Potential enhancements to 'hbond'

Amber-MD / cpptraj

Biomolecular simulation trajectory/data analysis.

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Potential enhancements to 'hbond' #392

Open drroe opened 8 years ago

drroe commented 8 years ago

[ ] nointrares keyword?
[x] bridging time series?
[x] Ignore UA - V -UA bridges with nointramol hbond
[x] allow bridges within one residue
[x] hbond bridging track atom numbers
[x] Add option to 'hbond' to only keep series above certain cutoff; Something like seriescut 0.2 which will keep all series with occupancy >= 0.2.
[ ] Water-water hbond tracking.
[ ] Record standard deviation for distance/angle.
[ ] 'byresidue' option
[x] Be able to generate a sparse 2D matrix (by atom or by residue) containing fraction hydrogen bonds present for atom/residue pairs.
[ ] Option to report/calculate hydrogen bonds based on H-A distance.
[ ] Auto-detect solvent hydrogen bond sites.
[ ] Option to print detected donors/acceptors to a file.
[ ] Track bridging interactions of higher orders (e.g. U-V-V-U).

hainm commented 7 years ago

@drroe

per solvent bridge hbond ID:

354(11+12+) means solute 354 is bridge between res 11 and 12? is index 0-based or 1-based? what does the extra '+' in 12+ mean?

drroe commented 7 years ago

is index 0-based or 1-based?

1-based.

what does the extra '+' in 12+ mean?

Nothing special - every residue number has a + after it.

envirodug commented 7 years ago

@drroe, for the bridgebyatom new feature in hbond (thanks for this!), is it possible to add a few new features (or is it already possible to do this)?

An option to only report heavy atoms in the output (e.g. instead of detailing hbonds to Lys HZ1, HZ2, and HZ3, just report to NZ).
Map the atom numbers to the residue number and name and print to the output file (e.g. including 1:GLU, 2:ASP, etc. as in the hbond calculation without specifying bridgebyatom in the options).

drroe commented 7 years ago

An option to only report heavy atoms in the output (e.g. instead of detailing hbonds to Lys HZ1, HZ2, and HZ3, just report to NZ).

You mean in the average output right? An option doesn't exist for doing this yet - I'll put it on the to-do list.

Map the atom numbers to the residue number and name and print to the output file (e.g. including 1:GLU, 2:ASP, etc. as in the hbond calculation without specifying bridgebyatom in the options).

Does the printatomnum keyword do what you want?