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Add CMAP support (currently just Amber topology files)

Open chryswoods opened this issue 10 months ago • 2 comments

Changes proposed in this pull request:

This PR introduces support for CMAP terms (in the cmap property), with reading and writing of these parameters currently only possible via Amber topology files.

The plan is to expand support to Gromacs topology files in the next PR.

  • I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
  • I confirm that I have added a test for any new functionality in this pull request: [y]
  • I confirm that I have added documentation (e.g. a new tutorial page or detailed guide) for any new functionality in this pull request: [n/a]
  • I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y]
  • I confirm that I have permission to release this code under the GPL3 license: [y]

Suggested reviewers:

@lohedges

Any additional context of information?

I will create a new branch from here (e.g. feature_cmap_gro) to work on Gromacs support.

(you can also attach files by dragging & dropping)

chryswoods avatar Apr 25 '25 05:04 chryswoods

All builds appear to fail during the wrapper compilation, albeit at different points.

For Linux, the error is:

In file included from /home/runner/miniconda3/envs/sire_build/conda-bld/sire_1745558259284/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/pkgs/sire-2025.1.0/include/Sire/SireError/errors.h:31,
                 from /home/runner/miniconda3/envs/sire_build/conda-bld/sire_1745558259284/work/wrapper/python/main.cpp:14:
/home/runner/miniconda3/envs/sire_build/conda-bld/sire_1745558259284/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/pkgs/sire-2025.1.0/include/Sire/sireglobal.h:91:10: fatal error: boost/current_function.hpp: No such file or directory
   91 | #include <boost/current_function.hpp>

For macOS it's related to gemmi, as seen in the other PR.

For Windows it's the apparent memory issue, so there's no actual error in the log (that I can see).

lohedges avatar Apr 28 '25 17:04 lohedges

Other than the CI issues, this is working nicely. I've tested via BioSimSpace and can parameterise using ff19SB just fine.

lohedges avatar May 12 '25 13:05 lohedges