Skip to content

Minimum mass for hydrogen guess in HydrogenBondAnalysis#2516

Merged
richardjgowers merged 34 commits intoMDAnalysis:developfrom
RMeli:issues/#2472-Hmass
Feb 12, 2020
Merged

Minimum mass for hydrogen guess in HydrogenBondAnalysis#2516
richardjgowers merged 34 commits intoMDAnalysis:developfrom
RMeli:issues/#2472-Hmass

Conversation

@RMeli
Copy link
Copy Markdown
Member

@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
Copy link
Copy Markdown
Member

@richardjgowers richardjgowers left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

couple silly questions

@codecov
Copy link
Copy Markdown

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

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 549c1a2...23cc898. Read the comment docs.

Copy link
Copy Markdown
Member

@IAlibay IAlibay left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Have a min_mass for HydrogenBondAnalysis.guess_hydrogens

4 participants