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// Copyright 2018 Global Phasing Ltd.
// Microbenchmark of gemmi::UnitCell::find_nearest_image().
#include "gemmi/model.hpp"
#include "gemmi/pdb.hpp"
#include "gemmi/calculate.hpp"
#include "gemmi/neighbor.hpp"
#include "gemmi/select.hpp" // count_atom_sites
#include <benchmark/benchmark.h>
static const char* path;
static void read_pdb_file(benchmark::State& state) {
for (auto _ : state) {
gemmi::Structure st = gemmi::read_pdb_file(path);
benchmark::DoNotOptimize(st);
}
}
static void find_atom_image(benchmark::State& state) {
using namespace gemmi;
Structure st = read_pdb_file(path);
const Model& model = st.models[0];
Position ref = model.chains.at(0).residues.at(0).atoms.at(0).pos;
for (auto _ : state) {
double sum_dist = 0;
for (const Chain& ch1 : model.chains)
for (const Residue& res1 : ch1.residues)
for (const Atom& a1 : res1.atoms) {
NearestImage im = st.cell.find_nearest_image(ref, a1.pos, Asu::Any);
sum_dist += im.dist_sq;
}
benchmark::DoNotOptimize(sum_dist);
}
}
static void neighbor_search_ctor(benchmark::State& state) {
using namespace gemmi;
Structure st = read_pdb_file(path);
for (auto _ : state) {
NeighborSearch ns(st.models.at(0), st.cell, 5.0);
benchmark::DoNotOptimize(ns);
}
}
static void neighbor_search_find(benchmark::State& state) {
using namespace gemmi;
Structure st = read_pdb_file(path);
const Model& model = st.models[0];
Position ref = model.chains.at(0).residues.at(2).atoms.at(0).pos;
NeighborSearch ns(st.models.at(0), st.cell, 5.0);
for (auto _ : state) {
auto r = ns.find_atoms(ref, '\0', 0, 4);
benchmark::DoNotOptimize(r);
}
}
static void neighbor_search_for_each(benchmark::State& state) {
using namespace gemmi;
Structure st = read_pdb_file(path);
const Model& model = st.models[0];
Position ref = model.chains.at(0).residues.at(2).atoms.at(0).pos;
NeighborSearch ns(st.models.at(0), st.cell, 5.0);
for (auto _ : state) {
double sum = 0;
ns.for_each(ref, '\0', 4,
[&sum](NeighborSearch::Mark&, double d) { sum += d; });
benchmark::DoNotOptimize(sum);
}
}
static void calculate_box(benchmark::State& state) {
using namespace gemmi;
Structure st = read_pdb_file(path);
for (auto _ : state) {
Box<Position> box = calculate_box(st);
benchmark::DoNotOptimize(box);
}
}
static void fractional_box(benchmark::State& state) {
using namespace gemmi;
Structure st = read_pdb_file(path);
for (auto _ : state) {
Box<Fractional> box = calculate_fractional_box(st);
benchmark::DoNotOptimize(box);
}
}
static bool has_hydrogen_with_levels(const gemmi::Structure& st) {
for (const gemmi::Model& model : st.models)
for (const gemmi::Chain& chain : model.chains)
for (const gemmi::Residue& res : chain.residues)
for (const gemmi::Atom& atom : res.atoms)
if (atom.is_hydrogen())
return true;
return false;
}
static bool has_hydrogen_with_cra(const gemmi::Structure& st) {
for (const gemmi::Model& model : st.models)
for (gemmi::const_CRA cra : model.all())
if (cra.atom->is_hydrogen())
return true;
return false;
}
static bool has_hydrogen_with_selection(const gemmi::Structure& st) {
gemmi::Selection sel("[H,D]");
return count_atom_sites(st, &sel) != 0;
}
static void has_hydrogen1(benchmark::State& state) {
using namespace gemmi;
Structure st = read_pdb_file(path);
for (auto _ : state) {
bool has_hydr = has_hydrogen_with_levels(st);
benchmark::DoNotOptimize(has_hydr);
}
}
static void has_hydrogen2(benchmark::State& state) {
using namespace gemmi;
Structure st = read_pdb_file(path);
for (auto _ : state) {
bool has_hydr = has_hydrogen_with_cra(st);
benchmark::DoNotOptimize(has_hydr);
}
}
static void has_hydrogen3(benchmark::State& state) {
using namespace gemmi;
Structure st = read_pdb_file(path);
for (auto _ : state) {
bool has_hydr = has_hydrogen_with_selection(st);
benchmark::DoNotOptimize(has_hydr);
}
}
int main(int argc, char** argv) {
benchmark::RegisterBenchmark("read_pdb_file", read_pdb_file);
benchmark::RegisterBenchmark("find_atom_image", find_atom_image);
benchmark::RegisterBenchmark("neighbor_search_ctor", neighbor_search_ctor);
benchmark::RegisterBenchmark("neighbor_search_find", neighbor_search_find);
benchmark::RegisterBenchmark("neighbor_search_for_each",
neighbor_search_for_each);
benchmark::RegisterBenchmark("calculate_box", calculate_box);
benchmark::RegisterBenchmark("fractional_box", fractional_box);
benchmark::RegisterBenchmark("has_hydrogen1", has_hydrogen1);
benchmark::RegisterBenchmark("has_hydrogen2", has_hydrogen2);
benchmark::RegisterBenchmark("has_hydrogen3", has_hydrogen3);
benchmark::Initialize(&argc, argv);
if (argc < 2) {
printf("Call it with path to a pdb file as an argument.\n");
return 1;
}
path = argv[argc-1];
{
gemmi::Structure st = gemmi::read_pdb_file(path);
printf("PDB file: %s with %zu atom sites.\n",
st.name.c_str(), count_atom_sites(st.models.at(0)));
}
benchmark::RunSpecifiedBenchmarks();
benchmark::Shutdown();
}
/* Output from my desktop:
*/
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