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Add TICA, max/min distance calc, and data projection commands #1075

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merged 200 commits into from
Apr 25, 2024

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@drroe drroe commented Apr 25, 2024

Version 6.24.1.

Adds new commands to cpptraj: one for performing time-independent correlation analysis (TICA), one for calculating the minimum distance between atoms or pairs of residues/molecules, one for calculating the maximum distance, and one for projecting 1D data sets along eigenmodes.

New analysis command: tica

        { crdset <COORDS set name> [mask <mask>] |
          data <input set arg1> ... }
        [lag <time lag>] [map {kinetic|commute|none}]
        [name <output set name>] [out <file>] [cumvarout <file>]

New actions: mindist / maxdist

        mask1 <mask1> [mask2 <mask2>] [{byatom|byres|bymol}]
        [noimage] [name <setname>] [out <file>] [resoffset <#>]

New analysis command: projectdata

        evecs <evecs dataset> [name <name>] [out <outfile>] [beg <beg>] [end <end>]
        {[dihedrals <dataset arg>] | [data <dataset arg> ...]}

This is a useful (often faster) alternative to project for 1D data sets when you don't have to project coordinates. The projection command has also been updated to allow projection of regular 1D data sets (on e.g. TICA modes). The matrix command will be updated to allow covariance calculation on 1D data sets in another PR.

Adds tests and updates the manual.

@drroe drroe added new action New Command New command for cpptraj labels Apr 25, 2024
@drroe drroe self-assigned this Apr 25, 2024
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src/CoordCovarMatrix_Half.cpp Fixed Show fixed Hide fixed
src/CoordCovarMatrix_Half.cpp Fixed Show fixed Hide fixed
src/CoordCovarMatrix.cpp Fixed Show fixed Hide fixed
src/CoordCovarMatrix_Full.cpp Fixed Show fixed Hide fixed
src/CoordCovarMatrix_Full.cpp Fixed Show fixed Hide fixed
src/CoordCovarMatrix_Full.cpp Fixed Show fixed Hide fixed
src/CoordCovarMatrix_Full.cpp Fixed Show fixed Hide fixed
src/CoordCovarMatrix_Half.cpp Fixed Show fixed Hide fixed
src/CoordCovarMatrix_Half.cpp Fixed Show fixed Hide fixed
@drroe drroe merged commit bf9f5c3 into Amber-MD:master Apr 25, 2024
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@drroe drroe deleted the tica branch April 25, 2024 18:52
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