docs: full Doxygen API documentation for maps and grids#418
Merged
Conversation
- Create docs/api.rst with complete Map and Grid Data section - Add Doxygen/Breathe configuration (Doxyfile and conf.py extensions) - Document 9 header files: grid.hpp, ccp4.hpp, recgrid.hpp, dencalc.hpp, asumask.hpp, solmask.hpp, floodfill.hpp, fourier.hpp, reciproc.hpp Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
CV-GPhL
force-pushed
the
api-docs/maps-grids
branch
from
9b9ac69 to
79db2aa
Compare
grid.hpp: Afonine et al. (2018) for Catmull-Rom cubic_interpolation and tricubic_interpolation; replace informal Wikipedia/URL references. Co-authored-by: C. Vonrhein / CV-GPhL
Move the block to after all @param and @return tags, following standard Doxygen ordering. Co-authored-by: C. Vonrhein / CV-GPhL
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
This PR adds complete Doxygen API documentation for Gemmi's map and grid layer, covering 9 headers:
grid.hpp— 3D crystallographic grid template (Grid, GridBase, GridOp, interpolation, symmetrize)ccp4.hpp— CCP4/MRC map file format (Ccp4, MapSetup, read/write functions)recgrid.hpp— Reciprocal-space grid for FFT (ReciprocalGrid, half_l mode, Miller index access)dencalc.hpp— Electron density calculation from atomic model (DensityCalculator, Gaussian placement)asumask.hpp— Asymmetric unit masking (AsuBrick, MaskedGrid<T,V>, get_asu_mask)solmask.hpp— Solvent masking (SolventMasker, AtomicRadiiSet, mask_points_in_radius)floodfill.hpp— 3D flood-fill on grids (FloodFill<T,Land>, flood_fill_above)fourier.hpp— FFT operations between real and reciprocal space (transform_f_phi_to_map, transform_map_to_f_phi)reciproc.hpp— Reciprocal space utilities (ReciprocalAsu, for_all_reflections)Documentation standard
///triple-slash Doxygen comments throughout@brief; non-obvious parameters have@param/@return/@throws/@tparamLiterature references added
@par ReferencesDoxygen blocks added to cite primary sources in the rendered API docs:cubic_interpolation()ingrid.hpptricubic_interpolation()ingrid.hppDependencies
This PR depends on PR #413 (Doxygen/Breathe infrastructure) being merged first.
It follows PR #414 (core data structures), PR #415 (CIF handling), PR #416 (structure I/O), and PR #417 (reflection data) in the documentation series.
Series context
This is PR 6 of a planned series of 10 PRs adding incremental API documentation:
api-docs/infraapi-docs/core-structuresapi-docs/cifapi-docs/structure-ioapi-docs/reflectionapi-docs/maps-gridsapi-docs/calculationsapi-docs/chemistryapi-docs/scattering-mathapi-docs/io-utilsAttribution
Builds on and credits prior work in PR #402 (Paul Emsley / pemsley)