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Add bridge time series and split analysis to hbond command #948

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merged 34 commits into from
Feb 16, 2022

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@drroe drroe commented Feb 16, 2022

Version 6.2.9.

This PR adds two new functionalities to hbond:

  1. Adds the bseries keyword (and associated bseriesfile <filename> keyword) for saving time series data for bridges (similar to series for hydrogen bonds). Addresses an item in Potential enhancements to 'hbond' #392. The data sets are created with an aspect that includes the atom/residue indices being bridged for easier selection.
  2. Adds the splitframe <comma-separated-list> keyword for doing "split" analysis on hydrogen bond averaged data. Works similar to the splitframe keyword in clustering where overall results are reported, followed by the results for each individual part as delineated by the comma-separated list of frame numbers given to the splitframe keyword.

Example output (2 parts):

#Acceptor          DonorH        Donor   Frames         Frac      AvgDist       AvgAng  Frames1        Frac1     AvgDist1      AvgAng1  Frames2        Frac2     AvgDist2      AvgAng2
ILE_19@O         THR_12@H     THR_12@N       69       0.6900       2.8626     160.5248       37       0.3700       2.8638     160.2253       32       0.3200       2.8612     160.8711
VAL_2@O          GLU_13@H     GLU_13@N       59       0.5900       2.8517     159.8143       36       0.3600       2.8510     158.5372       23       0.2300       2.8527     161.8133

Both of these work in parallel as well. Adds a test and updates the manual.

@drroe drroe self-assigned this Feb 16, 2022
@drroe drroe merged commit 4ceec70 into Amber-MD:master Feb 16, 2022
@drroe drroe deleted the hbondsplit branch February 16, 2022 20:40
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