set up performance benchmarks (#8865)

Code/Bench/CMakeLists.txt

@@ -0,0 +1,18 @@
+add_executable(bench EXCLUDE_FROM_ALL smiles.cpp stereo.cpp)
+target_link_libraries(bench rdkitCatch SmilesParse CIPLabeler)
+
+if(RDK_BUILD_CPP_TESTS)
+  # add a fast version of the benchmarks to the default unit tests
+  # to protect the benchmarks from bit-rot
+  add_test(
+    NAME quickbench
+    COMMAND bench --benchmark-samples 1 --benchmark-warmup-time 0
+  )
+  
+  # ctest does not automatically build test executables
+  # so, like with other unit tests in this repo, we need to manually
+  # build the target before running ctest. This usually gets done with
+  # an `all` or an `install` build. We re-add bench to he `all` group
+  # to keep it similar to the other unit tests
+  set_target_properties(bench PROPERTIES EXCLUDE_FROM_ALL FALSE)
+endif(RDK_BUILD_CPP_TESTS)

Code/Bench/README.md

@@ -0,0 +1,12 @@
+# RDKit Benchmarks
+
+To run:
+
+```bash
+mkdir build
+cd build
+cmake ..
+cmake --build . --target bench -j "$(nproc)"
+# see `./Code/Bench/bench --help` for options
+./Code/Bench/bench
+```

Code/Bench/bench_common.hpp

@@ -0,0 +1,11 @@
+#pragma once
+
+namespace bench_common {
+constexpr const char *CASES[] = {
+    "COC1/C=C/OC2(C)Oc3c(C)c(O)c4c(O)c(c(/C=N/OC(c5ccccc5)c5ccccc5)cc4c3C2=O)NC(=O)/C(C)=C\\C=C\\C(C)C(O)C(C)C(O)C(C)C(OC(C)=O)C1C",
+    "Cn1cnc2n(C)c(=O)n(C)c(=O)c12",
+    "c1ccc2c(c1)c3ccccc3c4ccccc24",
+    "F[C@@H](Cl)[C@H](Br)[C@](I)(O)[C@@](N)(C#N)C(=O)O",
+    "C[S+](C)(C)[O-]",
+};
+}  // namespace bench_common

Code/Bench/smiles.cpp

@@ -0,0 +1,30 @@
+#include <catch2/catch_all.hpp>
+#include <string>
+
+#include "bench_common.hpp"
+
+#include <GraphMol/ROMol.h>
+#include <GraphMol/SmilesParse/SmilesParse.h>
+#include <GraphMol/SmilesParse/SmilesWrite.h>
+
+using namespace RDKit;
+
+TEST_CASE("SmilesToMol", "[smiles]") {
+  for (auto smiles : bench_common::CASES) {
+    BENCHMARK("SmilesToMol: " + std::string(smiles)) {
+      auto mol = v2::SmilesParse::MolFromSmiles(smiles);
+      REQUIRE(mol);
+      return mol;
+    };
+  }
+}
+
+TEST_CASE("MolToSmiles", "[smiles]") {
+  for (auto smiles : bench_common::CASES) {
+    auto mol = v2::SmilesParse::MolFromSmiles(smiles);
+    REQUIRE(mol);
+    BENCHMARK("MolToSmiles: " + std::string(smiles)) {
+      return MolToSmiles(*mol);
+    };
+  }
+}

Code/Bench/stereo.cpp

@@ -0,0 +1,33 @@
+#include <catch2/catch_all.hpp>
+#include <string>
+
+#include "bench_common.hpp"
+
+#include <GraphMol/CIPLabeler/CIPLabeler.h>
+#include <GraphMol/Chirality.h>
+#include <GraphMol/ROMol.h>
+#include <GraphMol/SmilesParse/SmilesParse.h>
+
+using namespace RDKit;
+
+TEST_CASE("Chirality::findPotentialStereo", "[stereo]") {
+  for (auto smiles : bench_common::CASES) {
+    auto mol = v2::SmilesParse::MolFromSmiles(smiles);
+    REQUIRE(mol);
+
+    BENCHMARK("Chirality::findPotentialStereo: " + std::string(smiles)) {
+      return Chirality::findPotentialStereo(*mol);
+    };
+  }
+}
+
+TEST_CASE("CIPLabeler::CIPLabeler", "[stereo]") {
+  for (auto smiles : bench_common::CASES) {
+    auto mol = v2::SmilesParse::MolFromSmiles(smiles);
+    REQUIRE(mol);
+
+    BENCHMARK("CIPLabeler::assignCIPLabels: " + std::string(smiles)) {
+      return Chirality::findPotentialStereo(*mol);
+    };
+  }
+}

Code/CMakeLists.txt

@@ -40,3 +40,5 @@ add_subdirectory(MinimalLib)
 if(RDK_BUILD_FUZZ_TARGETS)
   add_subdirectory(Fuzz)
 endif(RDK_BUILD_FUZZ_TARGETS)
+
+add_subdirectory(Bench)