Daniel R. Roe
Daniel R. Roe
This is a placeholder so I don't forget about it. When running tests, the `test_trajectory_writer` test reports an internal cpptraj error but soldiers on. I'm not sure if this is...
This fixes several warnings that would be generated by GNU compilers with `-Wall`, mostly signed/unsigned comparisons, adding preprocessor guards for OpenMP `#pragma`s, and initializing uninitialized variables. @andysim There is one...
Currently K-Means initialization is more or less random, followed by picking points distant from each other. There should be an option to use points of high density for initialization (similar...
Reported on the Amber mailing list on 3-15-2024 by user Hirosuke Hotta: ``` Dear cpptraj developers, Regarding cpptraj error with test "Test_SPAM". We found Test_SPAM (there are 2 tests in...
In collaboration with @ramirandaq @lexin-chen, expand the cluster analysis capabilities of cpptraj by adding clustering via extended similarity metrics (and more). Some background reading: https://link.springer.com/article/10.1186/s13321-021-00505-3 https://link.springer.com/article/10.1007/s10822-022-00444-7
The GIST output and Eww output are currently ASCII, which can be cumbersome for large numbers of voxels. Would be nice to have the option to write to e.g. NetCDF....
- [ ] `nointrares` keyword? - [x] bridging time series? - [x] Ignore UA - V -UA bridges with nointramol hbond - [x] allow bridges within one residue - [x]...
Related to #999 . - [ ] NetCDF4/HDF5 writes should work in parallel. - [ ] Cmake should know how to build with NetCDF4/HDF5. - [ ] The `-libstatic` configure...
GIST in CPPTRAJ now has a lot of functionality thanks to all the work being done from @fwaibl @tkurtzman @EricChen521 @jokr91 @gosldorf and others. I think that developing some tutorials...
Specifically `vector corrplane` has two equally correct solutions, but when calculating angles from `corrplane` you typically want the acute one.