now parses ITP *and* TOP files from GROMACS, reads #include files, and
substitutes #define variables both from the file and when passed in as a keyword
argument. The directives parsed into bonds, angles, impropers, and dihedrals now
* ITPParser now parses ITP *and* TOP files from GROMACS, reads #include files, and
substitutes #define variables both from the file and when passed in as a keyword
argument. The directives parsed into bonds, angles, impropers, and dihedrals now
match TPRParser. (PR #2408)
* Added parmed to setup.py

Expand All @@ -71,14 +71,15 @@ Enhancements
* Added match_atoms keyword to analysis.align (Issue #2285, PR #2380)
* Added wrap/unwrap transformations (PR #2038)
* Read TPR files from Gromacs 2020 (Issue #2412 and #2428)
* Added analysis.align.AverageStructure to get the average structure of an
* Added analysis.align.AverageStructure to get the average structure of an
out-of-memory trajectory (Issue #2039)
* Added _add_TopologyObjects, _delete_TopologyObjects, and public convenience
* Added _add_TopologyObjects, _delete_TopologyObjects, and public convenience
methods to Universe. Added type and order checking to _Connection
topologyattrs. (PR #2382)
* Added radius_cut_q as a method to contacts.Contacts (PR #2458)
* Added ParmEdParser, ParmEdReader and ParmEdConverter to
* Added ParmEdParser, ParmEdReader and ParmEdConverter to
convert between a parmed.Structure and MDAnalysis Universe (PR #2404)
* Improve the distance search in water bridge analysis with capped_distance (PR #2480)

Changes
* Removes `save()` function from contacts, diffusionmap, hole, LinearDensity,
Expand Down Expand Up @@ -122,7 +123,7 @@ Enhancements
* improved atom element guessing in topology.guessers to check for elements
after the first element (#2313)
* added the zero-based index selection keyword (Issue #1959)
* added position averaging transformation that makes use of the
* added position averaging transformation that makes use of the
transformations API (PR #2208)
* added find_hydrogen_donors to analysis.bonds.hbond_autocorrel to
automatically determine donors where possible (#2181)
Expand Down Expand Up @@ -156,7 +157,7 @@ Enhancements
* added functionality to write files in compressed form(gz,bz2). (Issue #2216,
PR #2221)
* survival probability additions: residues, intermittency, step with performance,
(PR #2226)
(PR #2226)
* added unwrap keyword to center (PR #2275)
* added unwrap keyword to center_of_geometry (PR #2279)
* added unwrap keyword to center_of_mass (PR #2286)
Expand Down Expand Up @@ -233,7 +234,7 @@ Deprecations
method to be used, this is done automatically in run()

Testsuite
* Raised minimum pytest version to 3.3.0, warns now uses the `match`
* Raised minimum pytest version to 3.3.0, warns now uses the `match`
argument instead of `match_expr` (Issue #2329)
* Add tests for the new water bridge analysis (PR #2087)

Expand All @@ -256,7 +257,7 @@ Fixes
* Fixed reading PDB files with DOS line ending (#2128)

Deprecations
* Default ``filename`` directory of align.AlignTraj is deprecated and
* Default ``filename`` directory of align.AlignTraj is deprecated and
will change in 1.0 to the current directory.

10/09/18 tylerjereddy, richardjgowers, palnabarun, orbeckst, kain88-de, zemanj,
Expand Down Expand Up @@ -1828,7 +1829,7 @@ Testsuite
MDAnalysisTestData package with a higher release number is available.

Testsuite

* Split off test data trajectories and structures from
MDAnalaysis/tests/data into separate package. (Issue 28)
* Numbering matches the earliest MDAnalysis release for which the data is
Expand Down
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