Add options for substructure searching (#2254)

* first pass at adding a SubstructMatchParameter struct * start moving the rest of the backend to use the parameters * backend at least mostly moved over * add aromaticMatchesConjugated add tests * switch over the MolBundle too Add templates to reduce duplicated code * support older compilers let's see if it works... * add SubstructMatchParameters to Python wrapper * remove some deprecations and warnings * damn compilers * parameter support for bundles in python wrapper * add the parameters to the java wrappers * response to review
2026-06-03 21:44:30 +08:00 · 2019-02-08 14:10:10 +00:00
parent 8524652a86
commit a102eaf932
12 changed files with 846 additions and 528 deletions
--- a/Code/GraphMol/Substruct/catch_tests.cpp
+++ b/Code/GraphMol/Substruct/catch_tests.cpp
@@ -0,0 +1,92 @@
+//
+//  Copyright (C) 2019 Greg Landrum
+//
+//   @@ All Rights Reserved @@
+//  This file is part of the RDKit.
+//  The contents are covered by the terms of the BSD license
+//  which is included in the file license.txt, found at the root
+//  of the RDKit source tree.
+//
+
+#define CATCH_CONFIG_MAIN
+#include "catch.hpp"
+
+#include <tuple>
+
+#include <GraphMol/RDKitBase.h>
+#include <GraphMol/SmilesParse/SmilesParse.h>
+#include <GraphMol/Substruct/SubstructMatch.h>
+
+using namespace RDKit;
+typedef std::tuple<std::string, std::string, size_t> matchCase;
+
+TEST_CASE("substructure parameters", "[substruct]") {
+  SECTION("chirality") {
+    auto mol1 = "CCC[C@@H]1CN(CCC)CCN1"_smiles;
+    auto mol2 = "CCC[C@H]1CN(CCC)CCN1"_smiles;
+    REQUIRE(mol1);
+    REQUIRE(mol2);
+
+    SubstructMatchParameters ps;
+    // default is to ignore chirality:
+    CHECK(SubstructMatch(*mol1, *mol2, ps).size() == 1);
+    CHECK(SubstructMatch(*mol1, *mol1, ps).size() == 1);
+
+    ps.useChirality = true;
+    CHECK(SubstructMatch(*mol1, *mol2, ps).size() == 0);
+    CHECK(SubstructMatch(*mol1, *mol1, ps).size() == 1);
+  }
+  SECTION("conjugated matching aromaticity 1") {
+    auto mol1 = "C1=COC=C1"_smiles;
+    REQUIRE(mol1);
+    RWMol mol2(*mol1);
+    MolOps::Kekulize(mol2);
+    SubstructMatchParameters ps;
+    CHECK(SubstructMatch(*mol1, mol2, ps).size() == 0);
+    CHECK(SubstructMatch(mol2, *mol1, ps).size() == 0);
+
+    ps.aromaticMatchesConjugated = true;
+    CHECK(SubstructMatch(*mol1, mol2, ps).size() == 1);
+    CHECK(SubstructMatch(mol2, *mol1, ps).size() == 1);
+  }
+  SECTION("conjugated matching aromaticity 2") {
+    auto mol1 = "c1ccccc1"_smiles;
+    REQUIRE(mol1);
+    RWMol mol2(*mol1);
+    MolOps::Kekulize(mol2);
+    SubstructMatchParameters ps;
+    CHECK(SubstructMatch(*mol1, mol2, ps).size() == 0);
+    CHECK(SubstructMatch(mol2, *mol1, ps).size() == 0);
+
+    ps.aromaticMatchesConjugated = true;
+    CHECK(SubstructMatch(*mol1, mol2, ps).size() == 1);
+    CHECK(SubstructMatch(mol2, *mol1, ps).size() == 1);
+  }
+
+  SECTION("conjugated matching aromaticity bulk") {
+    std::vector<matchCase> examples;
+    examples.push_back(std::make_tuple(std::string("c1ccccc1"), std::string("C1CCCCC1"), 0));
+    examples.push_back(std::make_tuple(std::string("C1CCCCC1"), std::string("c1ccccc1"), 0));
+    examples.push_back(std::make_tuple(std::string("O=C1C=CC(=O)C=C1"), std::string("c1ccccc1"), 1));
+    SubstructMatchParameters ps;
+    ps.aromaticMatchesConjugated = true;
+    for (const auto &example : examples) {
+      // std::cerr << "   " << std::get<0>(example) << " - "
+      //           << std::get<1>(example) << std::endl;
+      std::unique_ptr<RWMol> m1(SmilesToMol(std::get<0>(example)));
+      REQUIRE(m1);
+      std::unique_ptr<RWMol> m2(SmilesToMol(std::get<1>(example)));
+      CHECK(SubstructMatch(*m1, *m2, ps).size() == std::get<2>(example));
+    }
+  }
+  SECTION("looping") {
+    auto mol1 = "CC(=O)C(=O)C(=O)"_smiles;
+    auto mol2 = "C=O"_smiles;
+    REQUIRE(mol1);
+    REQUIRE(mol2);
+    for( auto match : SubstructMatch(*mol1,*mol2)){
+      CHECK(match.size()==2);
+    }
+  }
+
+}