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9822e9439c
* [WIP-ENH]: Support greater use of `findAtomEnvironmentOfRadiusN()` This PR is the feature support for PR 4262. I am not so confident when coding the C++ as it is my first time hands-on experience There are still many thing that should be done but I still need several support * Update MolOps.cpp * Fix build error Fix according to this? https://www.boost.org/doc/libs/1_42_0/libs/python/doc/v2/object.html#object-spec-ctors * Fix build error * Fix test2.cpp * Fix `include` issue * Fixed as requested * Update Subgraphs.cpp * Update Subgraphs.cpp * Update Subgraphs.cpp * Fix reported error, correct doc * Update MolOps.cpp * Update test and fix error * Fix default argument * Fix duplication * Update Subgraphs.cpp * Fix test bug * Updated a test and fix reported error * Update Subgraphs.cpp * Fix reported error * Update test2.cpp * Fix reported error of memleak and introduce new function * Fix incorrect variable * Update test2.cpp * Update test2.cpp * Update MolOps.cpp * Update MolOps.cpp * Fix algorithm & Add test docs * Update test2.cpp * Update Subgraphs.cpp * New argument `bondDist` - Optimize the `FindAtomEnvFromMToN` Documentation is syncronized the meaning between C++ and Python - New argument `bondDist` - `findAtomEnvironmentOfRadiusMToN()` now called once instead of twice due to the introduction of `bondDist` * Update Subgraphs.cpp * Update test2.cpp * Fix casting * Correct the test * Update Subgraphs.cpp * Remove buggy function and replace argument position * Update Subgraphs.h * Fix build failed * Optimization Reduce graph expansion if it is the last radius * Adjust codebase based on review - Update Copyright - Add doc to prove optimization * suggested changes Co-authored-by: greg landrum <greg.landrum@gmail.com>
393 lines
12 KiB
C++
393 lines
12 KiB
C++
//
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// Copyright (C) 2003-2022 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 <RDGeneral/test.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/SmilesParse/SmartsWrite.h>
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#include <GraphMol/Subgraphs/Subgraphs.h>
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#include <GraphMol/Subgraphs/SubgraphUtils.h>
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#include <iostream>
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#include <algorithm>
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using namespace std;
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using namespace RDKit;
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std::string canon(std::string smiles) {
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unique_ptr<ROMol> m(SmilesToMol(smiles));
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const bool useStereo = true;
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return MolToSmiles(*m, useStereo);
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}
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void test1() {
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std::cout << "-----------------------\n Test1: pathToSubmol" << std::endl;
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{
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std::string smiles = "CC1CC1";
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RWMol *mol = SmilesToMol(smiles);
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TEST_ASSERT(mol);
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PATH_LIST sgs;
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sgs = findAllSubgraphsOfLengthN(*mol, 3, false, 0);
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TEST_ASSERT(sgs.size() == 3);
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for (const auto &tmp : sgs) {
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TEST_ASSERT(tmp[0] == 0);
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TEST_ASSERT(tmp.size() == 3);
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ROMol *frag = Subgraphs::pathToSubmol(*mol, tmp, false);
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smiles = MolToSmiles(*frag, true, false, 0, false);
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if (tmp[1] == 1) {
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if (tmp[2] == 2) {
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TEST_ASSERT(smiles == "CCCC");
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} else if (tmp[2] == 3) {
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TEST_ASSERT(smiles == "CC(C)C");
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} else {
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TEST_ASSERT(0);
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}
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} else if (tmp[1] == 3) {
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if (tmp[2] == 2) {
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TEST_ASSERT(smiles == "CCCC");
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} else if (tmp[2] == 1) {
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TEST_ASSERT(smiles == "CC(C)C");
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} else {
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TEST_ASSERT(0);
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}
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} else {
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TEST_ASSERT(0);
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}
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delete frag;
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}
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delete mol;
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}
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std::cout << "Finished" << std::endl;
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}
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void test2() {
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std::cout << "-----------------------\n Test2: Atom Environments"
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<< std::endl;
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{
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std::string smiles = "CC1CC1";
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RWMol *mol = SmilesToMol(smiles);
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TEST_ASSERT(mol);
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PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mol, 1, 0);
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TEST_ASSERT(pth.size() == 1);
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TEST_ASSERT(pth[0] == 0);
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pth = findAtomEnvironmentOfRadiusN(*mol, 2, 0);
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TEST_ASSERT(pth.size() == 3);
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TEST_ASSERT(pth[0] == 0);
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pth = findAtomEnvironmentOfRadiusN(*mol, 3, 0);
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TEST_ASSERT(pth.size() == 4);
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TEST_ASSERT(pth[0] == 0);
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pth = findAtomEnvironmentOfRadiusN(*mol, 4, 0);
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TEST_ASSERT(pth.size() == 0);
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pth = findAtomEnvironmentOfRadiusN(*mol, 1, 1);
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TEST_ASSERT(pth.size() == 3);
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pth = findAtomEnvironmentOfRadiusN(*mol, 2, 1);
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TEST_ASSERT(pth.size() == 4);
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pth = findAtomEnvironmentOfRadiusN(*mol, 3, 1);
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TEST_ASSERT(pth.size() == 0);
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delete mol;
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}
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{
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std::string smiles = "CC1CC1";
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RWMol *mol = SmilesToMol(smiles);
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TEST_ASSERT(mol);
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ROMol *mH = MolOps::addHs(static_cast<const ROMol &>(*mol));
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PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mH, 1, 0);
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TEST_ASSERT(pth.size() == 1);
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TEST_ASSERT(pth[0] == 0);
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pth = findAtomEnvironmentOfRadiusN(*mH, 1, 0, true);
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TEST_ASSERT(pth.size() == 4);
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delete mol;
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delete mH;
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}
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{
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std::string smiles = "O=C(O)CCCC=CC(C1C(O)CC(O)C1(C=CC(O)CCCCC))";
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RWMol *mol = SmilesToMol(smiles);
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TEST_ASSERT(mol);
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smiles = MolToSmiles(*mol);
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PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mol, 2, 9);
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TEST_ASSERT(pth.size() == 8);
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ROMol *frag = Subgraphs::pathToSubmol(*mol, pth, false);
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smiles = MolToSmiles(*frag, true, false, 0, false);
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TEST_ASSERT(canon(smiles) == canon("C(C(C(O)C)C(C)C)C"));
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delete frag;
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delete mol;
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}
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std::cout << "Finished" << std::endl;
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}
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void test3() {
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std::cout << "-----------------------" << std::endl;
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std::cout << "Test 3: Atom Environments (Extension)" << std::endl;
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{
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std::string smiles = "C=NC";
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unsigned int rootedAtAtom = 2;
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RWMol *mol = SmilesToMol(smiles);
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TEST_ASSERT(mol);
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ROMol *mH = MolOps::addHs(static_cast<const ROMol &>(*mol));
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PATH_TYPE pth =
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findAtomEnvironmentOfRadiusN(*mH, 2, rootedAtAtom, false, true);
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TEST_ASSERT(pth.size() == 2);
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pth = findAtomEnvironmentOfRadiusN(*mH, 2, rootedAtAtom, true, true);
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TEST_ASSERT(pth.size() == 5);
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pth = findAtomEnvironmentOfRadiusN(*mH, 3, rootedAtAtom, false, true);
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TEST_ASSERT(pth.size() == 0);
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pth = findAtomEnvironmentOfRadiusN(*mH, 3, rootedAtAtom, true, true);
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TEST_ASSERT(pth.size() == 7);
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pth = findAtomEnvironmentOfRadiusN(*mH, 3, rootedAtAtom, true, false);
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TEST_ASSERT(pth.size() == 7);
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pth = findAtomEnvironmentOfRadiusN(*mH, 3, rootedAtAtom, false, false);
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TEST_ASSERT(pth.size() == 2);
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pth = findAtomEnvironmentOfRadiusN(*mH, 4, rootedAtAtom, false, true);
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TEST_ASSERT(pth.size() == 0);
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pth = findAtomEnvironmentOfRadiusN(*mH, 4, rootedAtAtom, true, true);
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TEST_ASSERT(pth.size() == 0);
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pth = findAtomEnvironmentOfRadiusN(*mH, 4, rootedAtAtom, true, false);
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TEST_ASSERT(pth.size() == 7);
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pth = findAtomEnvironmentOfRadiusN(*mH, 4, rootedAtAtom, false, false);
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TEST_ASSERT(pth.size() == 2);
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delete mol;
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delete mH;
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}
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{
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std::string smiles = "C=NO"; // C(0)=N(1)O(2)
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unsigned int rootedAtAtom = 2;
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std::unordered_map<unsigned int, unsigned int> cAtomMap;
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RWMol *mol = SmilesToMol(smiles);
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TEST_ASSERT(mol);
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ROMol *mH = MolOps::addHs(static_cast<const ROMol &>(*mol));
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PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mH, 2, rootedAtAtom, false,
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true, &cAtomMap);
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TEST_ASSERT(cAtomMap.size() == 3);
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TEST_ASSERT(cAtomMap[rootedAtAtom] == 0);
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TEST_ASSERT(cAtomMap[1] == 1);
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TEST_ASSERT(cAtomMap[0] == 2);
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cAtomMap.clear();
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pth = findAtomEnvironmentOfRadiusN(*mH, 2, rootedAtAtom, false, false,
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&cAtomMap);
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TEST_ASSERT(cAtomMap.size() == 3);
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TEST_ASSERT(cAtomMap[rootedAtAtom] == 0);
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TEST_ASSERT(cAtomMap[1] == 1);
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TEST_ASSERT(cAtomMap[0] == 2);
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cAtomMap.clear();
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pth = findAtomEnvironmentOfRadiusN(*mH, 2, rootedAtAtom, true, true,
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&cAtomMap);
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TEST_ASSERT(cAtomMap.size() == 4);
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TEST_ASSERT(cAtomMap[rootedAtAtom] == 0);
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TEST_ASSERT(cAtomMap[1] == 1);
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TEST_ASSERT(cAtomMap[5] == 1);
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TEST_ASSERT(cAtomMap[0] == 2);
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cAtomMap.clear();
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pth = findAtomEnvironmentOfRadiusN(*mH, 2, rootedAtAtom, true, false,
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&cAtomMap);
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TEST_ASSERT(cAtomMap.size() == 4);
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TEST_ASSERT(cAtomMap[rootedAtAtom] == 0);
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TEST_ASSERT(cAtomMap[1] == 1);
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TEST_ASSERT(cAtomMap[5] == 1);
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TEST_ASSERT(cAtomMap[0] == 2);
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cAtomMap.clear();
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pth = findAtomEnvironmentOfRadiusN(*mH, 4, rootedAtAtom, false, true,
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&cAtomMap);
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TEST_ASSERT(pth.size() == 0);
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TEST_ASSERT(cAtomMap.size() == 0);
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pth = findAtomEnvironmentOfRadiusN(*mH, 4, rootedAtAtom, true, true,
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&cAtomMap);
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TEST_ASSERT(pth.size() == 0);
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TEST_ASSERT(cAtomMap.size() == 0);
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pth = findAtomEnvironmentOfRadiusN(*mH, 4, rootedAtAtom, false, false,
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&cAtomMap);
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TEST_ASSERT(pth.size() == 2);
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TEST_ASSERT(cAtomMap.size() == 3);
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TEST_ASSERT(cAtomMap[rootedAtAtom] == 0);
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TEST_ASSERT(cAtomMap[1] == 1);
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TEST_ASSERT(cAtomMap[0] == 2);
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cAtomMap.clear();
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pth = findAtomEnvironmentOfRadiusN(*mH, 4, rootedAtAtom, true, false,
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&cAtomMap);
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TEST_ASSERT(pth.size() == 5);
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TEST_ASSERT(cAtomMap.size() == 6);
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TEST_ASSERT(cAtomMap[rootedAtAtom] == 0);
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TEST_ASSERT(cAtomMap[1] == 1);
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TEST_ASSERT(cAtomMap[5] == 1);
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TEST_ASSERT(cAtomMap[0] == 2);
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TEST_ASSERT(cAtomMap[3] == 3);
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TEST_ASSERT(cAtomMap[4] == 3);
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cAtomMap.clear();
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delete mol;
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delete mH;
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}
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{
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std::string smiles = "c1cc[nH]c1";
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unsigned int rootedAtAtom = 1;
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std::unordered_map<unsigned int, unsigned int> cAtomMap;
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RWMol *mol = SmilesToMol(smiles);
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TEST_ASSERT(mol);
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// This test worked on ring system to guarantee that the atom ID
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// is marked correctly with the search radius
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PATH_TYPE pth;
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unsigned int size;
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for (size = 2; size < 4; size++) {
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pth = findAtomEnvironmentOfRadiusN(*mol, size, rootedAtAtom, false, true,
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&cAtomMap);
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TEST_ASSERT(cAtomMap.size() == 5);
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TEST_ASSERT(cAtomMap[rootedAtAtom] == 0);
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TEST_ASSERT(cAtomMap[0] == 1);
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TEST_ASSERT(cAtomMap[2] == 1);
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TEST_ASSERT(cAtomMap[3] == 2);
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TEST_ASSERT(cAtomMap[4] == 2);
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cAtomMap.clear();
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}
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for (size = 4; size < 6; size++) {
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pth = findAtomEnvironmentOfRadiusN(*mol, size, rootedAtAtom, false, false,
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&cAtomMap);
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TEST_ASSERT(cAtomMap.size() == 5);
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TEST_ASSERT(cAtomMap[rootedAtAtom] == 0);
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TEST_ASSERT(cAtomMap[0] == 1);
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TEST_ASSERT(cAtomMap[2] == 1);
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TEST_ASSERT(cAtomMap[3] == 2);
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TEST_ASSERT(cAtomMap[4] == 2);
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cAtomMap.clear();
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}
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delete mol;
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}
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{
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std::string smiles = "c1cc[nH]c1";
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unsigned int rootedAtAtom = 1;
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std::unordered_map<unsigned int, unsigned int> cAtomMap;
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RWMol *mol = SmilesToMol(smiles);
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TEST_ASSERT(mol);
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PATH_TYPE pth1 = findAtomEnvironmentOfRadiusN(*mol, 2, rootedAtAtom);
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PATH_TYPE pth2 = findAtomEnvironmentOfRadiusN(*mol, 2, rootedAtAtom, false);
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PATH_TYPE pth3 = findAtomEnvironmentOfRadiusN(*mol, 2, rootedAtAtom, true);
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PATH_TYPE pth4 =
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findAtomEnvironmentOfRadiusN(*mol, 2, rootedAtAtom, false, false);
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PATH_TYPE pth5 =
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findAtomEnvironmentOfRadiusN(*mol, 2, rootedAtAtom, false, true);
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PATH_TYPE pth6 = findAtomEnvironmentOfRadiusN(*mol, 2, rootedAtAtom, false,
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false, &cAtomMap);
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cAtomMap.clear();
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PATH_TYPE pth7 = findAtomEnvironmentOfRadiusN(*mol, 2, rootedAtAtom, false,
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true, &cAtomMap);
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cAtomMap.clear();
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delete mol;
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}
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std::cout << "Finished" << std::endl;
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}
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void testGithubIssue103() {
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std::cout << "-----------------------\n Testing github Issue103: "
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"stereochemistry and pathToSubmol"
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<< std::endl;
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{
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std::string smiles = "O=C(O)C(=O)C[C@@]1(C(=O)O)C=C[C@H](O)C=C1";
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RWMol *mol = SmilesToMol(smiles);
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TEST_ASSERT(mol);
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PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mol, 2, 12);
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TEST_ASSERT(pth.size() == 5);
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ROMol *frag = Subgraphs::pathToSubmol(*mol, pth, false);
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smiles = MolToSmiles(*frag, true);
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TEST_ASSERT(canon(smiles) == canon("C=CC(O)C=C"));
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delete frag;
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delete mol;
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}
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{
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std::string smiles = "O=C(O)C(=O)C[C@@]1(C(=O)O)C=C[C@H](O)C=C1";
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RWMol *mol = SmilesToMol(smiles);
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TEST_ASSERT(mol);
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PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mol, 2, 12);
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TEST_ASSERT(pth.size() == 5);
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ROMol *frag = Subgraphs::pathToSubmol(*mol, pth, false);
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smiles = MolToSmarts(*frag);
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TEST_ASSERT(smiles == "[#6]=[#6]-[#6@H](-[#8])-[#6]=[#6]");
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delete frag;
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delete mol;
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}
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{
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std::string smiles = "O=C(O)C(=O)C[C@@]1(C(=O)O)C=C[C@H](O)C=C1";
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RWMol *mol = SmilesToMol(smiles);
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TEST_ASSERT(mol);
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PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mol, 2, 12);
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TEST_ASSERT(pth.size() == 5);
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ROMol *frag = Subgraphs::pathToSubmol(*mol, pth, true);
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smiles = MolToSmarts(*frag);
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TEST_ASSERT(smiles == "[#6]=[#6]-[#6@](-[#8])-[#6]=[#6]");
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delete frag;
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delete mol;
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}
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std::cout << "Finished" << std::endl;
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}
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void testGithubIssue2647() {
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std::cout << "-----------------------\n Testing github Issue103: "
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"more stereochemistry and pathToSubmol (path needs to be in "
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"sorted order)"
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<< std::endl;
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std::string smiles = "I[C@](F)(Br)O";
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std::unique_ptr<ROMol> mol(SmilesToMol(smiles));
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std::vector<int> path = {0, 3, 2, 1};
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const bool useQuery = false;
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std::unique_ptr<ROMol> mol2(Subgraphs::pathToSubmol(*mol, path, useQuery));
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TEST_ASSERT(MolToSmiles(*mol2) == MolToSmiles(*mol));
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std::cout << "Finished" << std::endl;
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}
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// -------------------------------------------------------------------
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int main() {
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test1();
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test2();
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test3();
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testGithubIssue103();
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testGithubIssue2647();
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return 0;
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}
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