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21225e63b3
* move testSubstructMatch to catch2 * modernization * modernization * switch to catch2 * modernize * convert to catch2 * update * move to catch * please be quiet * move to catch2 * changes in response to review --------- Co-authored-by: = <=>
556 lines
16 KiB
C++
556 lines
16 KiB
C++
//
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// Copyright (C) 2003-2026 Greg Landrum and other RDKit contributors
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <catch2/catch_all.hpp>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/Subgraphs/Subgraphs.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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using namespace std;
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using namespace RDKit;
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TEST_CASE("testSubgraphs", "[subgraphs]") {
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// build: CCC(C)CC
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RWMol mol;
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bool updateLabel = true;
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bool takeOwnership = true;
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addBond(0, 1, Bond::SINGLE);
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mol.addBond(1, 2, Bond::SINGLE);
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mol.addBond(2, 3, Bond::SINGLE);
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mol.addBond(2, 4, Bond::SINGLE);
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mol.addBond(3, 5, Bond::SINGLE);
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PATH_LIST tmp;
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PATH_LIST::iterator i;
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int totPs = 0;
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tmp = findAllSubgraphsOfLengthN(mol, 1);
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CHECK(tmp.size() == 5);
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totPs += tmp.size();
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tmp = findAllSubgraphsOfLengthN(mol, 2);
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CHECK(tmp.size() == 5);
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totPs += tmp.size();
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tmp = findAllSubgraphsOfLengthN(mol, 3);
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CHECK(tmp.size() == 5);
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totPs += tmp.size();
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tmp = findAllSubgraphsOfLengthN(mol, 4);
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CHECK(tmp.size() == 3);
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totPs += tmp.size();
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tmp = findAllSubgraphsOfLengthN(mol, 5);
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CHECK(tmp.size() == 1);
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totPs += tmp.size();
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tmp = findAllSubgraphsOfLengthN(mol, 6);
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CHECK(tmp.empty());
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totPs += tmp.size();
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// now use the direct range function and check that we get the
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// same answer
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INT_PATH_LIST_MAP tmpm;
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tmpm = findAllSubgraphsOfLengthsMtoN(mol, 1, 6);
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int newTot, idx;
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newTot = 0;
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for (idx = 1; idx <= 6; idx++) {
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newTot += tmpm[idx].size();
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}
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CHECK(totPs == newTot);
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// add an H and make sure things don't change:
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mol.addAtom(new Atom(1), updateLabel, takeOwnership);
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mol.addBond(5, 6, Bond::SINGLE);
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tmp = findAllSubgraphsOfLengthN(mol, 1);
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CHECK(tmp.size() == 5);
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tmp = findAllSubgraphsOfLengthN(mol, 2);
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CHECK(tmp.size() == 5);
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tmp = findAllSubgraphsOfLengthN(mol, 3);
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CHECK(tmp.size() == 5);
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tmp = findAllSubgraphsOfLengthN(mol, 4);
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CHECK(tmp.size() == 3);
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tmp = findAllSubgraphsOfLengthN(mol, 5);
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CHECK(tmp.size() == 1);
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tmp = findAllSubgraphsOfLengthN(mol, 6);
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CHECK(tmp.empty());
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}
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TEST_CASE("testSubgraphs2a", "[subgraphs]") {
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// these have been moved here from test2.cpp
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auto mol = "C1CC2C1N2"_smiles;
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REQUIRE(mol);
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int nAll = 0;
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int nUnique = 0;
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for (unsigned int i = 1; i < 7; ++i) {
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PATH_LIST tmp;
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tmp = findAllSubgraphsOfLengthN(*mol, i);
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nAll += tmp.size();
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tmp = findUniqueSubgraphsOfLengthN(*mol, i);
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nUnique += tmp.size();
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}
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CHECK(nAll == 49);
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CHECK(nUnique == 21);
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}
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TEST_CASE("testSubgraphs2", "[subgraphs]") {
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// these have been moved here from test2.cpp
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auto mol = "C12C3C4C1C1C2C3N41"_smiles;
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REQUIRE(mol);
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int nAll = 0;
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int nUnique = 0;
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int i;
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for (i = 1; i < 13; i++) {
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PATH_LIST tmp;
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tmp = findAllSubgraphsOfLengthN(*mol, i);
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nAll += tmp.size();
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tmp = findUniqueSubgraphsOfLengthN(*mol, i);
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nUnique += tmp.size();
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}
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CHECK(nAll == 2433);
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CHECK(nUnique == 300);
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mol = "CCC(O)C(c1ccccc1)CC(C)N(C)C"_smiles;
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REQUIRE(mol);
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nAll = 0;
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nUnique = 0;
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for (i = 1; i < 18; i++) {
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PATH_LIST tmp;
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tmp = findAllSubgraphsOfLengthN(*mol, i);
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nAll += tmp.size();
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tmp = findUniqueSubgraphsOfLengthN(*mol, i);
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nUnique += tmp.size();
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}
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CHECK(nAll == 1990);
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CHECK(nUnique == 907);
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}
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void dumpVIV(PATH_LIST v) {
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PATH_LIST::iterator i;
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PATH_TYPE::iterator j;
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for (i = v.begin(); i != v.end(); i++) {
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for (j = i->begin(); j != i->end(); j++) {
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std::cout << *j << " ";
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}
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std::cout << std::endl;
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}
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}
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TEST_CASE("testPaths", "[subgraphs]") {
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// build: CCC(C)CC
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RWMol mol;
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bool updateLabel = true;
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bool takeOwnership = true;
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addBond(0, 1, Bond::SINGLE);
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mol.addBond(1, 2, Bond::SINGLE);
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mol.addBond(2, 3, Bond::SINGLE);
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mol.addBond(2, 4, Bond::SINGLE);
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mol.addBond(3, 5, Bond::SINGLE);
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PATH_LIST tmp;
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//
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// Retrieve using bonds
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//
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tmp = findAllPathsOfLengthN(mol, 1);
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CHECK(tmp.size() == 5);
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tmp = findAllPathsOfLengthN(mol, 2);
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CHECK(tmp.size() == 5);
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tmp = findAllPathsOfLengthN(mol, 3);
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CHECK(tmp.size() == 4);
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tmp = findAllPathsOfLengthN(mol, 4);
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CHECK(tmp.size() == 1);
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tmp = findAllPathsOfLengthN(mol, 5);
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CHECK(tmp.empty());
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tmp = findAllPathsOfLengthN(mol, 6);
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CHECK(tmp.empty());
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//
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// Retrieve using atoms, which gives the results shifted by
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// one (it takes two atoms to make one bond)
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//
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tmp = findAllPathsOfLengthN(mol, 1, false);
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CHECK(tmp.size() == 6);
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tmp = findAllPathsOfLengthN(mol, 2, false);
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CHECK(tmp.size() == 5);
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tmp = findAllPathsOfLengthN(mol, 3, false);
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CHECK(tmp.size() == 5);
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tmp = findAllPathsOfLengthN(mol, 4, false);
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CHECK(tmp.size() == 4);
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tmp = findAllPathsOfLengthN(mol, 5, false);
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CHECK(tmp.size() == 1);
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tmp = findAllPathsOfLengthN(mol, 6, false);
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CHECK(tmp.empty());
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//
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// try m->n
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//
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INT_PATH_LIST_MAP pths;
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pths = findAllPathsOfLengthsMtoN(mol, 1, 6);
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CHECK(pths[1].size() == 5);
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CHECK(pths[2].size() == 5);
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CHECK(pths[3].size() == 4);
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CHECK(pths[4].size() == 1);
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CHECK(pths[5].empty());
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CHECK(pths[6].empty());
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pths = findAllPathsOfLengthsMtoN(mol, 1, 6, false);
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CHECK(pths[1].size() == 6);
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CHECK(pths[2].size() == 5);
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CHECK(pths[3].size() == 5);
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CHECK(pths[4].size() == 4);
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CHECK(pths[5].size() == 1);
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CHECK(pths[6].empty());
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//
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// add an atom, close the ring and re-check a couple indices:
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// (leaves us with CC1CCCCC1)
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//
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addBond(5, 6, Bond::SINGLE);
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mol.addBond(0, 6, Bond::SINGLE);
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tmp = findAllPathsOfLengthN(mol, 4);
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CHECK(tmp.size() == 8);
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tmp = findAllPathsOfLengthN(mol, 5, false);
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CHECK(tmp.size() == 8);
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}
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TEST_CASE("testPaths2", "[subgraphs]") {
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// build: CCC(C)CC
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RWMol mol;
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bool updateLabel = true;
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bool takeOwnership = true;
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addBond(0, 1, Bond::SINGLE);
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mol.addBond(1, 2, Bond::SINGLE);
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mol.addBond(2, 3, Bond::SINGLE);
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mol.addBond(2, 0, Bond::SINGLE);
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//
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// Retrieve using bonds
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//
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PATH_LIST tmp = findAllPathsOfLengthN(mol, 3);
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// std::cout << "\n3:" << std::endl;
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// dumpVIV(tmp);
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CHECK(tmp.size() == 3);
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}
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TEST_CASE("testUniqueSubgraphs", "[subgraphs]") {
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// build: CCC(C)CC
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RWMol mol;
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bool updateLabel = true;
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bool takeOwnership = true;
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addAtom(new Atom(6), updateLabel, takeOwnership);
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mol.addBond(0, 1, Bond::SINGLE);
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mol.addBond(1, 2, Bond::SINGLE);
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mol.addBond(2, 3, Bond::SINGLE);
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mol.addBond(2, 4, Bond::SINGLE);
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mol.addBond(3, 5, Bond::SINGLE);
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PATH_LIST tmp;
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PATH_LIST::iterator i;
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tmp = findAllSubgraphsOfLengthN(mol, 1);
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CHECK(tmp.size() == 5);
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tmp = findAllSubgraphsOfLengthN(mol, 2);
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CHECK(tmp.size() == 5);
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tmp = findUniqueSubgraphsOfLengthN(mol, 2);
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CHECK(tmp.size() == 1);
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tmp = findAllSubgraphsOfLengthN(mol, 3);
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CHECK(tmp.size() == 5);
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tmp = findUniqueSubgraphsOfLengthN(mol, 3);
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CHECK(tmp.size() == 2);
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tmp = findAllSubgraphsOfLengthN(mol, 4);
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CHECK(tmp.size() == 3);
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tmp = findUniqueSubgraphsOfLengthN(mol, 4);
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CHECK(tmp.size() == 2);
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tmp = findAllSubgraphsOfLengthN(mol, 5);
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CHECK(tmp.size() == 1);
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tmp = findUniqueSubgraphsOfLengthN(mol, 5);
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CHECK(tmp.size() == 1);
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tmp = findAllSubgraphsOfLengthN(mol, 6);
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CHECK(tmp.empty());
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tmp = findUniqueSubgraphsOfLengthN(mol, 6);
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CHECK(tmp.empty());
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// add an H and make sure things don't change:
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mol.addAtom(new Atom(1), updateLabel, takeOwnership);
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mol.addBond(5, 6, Bond::SINGLE);
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tmp = findAllSubgraphsOfLengthN(mol, 2);
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CHECK(tmp.size() == 5);
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tmp = findUniqueSubgraphsOfLengthN(mol, 2);
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CHECK(tmp.size() == 1);
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tmp = findAllSubgraphsOfLengthN(mol, 3);
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CHECK(tmp.size() == 5);
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tmp = findUniqueSubgraphsOfLengthN(mol, 3);
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CHECK(tmp.size() == 2);
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tmp = findAllSubgraphsOfLengthN(mol, 4);
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CHECK(tmp.size() == 3);
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tmp = findUniqueSubgraphsOfLengthN(mol, 4);
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CHECK(tmp.size() == 2);
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tmp = findAllSubgraphsOfLengthN(mol, 5);
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CHECK(tmp.size() == 1);
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tmp = findUniqueSubgraphsOfLengthN(mol, 5);
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CHECK(tmp.size() == 1);
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tmp = findAllSubgraphsOfLengthN(mol, 6);
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CHECK(tmp.empty());
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tmp = findUniqueSubgraphsOfLengthN(mol, 6);
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CHECK(tmp.empty());
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}
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TEST_CASE("testUniqueSubgraphs2", "[subgraphs]") {
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// moved here from test2.cpp
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auto mol = "O=C(O)CCCC=CC(C1C(O)CC(O)C1(C=CC(O)CCCCC))"_smiles;
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REQUIRE(mol);
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int nAll = 0;
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int nUnique = 0;
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for (int i = 1; i < 26; i++) {
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PATH_LIST tmp;
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tmp = findAllSubgraphsOfLengthN(*mol, i);
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// std::cout << i << "\t" << tmp.size();
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nAll += tmp.size();
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tmp = findUniqueSubgraphsOfLengthN(*mol, i);
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// std::cout << "\t" << tmp.size() << std::endl;;
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nUnique += tmp.size();
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}
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CHECK(nAll == 6435);
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CHECK(nUnique == 5618);
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}
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TEST_CASE("testLeak", "[subgraphs]") {
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// moved here from test2.cpp
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// testing for a core leak (Issue 42)
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auto mol = "O=C(O)CCCC=CC(C1C(O)CC(O)C1(C=CC(O)CCCCC))"_smiles;
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REQUIRE(mol);
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for (int rep = 0; rep < 100; rep++) {
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int nAll = 0;
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int nUnique = 0;
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for (int i = 1; i < 26; i++) {
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PATH_LIST tmp;
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tmp = findAllSubgraphsOfLengthN(*mol, i);
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// std::cout << i << "\t" << tmp.size();
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nAll += tmp.size();
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tmp = findUniqueSubgraphsOfLengthN(*mol, i);
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// std::cout << "\t" << tmp.size() << std::endl;;
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nUnique += tmp.size();
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}
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CHECK(nAll == 6435);
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CHECK(nUnique == 5618);
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}
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}
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TEST_CASE("testRootedSubgraphs", "[subgraphs]") {
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{
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auto mol = "CC1CC1"_smiles;
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REQUIRE(mol);
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PATH_LIST tmp;
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tmp = findAllSubgraphsOfLengthN(*mol, 1, false, 0);
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CHECK(tmp.size() == 1);
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tmp = findAllSubgraphsOfLengthN(*mol, 2, false, 0);
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CHECK(tmp.size() == 2);
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tmp = findAllSubgraphsOfLengthN(*mol, 3, false, 0);
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CHECK(tmp.size() == 3);
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tmp = findUniqueSubgraphsOfLengthN(*mol, 2, false, false, 0);
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CHECK(tmp.size() == 1);
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tmp = findUniqueSubgraphsOfLengthN(*mol, 3, false, false, 0);
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CHECK(tmp.size() == 2);
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INT_PATH_LIST_MAP tmpm;
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tmpm = findAllSubgraphsOfLengthsMtoN(*mol, 1, 3, false, 0);
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CHECK(tmpm[1].size() == 1);
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CHECK(tmpm[2].size() == 2);
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CHECK(tmpm[3].size() == 3);
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// edge case:
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tmp = findAllSubgraphsOfLengthN(*mol, 1, false, 10);
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CHECK(tmp.empty());
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}
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{ // tests for sf.net issue 250
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auto mol = "C1CC1C"_smiles;
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REQUIRE(mol);
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PATH_LIST tmp;
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tmp = findAllSubgraphsOfLengthN(*mol, 1, false, 3);
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CHECK(tmp.size() == 1);
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tmp = findAllSubgraphsOfLengthN(*mol, 2, false, 3);
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CHECK(tmp.size() == 2);
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tmp = findAllSubgraphsOfLengthN(*mol, 3, false, 3);
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CHECK(tmp.size() == 3);
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tmp = findUniqueSubgraphsOfLengthN(*mol, 2, false, false, 3);
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CHECK(tmp.size() == 1);
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tmp = findUniqueSubgraphsOfLengthN(*mol, 3, false, false, 3);
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CHECK(tmp.size() == 2);
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INT_PATH_LIST_MAP tmpm;
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tmpm = findAllSubgraphsOfLengthsMtoN(*mol, 1, 3, false, 3);
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CHECK(tmpm[1].size() == 1);
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CHECK(tmpm[2].size() == 2);
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CHECK(tmpm[3].size() == 3);
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// edge case:
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tmp = findAllSubgraphsOfLengthN(*mol, 1, false, 10);
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CHECK(tmp.empty());
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}
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{
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auto mol = "CC1CC1"_smiles;
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REQUIRE(mol);
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INT_PATH_LIST_MAP tmpm;
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tmpm = findAllSubgraphsOfLengthsMtoN(*mol, 1, 2, false, 0);
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CHECK(tmpm[1].size() == 1);
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CHECK(tmpm[2].size() == 2);
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CHECK(tmpm[3].empty());
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tmpm = findAllSubgraphsOfLengthsMtoN(*mol, 1, 3, false, 0);
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CHECK(tmpm[1].size() == 1);
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CHECK(tmpm[2].size() == 2);
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CHECK(tmpm[3].size() == 3);
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}
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{ // tests for sf.net issue 250
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auto mol = "C1CC1C"_smiles;
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REQUIRE(mol);
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INT_PATH_LIST_MAP tmpm;
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tmpm = findAllSubgraphsOfLengthsMtoN(*mol, 1, 2, false, 3);
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CHECK(tmpm[1].size() == 1);
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CHECK(tmpm[2].size() == 2);
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CHECK(tmpm[3].empty());
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tmpm = findAllSubgraphsOfLengthsMtoN(*mol, 1, 3, false, 3);
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CHECK(tmpm[1].size() == 1);
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CHECK(tmpm[2].size() == 2);
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CHECK(tmpm[3].size() == 3);
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}
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}
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TEST_CASE("testRootedPaths", "[subgraphs]") {
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{
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auto mol = "CC1CC1"_smiles;
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REQUIRE(mol);
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PATH_LIST tmp;
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// bond paths:
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tmp = findAllPathsOfLengthN(*mol, 1, true, false, 0);
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CHECK(tmp.size() == 1);
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tmp = findAllPathsOfLengthN(*mol, 2, true, false, 0);
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CHECK(tmp.size() == 2);
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tmp = findAllPathsOfLengthN(*mol, 3, true, false, 0);
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CHECK(tmp.size() == 2);
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// edge case:
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tmp = findAllPathsOfLengthN(*mol, 1, true, false, 10);
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CHECK(tmp.empty());
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// atom paths:
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tmp = findAllPathsOfLengthN(*mol, 1, false, false, 0);
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CHECK(tmp.size() == 1);
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tmp = findAllPathsOfLengthN(*mol, 2, false, false, 0);
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CHECK(tmp.size() == 1);
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tmp = findAllPathsOfLengthN(*mol, 3, false, false, 0);
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CHECK(tmp.size() == 2);
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tmp = findAllPathsOfLengthN(*mol, 4, false, false, 0);
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CHECK(tmp.size() == 2);
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}
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{ // tests for sf.net issue 250
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auto mol = "C1CC1C"_smiles;
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REQUIRE(mol);
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PATH_LIST tmp;
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|
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// bond paths:
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tmp = findAllPathsOfLengthN(*mol, 1, true, false, 3);
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CHECK(tmp.size() == 1);
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tmp = findAllPathsOfLengthN(*mol, 2, true, false, 3);
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CHECK(tmp.size() == 2);
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tmp = findAllPathsOfLengthN(*mol, 3, true, false, 3);
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CHECK(tmp.size() == 2);
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// edge case:
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tmp = findAllPathsOfLengthN(*mol, 1, true, false, 10);
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CHECK(tmp.empty());
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// atom paths:
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tmp = findAllPathsOfLengthN(*mol, 1, false, false, 3);
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CHECK(tmp.size() == 1);
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tmp = findAllPathsOfLengthN(*mol, 2, false, false, 3);
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CHECK(tmp.size() == 1);
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tmp = findAllPathsOfLengthN(*mol, 3, false, false, 3);
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CHECK(tmp.size() == 2);
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tmp = findAllPathsOfLengthN(*mol, 4, false, false, 3);
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CHECK(tmp.size() == 2);
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}
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{
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auto mol = "CC1CC1"_smiles;
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REQUIRE(mol);
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INT_PATH_LIST_MAP tmpm;
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tmpm = findAllPathsOfLengthsMtoN(*mol, 1, 2, false, false, 0);
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CHECK(tmpm[1].size() == 1);
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CHECK(tmpm[2].size() == 1);
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CHECK(tmpm[3].empty());
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tmpm = findAllPathsOfLengthsMtoN(*mol, 1, 3, false, false, 0);
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CHECK(tmpm[1].size() == 1);
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CHECK(tmpm[2].size() == 1);
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CHECK(tmpm[3].size() == 2);
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}
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{ // tests for sf.net issue 250
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auto mol = "C1CC1C"_smiles;
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REQUIRE(mol);
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|
|
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INT_PATH_LIST_MAP tmpm;
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tmpm = findAllPathsOfLengthsMtoN(*mol, 1, 2, false, false, 3);
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CHECK(tmpm[1].size() == 1);
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CHECK(tmpm[2].size() == 1);
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CHECK(tmpm[3].empty());
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tmpm = findAllPathsOfLengthsMtoN(*mol, 1, 3, false, false, 3);
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CHECK(tmpm[1].size() == 1);
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CHECK(tmpm[2].size() == 1);
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CHECK(tmpm[3].size() == 2);
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}
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}
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