leonarski_fandClaude Opus 5
ac1e8b8603
Two test expectations that the changes under them made stale, and one overstated sentence in the docs. REPORT_VERSION was bumped to 12 without touching the line that pins it - the very line whose comment says a key added to the report is a contract change and this is where it has to be acknowledged. Acknowledged, and the absence of SOHNCKE_SPACE_GROUP on a fixture that is GIVEN its group rather than searching for one is now asserted too, since that is what makes the key's contract honest. The section documenting that the E^2 gate is what saves a screw from fabricated violations no longer holds, because there are now two independent defences: with the gate off, the absent class still sits at 2% of its own row, so the zone is dead per reflection and licenses the absence evidence to override the count. The section is kept rather than deleted - it now pins the second defence, and a future P2 there would mean the deferral has stopped licensing a zone that is genuinely extinct. The docs said SOHNCKE_SPACE_GROUP is written on every run. It is written on every run whose group came from the search; a run given its group with -S has no Sohncke candidate to name. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
623 lines
29 KiB
C++
623 lines
29 KiB
C++
#include <catch2/catch_all.hpp>
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#include "../image_analysis/scale_merge/SearchSpaceGroup.h"
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#include "gemmi/symmetry.hpp"
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#include <algorithm>
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#include <cmath>
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#include <cstdint>
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#include <string>
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#include <tuple>
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#include <unordered_set>
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#include <vector>
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namespace {
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struct HKL {
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int h = 0;
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int k = 0;
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int l = 0;
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bool operator==(const HKL& o) const noexcept {
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return h == o.h && k == o.k && l == o.l;
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}
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};
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struct HKLHash {
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size_t operator()(const HKL& x) const noexcept {
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auto mix = [](uint64_t v) {
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v ^= v >> 33;
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v *= 0xff51afd7ed558ccdULL;
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v ^= v >> 33;
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v *= 0xc4ceb9fe1a85ec53ULL;
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v ^= v >> 33;
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return v;
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};
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return static_cast<size_t>(
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mix(static_cast<uint64_t>(x.h)) ^
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(mix(static_cast<uint64_t>(x.k)) << 1) ^
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(mix(static_cast<uint64_t>(x.l)) << 2));
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}
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};
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double CalcSyntheticD(int h, int k, int l) {
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const double q2 = static_cast<double>(h * h + k * k + l * l);
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return 40.0 / std::sqrt(q2 + 1.0);
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}
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double SyntheticIntensityFromAsu(const gemmi::Op::Miller& asu) {
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uint64_t x = static_cast<uint64_t>((asu[0] + 31) * 73856093u) ^
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static_cast<uint64_t>((asu[1] + 37) * 19349663u) ^
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static_cast<uint64_t>((asu[2] + 41) * 83492791u);
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x ^= x >> 13;
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x *= 0x9e3779b97f4a7c15ULL;
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x ^= x >> 17;
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return 100.0 + static_cast<double>(x % 500);
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}
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std::vector<MergedReflection> GenerateMergedReflectionsForSpaceGroup(
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const gemmi::SpaceGroup& sg,
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int hmax = 8) {
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std::vector<MergedReflection> merged;
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std::unordered_set<HKL, HKLHash> added;
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const gemmi::GroupOps gops = sg.operations();
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const gemmi::ReciprocalAsu rasu(&sg);
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for (int h = -hmax; h <= hmax; ++h) {
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for (int k = -hmax; k <= hmax; ++k) {
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for (int l = -hmax; l <= hmax; ++l) {
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if (h == 0 && k == 0 && l == 0)
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continue;
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bool absent = false;
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gemmi::Op::Miller hkl{{h, k, l}};
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if (gops.is_systematically_absent(hkl))
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absent = true;
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const auto [asu, sign_plus] = rasu.to_asu_sign(hkl, gops);
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if (!sign_plus)
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continue;
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const HKL key{h, k, l};
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if (added.find(key) != added.end())
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continue;
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added.insert(key);
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merged.push_back(MergedReflection{
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.h = h,
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.k = k,
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.l = l,
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.I = absent ? 0.0 : SyntheticIntensityFromAsu(asu),
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.sigma = 1.0,
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.d = CalcSyntheticD(h, k, l)
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});
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}
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}
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}
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return merged;
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}
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}
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TEST_CASE("SearchSpaceGroup detects synthetic space groups") {
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struct Case {
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std::string input_name;
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std::string expected_short_name;
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};
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const std::vector<Case> cases = {
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{"P 1", "P1"},
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{"P 1 2 1", "P2"},
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{"P 3 2 1", "P321"},
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{"P 4 2 2", "P422"},
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{"P 4 3 2", "P432"},
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{"P 43 21 2", "P43212"},
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{"P 6 2 2", "P622"},
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{"C 1 2 1", "C2"},
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{"C 2 2 2", "C222"},
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{"I 4 3 2", "I432"},
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{"I 21 21 21", "I212121"},
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{"I 2 1 3", "I213"},
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};
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for (const auto& tc : cases) {
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DYNAMIC_SECTION(tc.expected_short_name) {
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const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name(tc.input_name);
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const auto merged = GenerateMergedReflectionsForSpaceGroup(sg);
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SearchSpaceGroupOptions opt;
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opt.merge_friedel = true;
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const auto result = SearchSpaceGroup(merged, opt);
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// Several inputs cannot be told apart from intensities alone: enantiomorphic partners
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// (P4_3 vs P4_1) and origin-ambiguous pairs (I2_12_12_1 vs I222, I2_13 vs I2_3) share
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// the same systematic absences. The search reports those as alternatives, so the
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// expected group must appear among the best group and its alternatives.
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std::vector<std::string> accepted;
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if (result.best_space_group.has_value())
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accepted.push_back(result.best_space_group->short_name());
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for (const auto& alt : result.alternatives)
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accepted.push_back(alt.short_name());
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INFO(SearchSpaceGroupResultToText(result));
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REQUIRE(result.best_space_group.has_value());
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CHECK(std::find(accepted.begin(), accepted.end(), tc.expected_short_name) != accepted.end());
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}
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}
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}
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// Regression: a real screw axis whose systematically-absent reflections carry a genuinely weak
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// intensity but an UNDER-estimated sigma (so their I/sigma clears the "present" cut) must still be
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// found. Reproduces a monoclinic 2_1 miss on weakly-diffracting monoclinic data, where the merged sigmas on
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// the 0k0-odd reflections were ~2x too small and faked screw-axis violations. The E^2 intensity gate
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// (present_e_squared) is what keeps those reflections classified absent.
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TEST_CASE("SearchSpaceGroup finds a screw axis despite under-estimated sigmas on absent reflections") {
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const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name("P 1 21 1");
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auto merged = GenerateMergedReflectionsForSpaceGroup(sg, 18);
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// Every systematically-absent (0k0, k odd) reflection: small-but-nonzero intensity (~2% of a
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// normal reflection) with a far-too-small sigma, so I/sigma ~ 27 fakes a "present" reflection.
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const gemmi::GroupOps gops = sg.operations();
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int absent_count = 0;
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for (auto& r : merged) {
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const gemmi::Op::Miller hkl{{r.h, r.k, r.l}};
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if (gops.is_systematically_absent(hkl)) {
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r.I = 8.0f;
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r.sigma = 0.3f;
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++absent_count;
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}
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}
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REQUIRE(absent_count >= 8); // enough predicted-absent reflections to be trusted
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SearchSpaceGroupOptions opt;
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opt.merge_friedel = true;
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SECTION("intensity gate on (default): screw recovered") {
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const auto result = SearchSpaceGroup(merged, opt);
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INFO(SearchSpaceGroupResultToText(result));
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REQUIRE(result.best_space_group.has_value());
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CHECK(result.best_space_group->short_name() == "P21");
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}
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SECTION("intensity gate off (I/sigma only): the deferral recovers the screw anyway") {
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// This section used to document the failure the E^2 gate fixes - with I/sigma alone the
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// too-small sigmas fake violations and the search fell back to the symmorphic group. There
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// are now TWO independent defences and the second one holds here without the first: the
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// fabricated violations are still counted, but the absent class sits at 2% of its own row,
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// so the zone is dead per reflection and carries no measured pseudo-translation, which is
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// what licenses the absence evidence to override the count.
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//
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// Kept rather than deleted, because it pins the two apart: if a future change makes this
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// read P2 again, the deferral has stopped licensing a zone that is genuinely extinct.
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opt.present_e_squared = 0.0;
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const auto result = SearchSpaceGroup(merged, opt);
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INFO(SearchSpaceGroupResultToText(result));
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REQUIRE(result.best_space_group.has_value());
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CHECK(result.best_space_group->short_name() == "P21");
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}
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}
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// Regression: the E^2 gate above compares a reflection to the mean of its RESOLUTION SHELL, which
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// falls off with resolution, while a systematically-absent reflection keeps a small non-decaying
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// residual (background / profile leakage). On a crystal whose axial rows are much stronger than an
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// average reflection, that turns the high-resolution residuals into screw-axis violations and the
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// screw is lost, although the reflections beside them in the same row are tens of times stronger.
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// A tetragonal 42_12 case failed exactly this way (18 of 47 absent 00l over the cut, all beyond
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// 3.7 A, at 1-2% of the l=4n reflections next to them). The threshold is therefore taken relative to
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// the axial row the screw constrains, not to the shell.
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TEST_CASE("SearchSpaceGroup finds a screw axis whose absent class is weak only within its own row") {
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const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name("P 43 21 2");
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auto merged = GenerateMergedReflectionsForSpaceGroup(sg, 12);
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// Axial rows 40x stronger than a general reflection, and an absent class carrying ~2% of its own
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// row - but half of a general reflection, so a threshold set against the shell calls every one of
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// them a violation while a threshold set against the row calls none.
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const gemmi::GroupOps gops = sg.operations();
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int absent_on_axis = 0;
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for (auto& r : merged) {
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const gemmi::Op::Miller hkl{{r.h, r.k, r.l}};
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if (gops.epsilon_factor_without_centering(hkl) <= 1)
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continue;
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if (gops.is_systematically_absent(hkl)) {
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r.I = 300.0f;
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r.sigma = 1.0f;
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++absent_on_axis;
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} else {
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r.I *= 40.0f;
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}
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}
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REQUIRE(absent_on_axis >= 8);
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SearchSpaceGroupOptions opt;
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opt.merge_friedel = true;
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const auto result = SearchSpaceGroup(merged, opt);
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INFO(SearchSpaceGroupResultToText(result));
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REQUIRE(result.best_space_group.has_value());
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// P4_1 2_1 2 and P4_3 2_1 2 are enantiomorphs and indistinguishable from intensities.
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std::vector<std::string> accepted{result.best_space_group->short_name()};
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for (const auto& alt : result.alternatives)
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accepted.push_back(alt.short_name());
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CHECK(std::find(accepted.begin(), accepted.end(), "P43212") != accepted.end());
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}
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// Regression: a screw's predicted-absent class is one row of reciprocal space, and that row is often
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// the one a rotation sweep records least - it lies near the spindle, where the blind cusp maps onto
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// itself and symmetry cannot fill it in. Counting the class therefore measures the geometry of the
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// sweep, not the strength of the evidence, and a count gate refused a monoclinic crystal its 2_1 for
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// having six 0k0-odd reflections rather than eight, every one of them measured at a thousandth of the
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// row beside them. The class is judged by ScrewZoneEvidence instead, which reads the contrast
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// against the row - so few-but-decisive is accepted and many-but-marginal is not.
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TEST_CASE("SearchSpaceGroup weighs a screw's absences by evidence, not by how many were recorded") {
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const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name("P 1 21 1");
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const gemmi::GroupOps gops = sg.operations();
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SearchSpaceGroupOptions opt;
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opt.merge_friedel = true;
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SECTION("five decisive absences, below min_absent_observed: the screw is still found") {
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auto merged = GenerateMergedReflectionsForSpaceGroup(sg, 18);
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// Keep five of the 0k0-odd reflections, at a thousandth of their row, and drop the rest - as a
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// sweep along the 2-fold does, leaving too few to satisfy a count but plenty to decide.
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int kept = 0;
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std::erase_if(merged, [&](MergedReflection& r) {
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if (!gops.is_systematically_absent(gemmi::Op::Miller{{r.h, r.k, r.l}}))
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return false;
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if (kept >= 5)
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return true;
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++kept;
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r.I = 0.5;
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return false;
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});
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REQUIRE(kept == 5);
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REQUIRE(kept < opt.min_absent_observed);
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const auto result = SearchSpaceGroup(merged, opt);
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INFO(SearchSpaceGroupResultToText(result));
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REQUIRE(result.best_space_group.has_value());
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CHECK(result.best_space_group->short_name() == "P21");
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}
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SECTION("a uniformly weak axial row decides nothing, however many absences it holds") {
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// The whole 0k0 row badly measured: the predicted-absent reflections are weak, but so is the
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// rest of their row, so there is no contrast and no screw to claim. A violation count cannot
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// see this - nothing on the row clears an absolute cut, so it reads zero violations and, with
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// enough reflections to satisfy the count, would claim the 2_1 from no evidence at all.
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auto merged = GenerateMergedReflectionsForSpaceGroup(sg, 18);
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int absent_on_row = 0;
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for (auto& r : merged) {
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if (r.h != 0 || r.l != 0)
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continue;
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const bool absent = gops.is_systematically_absent(gemmi::Op::Miller{{r.h, r.k, r.l}});
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r.I = absent ? 4.0 : 5.0;
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absent_on_row += absent ? 1 : 0;
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}
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REQUIRE(absent_on_row >= opt.min_absent_observed);
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const auto result = SearchSpaceGroup(merged, opt);
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INFO(SearchSpaceGroupResultToText(result));
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REQUIRE(result.best_space_group.has_value());
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CHECK(result.best_space_group->short_name() == "P2");
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}
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}
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// The operator correlation is on resolution-normalised E^2, not on raw I (see SearchSpaceGroup.cpp).
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// Both members of a symmetry pair sit at the same |s|, so on raw intensities the resolution fall-off
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// is variance shared perfectly between the two arms of every pair and reads as a correlation for ANY
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// pairing at all. These two cases pin that down from both sides.
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TEST_CASE("SearchSpaceGroup operator correlation reads symmetry, not the resolution fall-off",
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"[SearchSpaceGroup]") {
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// Intensities that are a smooth function of resolution times an INDEPENDENT per-reflection
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// factor: a Wilson-like fall-off with no symmetry in it whatsoever.
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auto radial_only = [](int hmax) {
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std::vector<MergedReflection> merged;
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for (int h = -hmax; h <= hmax; ++h)
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for (int k = -hmax; k <= hmax; ++k)
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for (int l = -hmax; l <= hmax; ++l) {
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if ((h == 0 && k == 0 && l == 0) || std::make_tuple(-h, -k, -l) < std::make_tuple(h, k, l))
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continue;
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const double d = CalcSyntheticD(h, k, l);
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const double falloff = std::exp(-30.0 / (d * d));
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// Deterministic, independent of any symmetry mate: reuse the hash on the raw index.
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const double jitter = SyntheticIntensityFromAsu(gemmi::Op::Miller{{h, k, l}}) / 350.0;
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const double I = 1.0e5 * falloff * jitter;
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merged.push_back(MergedReflection{
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.h = h, .k = k, .l = l, .I = I, .sigma = I / 20.0, .d = d});
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}
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return merged;
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};
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SearchSpaceGroupOptions opt;
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opt.merge_friedel = true;
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SECTION("a fall-off with no symmetry in it confirms no operator") {
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const auto result = SearchSpaceGroup(radial_only(8), opt);
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INFO(SearchSpaceGroupResultToText(result));
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REQUIRE(result.operator_scores.size() > 1);
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for (const auto& s : result.operator_scores) {
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INFO("operator " << s.op_triplet_hkl);
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CHECK(s.n_pairs >= opt.min_pairs_per_operator);
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CHECK(s.cc < opt.min_operator_cc);
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CHECK_FALSE(s.present);
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}
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CHECK(result.point_group_hm == "1");
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}
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SECTION("a real operator under the same fall-off is confirmed, and does not move with the cut") {
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// Same fall-off, but the intensities now carry a genuine monoclinic 2-fold.
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const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name("P 1 2 1");
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const gemmi::ReciprocalAsu rasu(&sg);
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const gemmi::GroupOps gops = sg.operations();
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auto merged = radial_only(8);
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for (auto& r : merged) {
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const auto [asu, plus] = rasu.to_asu_sign(gemmi::Op::Miller{{r.h, r.k, r.l}}, gops);
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const double falloff = std::exp(-30.0 / (r.d * r.d));
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r.I = 1.0e5 * falloff * SyntheticIntensityFromAsu(asu) / 350.0;
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r.sigma = r.I / 20.0;
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}
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auto two_fold_cc = [&](double d_min) {
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SearchSpaceGroupOptions o = opt;
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o.d_min_limit_A = d_min;
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const auto result = SearchSpaceGroup(merged, o);
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INFO(SearchSpaceGroupResultToText(result));
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REQUIRE(result.point_group_hm == "2");
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double cc = -2.0;
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for (const auto& s : result.operator_scores)
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if (s.present)
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cc = s.cc;
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REQUIRE(cc > opt.min_operator_cc);
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return cc;
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};
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// The whole point of normalising: how much of the fall-off is inside the merge no longer
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// moves the operator's score, so the search resolution cut cannot decide the symmetry.
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CHECK(std::fabs(two_fold_cc(0.0) - two_fold_cc(6.0)) < 0.05);
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}
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}
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// The enumeration reaches the settings gemmi does not call the reference one, and only when the cell
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// has the axes they name. Both halves are pinned here: `P 1 1 2_1` puts its 2-fold and its screw on
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// c, which no reference setting can express (Stage A never offers the rotation and Stage B never
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// offers the group), so without the two options the answer is P1; with them, and with a cell whose
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// unique axis IS c, it is named; and with a cell whose unique axis is b the same candidate is
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// refused rather than adopted on axes the crystal does not have.
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TEST_CASE("SearchSpaceGroup names a non-reference setting only on a cell that hosts it") {
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const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name("P 1 1 21");
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const auto merged = GenerateMergedReflectionsForSpaceGroup(sg, 12);
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SearchSpaceGroupOptions opt;
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opt.merge_friedel = true;
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SECTION("narrow enumeration cannot name it") {
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const auto result = SearchSpaceGroup(merged, opt);
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INFO(SearchSpaceGroupResultToText(result));
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REQUIRE(result.best_space_group.has_value());
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CHECK(result.best_space_group->number == 1);
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}
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SECTION("widened enumeration names it on a c-unique cell") {
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opt.cell = gemmi::UnitCell(40.0, 50.0, 60.0, 90.0, 90.0, 100.0);
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opt.enumerate_all_settings = true;
|
|
opt.enumerate_all_rotation_sets = true;
|
|
const auto result = SearchSpaceGroup(merged, opt);
|
|
INFO(SearchSpaceGroupResultToText(result));
|
|
REQUIRE(result.best_space_group.has_value());
|
|
CHECK(result.best_space_group->xhm() == "P 1 1 21");
|
|
}
|
|
|
|
SECTION("a b-unique cell refuses it") {
|
|
opt.cell = gemmi::UnitCell(40.0, 50.0, 60.0, 90.0, 100.0, 90.0);
|
|
opt.enumerate_all_settings = true;
|
|
opt.enumerate_all_rotation_sets = true;
|
|
const auto result = SearchSpaceGroup(merged, opt);
|
|
INFO(SearchSpaceGroupResultToText(result));
|
|
REQUIRE(result.best_space_group.has_value());
|
|
CHECK(result.best_space_group->number == 1);
|
|
}
|
|
}
|
|
|
|
// The screw axes of an orthorhombic crystal can lie on any pair of axes, and only one of the three
|
|
// namings of #18 is a reference setting. With the narrow enumeration the group that predicts a
|
|
// SUBSET of the real absences and nothing else wins on no evidence at all, so the reported group is
|
|
// wrong rather than low - the widening is what makes the correct one available.
|
|
TEST_CASE("SearchSpaceGroup names an orthorhombic screw pair on the axes it lies on") {
|
|
const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name("P 2 21 21");
|
|
const auto merged = GenerateMergedReflectionsForSpaceGroup(sg, 14);
|
|
|
|
SearchSpaceGroupOptions opt;
|
|
opt.merge_friedel = true;
|
|
opt.lattice_system = gemmi::CrystalSystem::Orthorhombic;
|
|
|
|
SECTION("narrow enumeration reports the wrong group") {
|
|
const auto result = SearchSpaceGroup(merged, opt);
|
|
INFO(SearchSpaceGroupResultToText(result));
|
|
REQUIRE(result.best_space_group.has_value());
|
|
CHECK(result.best_space_group->number != 18);
|
|
}
|
|
|
|
SECTION("widened enumeration reports it") {
|
|
opt.cell = gemmi::UnitCell(40.0, 50.0, 60.0, 90.0, 90.0, 90.0);
|
|
opt.enumerate_all_settings = true;
|
|
const auto result = SearchSpaceGroup(merged, opt);
|
|
INFO(SearchSpaceGroupResultToText(result));
|
|
REQUIRE(result.best_space_group.has_value());
|
|
CHECK(result.best_space_group->xhm() == "P 2 21 21");
|
|
}
|
|
}
|
|
|
|
// The centring half of the same widening. A, B and C centring on one orthorhombic cell are three
|
|
// different lattices, and only C is a reference setting, so an A-centred crystal used to have its
|
|
// centring refused (its absent class is not the one C predicts) and came out primitive. The
|
|
// candidate is now offered, and it has to be adopted from its own absences rather than from the
|
|
// metric, which cannot tell A from C at all.
|
|
TEST_CASE("SearchSpaceGroup names an A-centred orthorhombic lattice") {
|
|
const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name("A 2 2 2");
|
|
const auto merged = GenerateMergedReflectionsForSpaceGroup(sg, 12);
|
|
|
|
SearchSpaceGroupOptions opt;
|
|
opt.merge_friedel = true;
|
|
opt.lattice_system = gemmi::CrystalSystem::Orthorhombic;
|
|
|
|
SECTION("narrow enumeration cannot name it") {
|
|
const auto result = SearchSpaceGroup(merged, opt);
|
|
INFO(SearchSpaceGroupResultToText(result));
|
|
REQUIRE(result.best_space_group.has_value());
|
|
CHECK(result.best_space_group->centring_type() != 'A');
|
|
}
|
|
|
|
SECTION("widened enumeration names it") {
|
|
opt.cell = gemmi::UnitCell(40.0, 50.0, 60.0, 90.0, 90.0, 90.0);
|
|
opt.enumerate_all_settings = true;
|
|
const auto result = SearchSpaceGroup(merged, opt);
|
|
INFO(SearchSpaceGroupResultToText(result));
|
|
REQUIRE(result.best_space_group.has_value());
|
|
CHECK(result.best_space_group->xhm() == "A 2 2 2");
|
|
}
|
|
}
|
|
|
|
// The null the widening has to survive. Stage A's second pass offers the a- and c-unique 2-folds on
|
|
// any metric that could host them, which is every orthorhombic one - so a genuinely triclinic
|
|
// crystal sitting on a pseudo-orthorhombic cell is now offered three promotions where it used to be
|
|
// offered one. It must still be refused all three: the added candidates go through the same operator
|
|
// correlation as every other, and a rotation the intensities do not have scores nothing.
|
|
TEST_CASE("SearchSpaceGroup does not promote triclinic data on a pseudo-orthorhombic cell") {
|
|
const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name("P 1");
|
|
const auto merged = GenerateMergedReflectionsForSpaceGroup(sg, 10);
|
|
|
|
SearchSpaceGroupOptions opt;
|
|
opt.merge_friedel = true;
|
|
opt.lattice_system = gemmi::CrystalSystem::Orthorhombic;
|
|
opt.cell = gemmi::UnitCell(40.0, 50.0, 60.0, 90.0, 90.0, 90.0);
|
|
opt.enumerate_all_settings = true;
|
|
opt.enumerate_all_rotation_sets = true;
|
|
|
|
const auto result = SearchSpaceGroup(merged, opt);
|
|
INFO(SearchSpaceGroupResultToText(result));
|
|
REQUIRE(result.best_space_group.has_value());
|
|
CHECK(result.best_space_group->number == 1);
|
|
CHECK(result.point_group_order == 1);
|
|
}
|
|
|
|
// A zone whose predicted absences were never measurable must not outscore a zone that is genuinely
|
|
// dead. sum_u is a sum of max(0, E^2)/row_mean, so it is EXACTLY zero when every absent reflection in
|
|
// the zone merged non-positive - and the Beta tail then diverges, worth ~690 nats per reflection. That
|
|
// was harmless while the number only had to clear a bound; it is now summed across zones and ranks the
|
|
// candidates, so it made a candidate claiming a screw on an UNMEASURED row beat one whose rows are
|
|
// actually dead. The evidence is scored through the same entry point for both kinds of absence.
|
|
TEST_CASE("AbsenceEvidence does not reward a zone that was never measurable", "[SearchSpaceGroup]") {
|
|
// 2 absences that all merged non-positive, against a control of 8...
|
|
const double unmeasurable = AbsenceEvidence(0.0, 2, 8);
|
|
// ...against a genuinely dead zone: 6 absences at 1% of their row's mean, same control.
|
|
const double genuine = AbsenceEvidence(0.06, 6, 8);
|
|
|
|
CHECK(std::isfinite(unmeasurable));
|
|
CHECK(unmeasurable < genuine); // the ordering that was inverted
|
|
CHECK(unmeasurable < 20.0); // and it does not clear min_screw_absence_evidence
|
|
|
|
// The floor is far below any real measurement, so a genuine zone is untouched by it.
|
|
CHECK(genuine == Catch::Approx(22.0).margin(0.2));
|
|
CHECK(AbsenceEvidence(0.22, 22, 8) == Catch::Approx(65.4).margin(0.3));
|
|
|
|
// More dead reflections still means more evidence, which is the property the sum relies on.
|
|
CHECK(AbsenceEvidence(0.0, 6, 8) > AbsenceEvidence(0.0, 2, 8));
|
|
}
|
|
|
|
// ---------------------------------------------------------------------------------------------
|
|
// Glide planes (small-molecule space groups).
|
|
//
|
|
// A glide extinguishes a two-dimensional ZONE where a screw extinguishes a row, so it is the same
|
|
// absence test on a plane. What these cases pin is not that the test works - it is the two places
|
|
// it must NOT act: on a Sohncke group (a chiral crystal has no glide, and the corpus measurement
|
|
// that licensed this feature is a zero false-positive rate on 140 protein datasets), and on an
|
|
// inversion centre (Friedel's law makes it unmeasurable, so it must never be claimed).
|
|
// ---------------------------------------------------------------------------------------------
|
|
TEST_CASE("SearchSpaceGroup names a glide plane") {
|
|
struct Case {
|
|
std::string input_name;
|
|
std::string expected_xhm;
|
|
gemmi::UnitCell cell;
|
|
};
|
|
const gemmi::UnitCell monoclinic(11.0, 13.0, 17.0, 90.0, 101.0, 90.0);
|
|
const gemmi::UnitCell orthorhombic(11.0, 13.0, 17.0, 90.0, 90.0, 90.0);
|
|
|
|
const std::vector<Case> cases = {
|
|
// The reference setting, and the non-reference one the same group takes when the data are
|
|
// indexed with the glide on a: a setting names the mirror by AXIS, so both have to be
|
|
// reachable or a crystal indexed the other way round is named wrongly or not at all.
|
|
{"P 1 21/c 1", "P 1 21/c 1", monoclinic},
|
|
{"P 1 21/a 1", "P 1 21/a 1", monoclinic},
|
|
{"C 1 2/c 1", "C 1 2/c 1", monoclinic},
|
|
// Three glide planes at once: every zone must be dead, not just the best one.
|
|
{"P b c a", "P b c a", orthorhombic},
|
|
};
|
|
|
|
for (const auto& tc : cases) {
|
|
DYNAMIC_SECTION(tc.expected_xhm) {
|
|
const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name(tc.input_name);
|
|
const auto merged = GenerateMergedReflectionsForSpaceGroup(sg, 10);
|
|
|
|
SearchSpaceGroupOptions opt;
|
|
opt.merge_friedel = true;
|
|
opt.cell = tc.cell;
|
|
opt.enumerate_all_settings = true;
|
|
|
|
const auto result = SearchSpaceGroup(merged, opt);
|
|
INFO(SearchSpaceGroupResultToText(result));
|
|
REQUIRE(result.best_space_group.has_value());
|
|
CHECK(result.best_space_group->xhm() == tc.expected_xhm);
|
|
// The Sohncke answer is reported alongside on the same run, so a reader who knows the
|
|
// sample is chiral never has to process the images again to see it.
|
|
CHECK(result.sohncke_space_group.has_value());
|
|
CHECK(result.sohncke_space_group->is_sohncke());
|
|
REQUIRE_FALSE(result.glide_zones.empty());
|
|
for (const auto& z : result.glide_zones)
|
|
CHECK(z.evidence_per_reflection >= opt.min_glide_evidence_per_reflection);
|
|
}
|
|
}
|
|
}
|
|
|
|
// The inert direction, which is the one that matters: a chiral crystal has no glide plane, so on
|
|
// Sohncke data the glide machinery must add nothing at all - not a different group, not a zone.
|
|
TEST_CASE("SearchSpaceGroup claims no glide on Sohncke data") {
|
|
const gemmi::UnitCell monoclinic(11.0, 13.0, 17.0, 90.0, 101.0, 90.0);
|
|
for (const std::string name : {"P 1 21 1", "P 1 2 1", "C 1 2 1"}) {
|
|
DYNAMIC_SECTION(name) {
|
|
const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name(name);
|
|
const auto merged = GenerateMergedReflectionsForSpaceGroup(sg, 10);
|
|
|
|
SearchSpaceGroupOptions opt;
|
|
opt.merge_friedel = true;
|
|
opt.cell = monoclinic;
|
|
opt.enumerate_all_settings = true;
|
|
|
|
const auto result = SearchSpaceGroup(merged, opt);
|
|
INFO(SearchSpaceGroupResultToText(result));
|
|
REQUIRE(result.best_space_group.has_value());
|
|
CHECK(result.best_space_group->is_sohncke());
|
|
CHECK_FALSE(result.glide_space_group.has_value());
|
|
CHECK(result.glide_zones.empty());
|
|
}
|
|
}
|
|
}
|
|
|
|
// The centre of symmetry is NOT determinable and must never be claimed: Friedel's law makes the
|
|
// diffraction pattern centrosymmetric whether or not the crystal is, so P 1 2/m 1 predicts exactly
|
|
// what P 1 2 1 predicts. Data generated in the centrosymmetric group must still come out Sohncke -
|
|
// which is the enumeration refusing any non-Sohncke group whose absences a Sohncke one already has.
|
|
TEST_CASE("SearchSpaceGroup never claims an inversion centre") {
|
|
const gemmi::UnitCell monoclinic(11.0, 13.0, 17.0, 90.0, 101.0, 90.0);
|
|
const gemmi::SpaceGroup& sg = gemmi::get_spacegroup_by_name("P 1 2/m 1");
|
|
const auto merged = GenerateMergedReflectionsForSpaceGroup(sg, 10);
|
|
|
|
SearchSpaceGroupOptions opt;
|
|
opt.merge_friedel = true;
|
|
opt.cell = monoclinic;
|
|
opt.enumerate_all_settings = true;
|
|
|
|
const auto result = SearchSpaceGroup(merged, opt);
|
|
INFO(SearchSpaceGroupResultToText(result));
|
|
REQUIRE(result.best_space_group.has_value());
|
|
CHECK(result.best_space_group->is_sohncke());
|
|
CHECK_FALSE(result.glide_space_group.has_value());
|
|
}
|