Move the atomic-model code to image_analysis/structure_refinement/ and WriteModel to writer/
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
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Claude Opus 5.5
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// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include "ModelGrid.h"
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#include <algorithm>
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#include <array>
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#include <cmath>
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#include <utility>
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#include "gemmi/solmask.hpp" // SolventMasker
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#include "../../common/ParallelFor.h"
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namespace {
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using Table = gemmi::IT92<float>;
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// The box of grid points gemmi's Grid::use_points_in_box<true>() walks around one atom.
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struct AtomBox {
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gemmi::Fractional fpos;
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int du = 0, dv = 0, dw = 0;
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double radius = 0;
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};
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// The box of use_points_around<true>(fpos, radius, ..., false), sized and clamped as gemmi does it.
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AtomBox MakeAtomBox(const gemmi::Grid<float> &grid, const gemmi::Fractional &fpos, double radius) {
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AtomBox box;
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box.fpos = fpos;
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box.radius = radius;
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box.du = std::min(static_cast<int>(std::ceil(radius / grid.spacing[0])), grid.nu - 1);
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box.dv = std::min(static_cast<int>(std::ceil(radius / grid.spacing[1])), grid.nv - 1);
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box.dw = std::min(static_cast<int>(std::ceil(radius / grid.spacing[2])), grid.nw - 1);
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return box;
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}
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// gemmi's use_points_in_box<true>() run over a list of atoms (grid.hpp, do_use_points_in_box), in
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// parallel over the grid's w planes: a plane is one task, and it walks every atom whose box reaches
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// it, in list order, visiting only that plane's points. Every point is so handed exactly the calls
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// gemmi's serial loop over the atoms hands it, in the same order, and the grid comes out bit for bit
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// the same whatever the thread count. func_for(i) gives atom i's func(point, d2, delta), taken as a
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// local copy so that the compiler can hold it in registers while the atom's points are written.
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template <typename FuncFor>
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void UseAtomBoxesByPlane(gemmi::Grid<float> &grid, const std::vector<AtomBox> &boxes, size_t nthreads,
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FuncFor func_for) {
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const int nu = grid.nu, nv = grid.nv, nw = grid.nw;
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std::vector<std::vector<int>> plane_atoms(nw);
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for (int i = 0; i < static_cast<int>(boxes.size()); i++) {
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const int w0 = gemmi::iround(boxes[i].fpos.z * nw);
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for (int w = w0 - boxes[i].dw; w <= w0 + boxes[i].dw; w++) {
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std::vector<int> &atoms = plane_atoms[gemmi::modulo(w, nw)];
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if (atoms.empty() || atoms.back() != i)
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atoms.push_back(i);
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}
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}
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ParallelFor(nw, nthreads, [&](int plane) {
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for (int i : plane_atoms[plane]) {
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const AtomBox &b = boxes[i];
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const auto func = func_for(i);
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const double max_dist_sq = b.radius * b.radius;
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const gemmi::Fractional nctr(b.fpos.x * nu, b.fpos.y * nv, b.fpos.z * nw);
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const int u_lo = gemmi::iround(nctr.x) - b.du, u_hi = gemmi::iround(nctr.x) + b.du;
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const int v_lo = gemmi::iround(nctr.y) - b.dv, v_hi = gemmi::iround(nctr.y) + b.dv;
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const int w_lo = gemmi::iround(nctr.z) - b.dw, w_hi = gemmi::iround(nctr.z) + b.dw;
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const int u_0 = gemmi::modulo(u_lo, nu), v_0 = gemmi::modulo(v_lo, nv);
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gemmi::Fractional fdelta(nctr.x - u_lo, 0, 0);
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// The box's w that fall on this plane, ascending as gemmi walks them: one, unless the box is
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// wider than the cell.
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for (int w = w_lo + gemmi::modulo(plane - w_lo, nw); w <= w_hi; w += nw) {
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fdelta.z = nctr.z - w;
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for (int v = v_lo, v_ = v_0; v <= v_hi; ++v, v_ = (v_ + 1 == nv ? 0 : v_ + 1)) {
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fdelta.y = nctr.y - v;
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gemmi::Position delta(grid.orth_n.multiply(fdelta));
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const double dist_sq0 = gemmi::sq(delta.y) + gemmi::sq(delta.z);
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if (dist_sq0 > max_dist_sq)
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continue;
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float *t = &grid.data[grid.index_q(u_0, v_, plane)];
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for (int u = u_lo, u_ = u_0;;) {
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const double dist_sq = dist_sq0 + gemmi::sq(delta.x);
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if (!(dist_sq > max_dist_sq))
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func(*t, dist_sq, delta);
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if (u >= u_hi)
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break;
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++u;
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++u_;
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++t;
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if (u_ == nu) {
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u_ = 0;
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t -= nu;
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}
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delta.x -= grid.orth_n.a11;
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}
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}
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}
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}
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});
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}
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// gemmi's Grid::symmetrize() in parallel over the orbits found by OrbitLeaders(): each orbit is reduced
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// by one thread, into its leader, with gemmi's operands in gemmi's order, and the value written to its
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// leader and mates as gemmi writes it. Orbits share no points, so the grid is gemmi's, bit for bit.
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template <typename Func>
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void SymmetrizeOrbits(gemmi::Grid<float> &grid, const std::vector<size_t> &leaders, size_t nthreads,
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Func func) {
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const std::vector<gemmi::GridOp> ops = grid.get_scaled_ops_except_id();
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const size_t nu = grid.nu, nv = grid.nv;
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ParallelChunks(static_cast<int>(leaders.size()), nthreads, [&](int lo, int hi) {
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std::vector<size_t> mates(ops.size());
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for (int i = lo; i < hi; i++) {
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const size_t idx = leaders[i];
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const int u = static_cast<int>(idx % nu), v = static_cast<int>(idx / nu % nv),
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w = static_cast<int>(idx / (nu * nv));
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for (size_t k = 0; k < ops.size(); ++k) {
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const std::array<int, 3> t = ops[k].apply(u, v, w);
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mates[k] = grid.index_n(t[0], t[1], t[2]);
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}
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float value = grid.data[idx];
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for (size_t k : mates)
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value = func(value, grid.data[k]);
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grid.data[idx] = value;
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for (size_t k : mates)
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grid.data[k] = value;
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}
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});
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}
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std::vector<const gemmi::Atom *> ModelAtoms(const gemmi::Model &model) {
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std::vector<const gemmi::Atom *> atoms;
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for (const gemmi::Chain &ch : model.chains)
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for (const gemmi::Residue &r : ch.residues)
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for (const gemmi::Atom &a : r.atoms)
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atoms.push_back(&a);
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return atoms;
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}
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// One atom's density, added to a grid point as gemmi's do_add_atom_density_to_grid() adds it.
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struct AtomDensity {
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using CReal = Table::Coef::coef_type;
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using IsoSum = decltype(std::declval<const Table::Coef &>().precalculate_density_iso(CReal(), CReal()));
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using AnisoSum = decltype(std::declval<const Table::Coef &>().precalculate_density_aniso_b(
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gemmi::SMat33<CReal>(), CReal()));
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bool is_aniso = false;
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float occ = 0;
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IsoSum iso{};
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AnisoSum aniso{};
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void operator()(float &point, double r2, const gemmi::Position &delta) const {
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if (!is_aniso)
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point += float(occ * iso.calculate((CReal)r2));
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else
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point += float(occ * aniso.calculate(delta));
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}
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};
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} // namespace
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// The points gemmi's Grid::symmetrize() (grid.hpp) reduces the grid's orbits into, ascending. gemmi
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// walks the points by index and takes the orbit of every point it has not visited yet, so it reduces
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// each orbit into the orbit's lowest index - the point none of whose mates has a lower one. They depend
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// on the grid's size and space group only, so a zone finds them once for all its evaluations.
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std::vector<size_t> OrbitLeaders(const gemmi::Grid<float> &grid, size_t nthreads) {
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const std::vector<gemmi::GridOp> ops = grid.get_scaled_ops_except_id();
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if (ops.empty())
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return {}; // P1: nothing to symmetrize
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std::vector<std::vector<size_t>> plane_leaders(grid.nw);
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ParallelFor(grid.nw, nthreads, [&](int w) {
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for (int v = 0; v < grid.nv; ++v)
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for (int u = 0; u < grid.nu; ++u) {
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const size_t idx = grid.index_q(u, v, w);
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bool lowest = true;
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for (size_t k = 0; k < ops.size() && lowest; ++k) {
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const std::array<int, 3> t = ops[k].apply(u, v, w);
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lowest = grid.index_n(t[0], t[1], t[2]) >= idx;
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}
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if (lowest)
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plane_leaders[w].push_back(idx);
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}
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});
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std::vector<size_t> leaders;
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for (const std::vector<size_t> &l : plane_leaders)
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leaders.insert(leaders.end(), l.begin(), l.end());
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return leaders;
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}
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// DensityCalculator::put_model_density_on_grid() (gemmi dencalc.hpp, do_add_atom_density_to_grid)
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// with the atoms and the symmetry spread over the threads as above - the same grid, bit for bit. Each
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// atom's density coefficients and radius are worked out once, up front, rather than once per plane.
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void PutModelDensityOnGrid(gemmi::DensityCalculator<Table, float> &dc, const gemmi::Model &model,
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const std::vector<size_t> &orbit_leaders, size_t nthreads) {
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using CReal = AtomDensity::CReal;
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dc.initialize_grid();
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const std::vector<const gemmi::Atom *> atoms = ModelAtoms(model);
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const int n = static_cast<int>(atoms.size());
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std::vector<AtomBox> boxes(n);
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std::vector<AtomDensity> density(n);
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ParallelChunks(n, nthreads, [&](int lo, int hi) {
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for (int i = lo; i < hi; i++) {
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const gemmi::Atom &atom = *atoms[i];
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const auto &coef = Table::get(atom.element, atom.charge, atom.serial);
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const float addend = dc.addends.get(atom.element);
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const gemmi::Fractional fpos = dc.grid.unit_cell.fractionalize(atom.pos);
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AtomDensity &d = density[i];
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d.occ = atom.occ;
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d.is_aniso = atom.aniso.nonzero();
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if (!d.is_aniso) {
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const CReal b = static_cast<CReal>(atom.b_iso + dc.blur);
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d.iso = coef.precalculate_density_iso(b, addend);
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boxes[i] = MakeAtomBox(dc.grid, fpos, dc.estimate_radius(d.iso, b));
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} else {
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const auto aniso_b = atom.aniso.scaled(CReal(gemmi::u_to_b())).added_kI(CReal(dc.blur));
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const CReal b_max = std::max(std::max(aniso_b.u11, aniso_b.u22), aniso_b.u33);
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const double radius = dc.estimate_radius(coef.precalculate_density_iso(b_max, addend), b_max);
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d.aniso = coef.precalculate_density_aniso_b(aniso_b, addend);
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boxes[i] = MakeAtomBox(dc.grid, fpos, radius);
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}
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}
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});
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UseAtomBoxesByPlane(dc.grid, boxes, nthreads, [&](int i) { return density[i]; });
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SymmetrizeOrbits(dc.grid, orbit_leaders, nthreads, [](float a, float b) { return a + b; });
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}
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// SolventMasker(AtomicRadiiSet::Refmac).put_mask_on_grid() (gemmi solmask.hpp) with the atoms and the
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// symmetry spread over the threads as above - the same mask, bit for bit. The island removal and the
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// shrink that follow are gemmi's own, except that the shrink is skipped where it cannot change a point:
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// it looks at the grid offsets within rshrink of each point (set_margin_around), and on a grid whose
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// spacing is coarser than rshrink along all three axes there are none - which is every rigid-body zone -
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// yet it still walks the whole grid.
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void PutMaskOnGrid(gemmi::Grid<float> &grid, const gemmi::Model &model, const std::vector<size_t> &orbit_leaders,
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size_t nthreads) {
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const gemmi::SolventMasker masker(gemmi::AtomicRadiiSet::Refmac);
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masker.clear(grid);
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std::vector<AtomBox> boxes;
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for (const gemmi::Atom *atom : ModelAtoms(model)) {
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if ((masker.ignore_hydrogen && atom->is_hydrogen()) ||
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(masker.ignore_zero_occupancy_atoms && atom->occ <= 0))
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continue;
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double r = masker.constant_r + masker.rprobe;
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r += gemmi::refmac_radius_for_bulk_solvent(atom->element.elem);
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boxes.push_back(MakeAtomBox(grid, grid.unit_cell.fractionalize(atom->pos), r));
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}
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UseAtomBoxesByPlane(grid, boxes, nthreads, [](int) {
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return [](float &point, double, const gemmi::Position &) { point = 0.f; };
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});
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SymmetrizeOrbits(grid, orbit_leaders, nthreads, [](float a, float b) { return a < b ? a : b; });
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masker.remove_islands(grid);
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bool shrink_has_offsets = false;
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for (int i = 0; i < 3; i++)
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shrink_has_offsets = shrink_has_offsets || static_cast<int>(std::floor(masker.rshrink / grid.spacing[i])) > 0;
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if (shrink_has_offsets)
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masker.shrink(grid);
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}
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