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Turn waterdynamics.HydrogenBondLifetimes into function of HydrogenBondAnalysis #2547
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Hi @lilyminium, we have extracted the standalone Autocorrelation function with @p-j-smith (#2256). Once that's merged, we can proceed with your suggestion and add a hydrogen bond lifetime function to HydrogenBondAnalysis that makes use of this discrete autocorrelation function. The new functions will be available in MDAnalysis.analysis.utils. |
bieniekmateusz
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…ydrogen bond implementation. Fixes MDAnalysis#2547 and we depracate the waterdynamic.HydrogenBondLifetime because of MDAnalysis#2247. co-authored-by: p-j-smith <[email protected]>
bieniekmateusz
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…ydrogen bond implementation. Fixes MDAnalysis#2547 and we depracate the waterdynamic.HydrogenBondLifetime because of MDAnalysis#2247. co-authored-by: p-j-smith <[email protected]>
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orbeckst
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* Fixes #2547 * The standalone autocorrelation function is now used to calculate the hydrogen bond lifetime in the new implementation of the hydrogen bond analysis class. * Added ability to select groups between which to find hydrogen bonds.: new parameter "between" for hydrogen binding (backwards compatible): The `between` keyword can be used to specify pairs of groups between which hydrogen bonds will be calculated. Hydrogen bonds found other pairs of atom groups will be discarded. * We deprecate the waterdynamics.HydrogenBondLifetime class because of #2247. * Basic unit tests added to check the integration of the separate components * add docs with example * update CHANGELOG co-authored-by: p-j-smith <[email protected]>
PicoCentauri
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* Fixes MDAnalysis#2547 * The standalone autocorrelation function is now used to calculate the hydrogen bond lifetime in the new implementation of the hydrogen bond analysis class. * Added ability to select groups between which to find hydrogen bonds.: new parameter "between" for hydrogen binding (backwards compatible): The `between` keyword can be used to specify pairs of groups between which hydrogen bonds will be calculated. Hydrogen bonds found other pairs of atom groups will be discarded. * We deprecate the waterdynamics.HydrogenBondLifetime class because of MDAnalysis#2247. * Basic unit tests added to check the integration of the separate components * add docs with example * update CHANGELOG co-authored-by: p-j-smith <[email protected]>
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Is your feature request related to a problem? Please describe.
Given that
HydrogenBondLifetimes
just runs (the now deprecated) hbonds.HydrogenBondAnalysis under the hood, it seems it could be easily turned into a post-run() function of HydrogenBondAnalysis.Describe the solution you'd like
Turn it into a function of HydrogenBondAnalysis.
Describe alternatives you've considered
At least use the new class instead of the old one.
Additional context
This is the
run()
function:The text was updated successfully, but these errors were encountered: