leonarski_fandClaude Opus 5.5
9ad92b6bfe
A pure move. ModelValidation, RigidBodyRefine, RigidBodyGPU, ModelFFT, ModelGrid, ModelScaling, ModelMaskGPU, ModelScaleGPU and SigmaA - everything that works on an atomic model - become the JFJochStructureRefinement library, linked by JFJochImageAnalysis. WriteModel (the placed-model mmCIF/PDB writer) goes to writer/ as its own small JFJochModelWriter target, so JFJochWriter, which a writer-only build compiles, does not gain a gemmi dependency. Only include paths and CMake lists change. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
30 lines
1.5 KiB
C++
30 lines
1.5 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
|
|
// SPDX-License-Identifier: GPL-3.0-only
|
|
|
|
#pragma once
|
|
|
|
#include <cstddef>
|
|
#include <vector>
|
|
|
|
#include "gemmi/dencalc.hpp" // DensityCalculator
|
|
#include "gemmi/grid.hpp"
|
|
#include "gemmi/it92.hpp" // IT92 x-ray form factors
|
|
#include "gemmi/model.hpp"
|
|
|
|
// gemmi's gridding of a model - the density of DensityCalculator::put_model_density_on_grid() and the
|
|
// bulk-solvent mask of SolventMasker(AtomicRadiiSet::Refmac).put_mask_on_grid() - spread over
|
|
// `nthreads` threads of ParallelFor's pool. Every grid point receives the same operations in the same
|
|
// order as in gemmi's serial loops, so the grids are gemmi's, bit for bit, on any number of threads.
|
|
|
|
// The points gemmi's Grid::symmetrize() reduces the orbits of this grid's size and space group into
|
|
// (empty in P1). Both functions below take them, for a grid of the same size.
|
|
std::vector<size_t> OrbitLeaders(const gemmi::Grid<float> &grid, size_t nthreads);
|
|
|
|
// `dc` set up as for put_model_density_on_grid(): d_min, rate, blur, the grid's cell and group.
|
|
void PutModelDensityOnGrid(gemmi::DensityCalculator<gemmi::IT92<float>, float> &dc, const gemmi::Model &model,
|
|
const std::vector<size_t> &orbit_leaders, size_t nthreads);
|
|
|
|
// `grid` sized, with its cell and group set.
|
|
void PutMaskOnGrid(gemmi::Grid<float> &grid, const gemmi::Model &model, const std::vector<size_t> &orbit_leaders,
|
|
size_t nthreads);
|