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Minimum mass for hydrogen guess in HydrogenBondAnalysis #2516

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merged 34 commits into from
Feb 12, 2020

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RMeli
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@RMeli RMeli commented Feb 9, 2020

Fixes #2472

Changes made in this Pull Request:

  • Added a min_mass parameter (set to 0.9 by default) to guess_hydrogens in HydrogenBondAnalysis

When the mass can't be guessed it is usually set to 0.0. This could lead to an erroneous identification of hydrogen atoms.

PR Checklist

  • Tests?
  • CHANGELOG updated?
  • Issue raised/referenced?

RMeli and others added 29 commits August 7, 2019 18:41
@RMeli RMeli requested a review from IAlibay February 9, 2020 14:53
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@richardjgowers richardjgowers left a comment

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couple silly questions

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codecov bot commented Feb 9, 2020

Codecov Report

Merging #2516 into develop will increase coverage by 0.08%.
The diff coverage is 100%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop    #2516      +/-   ##
===========================================
+ Coverage    90.25%   90.33%   +0.08%     
===========================================
  Files          169      170       +1     
  Lines        23210    23146      -64     
  Branches      3008     2989      -19     
===========================================
- Hits         20948    20909      -39     
+ Misses        1655     1634      -21     
+ Partials       607      603       -4
Impacted Files Coverage Δ
...age/MDAnalysis/analysis/hbonds/hbond_autocorrel.py 88.05% <ø> (+0.09%) ⬆️
package/MDAnalysis/analysis/hole.py 72.01% <ø> (+0.04%) ⬆️
package/MDAnalysis/analysis/lineardensity.py 81.81% <ø> (+18.51%) ⬆️
package/MDAnalysis/analysis/diffusionmap.py 93.33% <ø> (+2.56%) ⬆️
package/MDAnalysis/analysis/psa.py 83.68% <ø> (+0.63%) ⬆️
...DAnalysis/analysis/hydrogenbonds/hbond_analysis.py 95.45% <100%> (+0.08%) ⬆️
package/MDAnalysis/coordinates/NAMDBIN.py 100% <100%> (ø)
...ckage/MDAnalysis/analysis/hbonds/hbond_analysis.py 81.6% <100%> (+0.78%) ⬆️
package/MDAnalysis/analysis/rms.py 92.8% <100%> (+0.13%) ⬆️
package/MDAnalysis/analysis/contacts.py 100% <100%> (ø) ⬆️
... and 18 more

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Couple of test suggestions.

@richardjgowers richardjgowers merged commit d873d36 into MDAnalysis:develop Feb 12, 2020
@RMeli RMeli deleted the issues/#2472-Hmass branch February 12, 2020 10:42
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Have a min_mass for HydrogenBondAnalysis.guess_hydrogens
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