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Moves hbond_autocorrel and removes old hbond code #3258

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Merged
IAlibay merged 9 commits into from
May 6, 2021
Merged

Moves hbond_autocorrel and removes old hbond code #3258

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66f9a5a
Moves hbond_autocorrel and removes old hbond code
IAlibay May 2, 2021
fc43502
Deprecated in situ instead
IAlibay May 2, 2021
2ad6b56
Fix docs
IAlibay May 2, 2021
6ec1efd
Merge branch 'mv-hbond' of https://github.com/IAlibay/mdanalysis into…
orbeckst May 5, 2021
12bbf4e
add output to test_api/submodule test
orbeckst May 5, 2021
eb3b637
moved hbonds.hbond_autocorrel to hydrogenbonds.hbond_autocorrel
orbeckst May 5, 2021
2145483
include hydrogenbonds.hbond_autocorrel in docs
orbeckst May 5, 2021
fe76676
fixed doc in hydrogenbonds.wbridge_analysis
orbeckst May 6, 2021
6a8dccd
Merge branch 'develop' into mv-hbond
orbeckst May 6, 2021
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11 changes: 8 additions & 3 deletions package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ Fixes
removed (Issue #3209)
* Fixed 'sphzone', 'sphlayer', 'cyzone', and 'cylayer' to return empty if the
zone/layer is empty, consistent with 'around' (Issue #2915)
* A Universe created from an ROMol with no atoms returns now a Universe
* A Universe created from an ROMol with no atoms returns now a Universe
with 0 atoms (Issue #3142)
* PDBParser will check for the presence of the chainID attribute of an
atom group and use these values instead of just using the end of segid.
Expand Down Expand Up @@ -114,10 +114,10 @@ Enhancements
* Switch GNMAnalysis to AnalysisBase (Issue #3243)
* Adds python 3.9 support (Issue #2974, PR #3027, #3245)
* Added an MDAnalysis shields.io badge to the README (Issue #3227, PR #3229)
* Added sort method to the atomgroup (Issue #2976, PR #3188)
* Added sort method to the atomgroup (Issue #2976, PR #3188)
* ITPParser now reads [ atomtypes ] sections in ITP files, used for charges
and masses not defined in the [ atoms ] sections
* Add `set_dimensions` transformation class for setting constant
* Add `set_dimensions` transformation class for setting constant
box dimensions for all timesteps in trajectory (Issue #2691)
* Added a ValueError raised when not given a gridcenter while
providing grid dimensions to DensityAnalysis, also added
Expand Down Expand Up @@ -174,6 +174,8 @@ Enhancements
checking if it can be used in parallel analysis. (Issue #2996, PR #2950)

Changes
* Deprecated analysis.hbonds.hbond_analysis has been removed in favour of
analysis.hydrogenbonds.hbond_analysis (Issues #2739, #2746)
* `GNMAnalysis`, `LinearDensity`, `PersistenceLength` and
`AnalysisFromFunction` use the `results` attribute.
* Fixed inaccurate docstring inside the RMSD class (Issue #2796, PR #3134)
Expand Down Expand Up @@ -220,6 +222,9 @@ Changes
* Added OpenMM coordinate and topology converters (Issue #2863, PR #2917)

Deprecations
* The analysis.hbonds.hbond_autocorrel code has been moved to
analysis.hydrogenbonds.hbond_autocorrel and will be removed
from analysis.hbonds in 3.0.0 (PR #3258)
* In 2.1.0 the TRZReader will default to a dt of 1.0 ps when failing to
read it from the input TRZ trajectory.

Expand Down
2 changes: 0 additions & 2 deletions package/MDAnalysis/analysis/hbonds/__init__.py
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Expand Up @@ -22,9 +22,7 @@
#

__all__ = [
'HydrogenBondAnalysis',
'HydrogenBondAutoCorrel', 'find_hydrogen_donors',
]

from .hbond_analysis import HydrogenBondAnalysis
from .hbond_autocorrel import HydrogenBondAutoCorrel, find_hydrogen_donors
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