Removing the deprecated module, see PR #2791 for more info.#2842
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orbeckst merged 7 commits intoMDAnalysis:developfrom Jul 14, 2020
Merged
Removing the deprecated module, see PR #2791 for more info.#2842orbeckst merged 7 commits intoMDAnalysis:developfrom
orbeckst merged 7 commits intoMDAnalysis:developfrom
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co-authored-by: p-j-smith <paul.smith@kcl.ac.uk>
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@@ Coverage Diff @@
## develop #2842 +/- ##
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Coverage 92.20% 92.20%
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Files 184 184
Lines 24103 24079 -24
Branches 3134 3115 -19
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- Hits 22224 22202 -22
+ Misses 1814 1812 -2
Partials 65 65
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orbeckst
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Please add an entry to CHANGELOG that the class was removed. See inline for comment on docs. Thanks!
| protein and residue 42. If the hydrogen bond lifetimes are very stable, we can | ||
| assume that residue 38 is hydrophilic, on the other hand, if the are very | ||
| unstable, we can assume that residue 38 is hydrophobic:: | ||
| The class Analyzing hydrogen bond lifetimes (HBL) |
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Instead of saying that it has been removed just say that there are other ways to analyze water dynamics is the ...lifetimes() method.
Add a See Also section for the hbond_analysis module.
co-authored-by: p-j-smith <paul.smith@kcl.ac.uk>
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Some small issues with the docs, see inline comments.
I also checked the docs for lifetime and there are some formatting issues. Could you please also fix the following in this PR
- lifetime: the first line Computes and returns the time-autocorrelation (HydrogenBondLifetimes) the summarizes the function is formatted as an enumeration(?). Should look like all other methods.
- under Example uses ... near In order to compute the hydrogen bond lifetime, after finding hydrogen bonds one can use the lifetime function: the text … hbonds.run() tau_timeseries, timeseries = hbonds.lifetime() should be formatted properly (as code block?)
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
co-authored-by: p-j-smith <paul.smith@kcl.ac.uk>
co-authored-by: p-j-smith <paul.smith@kcl.ac.uk>
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Thank you @bieniekmateusz and @p-j-smith ! |
PicoCentauri
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Mar 30, 2021
…alysis#2842) * remove the deprecated waterdynamics.HydrogenBondLifetimes class, see PR MDAnalysis#2791 for more info. * update waterdynamics docs and link to the replacement, hydrogenbonds.hbond_analysis.HydrogenBondAnalysis.liftetime * corrected doc formatting in hydrogenbonds.hbond_analysis * update CHANGELOG co-authored-by: p-j-smith <paul.smith@kcl.ac.uk>
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maintainability
deprecation
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Fixes
Changes made in this Pull Request:
I am not sure about the references. One way to go about this is to publish our own paper with @p-j-smith and then sort it out. Another is to remove original any reference to HBL straight away.
Related to PR #2791. Co-authored-by: @p-j-smith
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