@@ -20,6 +20,12 @@
 using namespace std;
 using namespace RDKit;
 
+std::string canon(std::string smiles) {
+  unique_ptr<ROMol> m(SmilesToMol(smiles));
+  const bool useStereo = true;
+  return MolToSmiles(*m, useStereo);
+}
+
 void test1() {
   std::cout << "-----------------------\n Test1: pathToSubmol" << std::endl;
   {
//
//  Copyright (C) 2003-2018 Greg Landrum and Rational Discovery LLC
//
//   @@ 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.
//
#include <RDGeneral/test.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <GraphMol/Subgraphs/Subgraphs.h>
#include <GraphMol/Subgraphs/SubgraphUtils.h>
#include <boost/foreach.hpp>

#include <iostream>
using namespace std;
using namespace RDKit;

void test1() {
  std::cout << "-----------------------\n Test1: pathToSubmol" << std::endl;
  {
    std::string smiles = "CC1CC1";
    RWMol *mol = SmilesToMol(smiles);
    TEST_ASSERT(mol);

    PATH_LIST sgs;
    sgs = findAllSubgraphsOfLengthN(*mol, 3, false, 0);
    TEST_ASSERT(sgs.size() == 3);
    BOOST_FOREACH (PATH_TYPE tmp, sgs) {
      TEST_ASSERT(tmp[0] == 0);
      TEST_ASSERT(tmp.size() == 3);
      ROMol *frag = Subgraphs::pathToSubmol(*mol, tmp, false);
      smiles = MolToSmiles(*frag, true, false, 0, false);
      if (tmp[1] == 1) {
        if (tmp[2] == 2) {
          TEST_ASSERT(smiles == "CCCC");
        } else if (tmp[2] == 3) {
          TEST_ASSERT(smiles == "CC(C)C");
        } else {
          TEST_ASSERT(0);
        }
      } else if (tmp[1] == 3) {
        if (tmp[2] == 2) {
          TEST_ASSERT(smiles == "CCCC");
        } else if (tmp[2] == 1) {
          TEST_ASSERT(smiles == "CC(C)C");
        } else {
          TEST_ASSERT(0);
        }
      } else {
        TEST_ASSERT(0);
      }
      delete frag;
    }
    delete mol;
  }
  std::cout << "Finished" << std::endl;
}

void test2() {
  std::cout << "-----------------------\n Test2: Atom Environments"
            << std::endl;
  {
    std::string smiles = "CC1CC1";
    RWMol *mol = SmilesToMol(smiles);
    TEST_ASSERT(mol);

    PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mol, 1, 0);
    TEST_ASSERT(pth.size() == 1);
    TEST_ASSERT(pth[0] == 0);

    pth = findAtomEnvironmentOfRadiusN(*mol, 2, 0);
    TEST_ASSERT(pth.size() == 3);
    TEST_ASSERT(pth[0] == 0);

    pth = findAtomEnvironmentOfRadiusN(*mol, 3, 0);
    TEST_ASSERT(pth.size() == 4);
    TEST_ASSERT(pth[0] == 0);

    pth = findAtomEnvironmentOfRadiusN(*mol, 4, 0);
    TEST_ASSERT(pth.size() == 0);

    pth = findAtomEnvironmentOfRadiusN(*mol, 1, 1);
    TEST_ASSERT(pth.size() == 3);

    pth = findAtomEnvironmentOfRadiusN(*mol, 2, 1);
    TEST_ASSERT(pth.size() == 4);

    pth = findAtomEnvironmentOfRadiusN(*mol, 3, 1);
    TEST_ASSERT(pth.size() == 0);

    delete mol;
  }

  {
    std::string smiles = "CC1CC1";
    RWMol *mol = SmilesToMol(smiles);
    TEST_ASSERT(mol);
    ROMol *mH = MolOps::addHs(static_cast<const ROMol &>(*mol));

    PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mH, 1, 0);
    TEST_ASSERT(pth.size() == 1);
    TEST_ASSERT(pth[0] == 0);

    pth = findAtomEnvironmentOfRadiusN(*mH, 1, 0, true);
    TEST_ASSERT(pth.size() == 4);

    delete mol;
    delete mH;
  }

  {
    std::string smiles = "O=C(O)CCCC=CC(C1C(O)CC(O)C1(C=CC(O)CCCCC))";
    RWMol *mol = SmilesToMol(smiles);
    TEST_ASSERT(mol);
    smiles = MolToSmiles(*mol);

    PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mol, 2, 9);
    TEST_ASSERT(pth.size() == 8);
    ROMol *frag = Subgraphs::pathToSubmol(*mol, pth, false);
    smiles = MolToSmiles(*frag, true, false, 0, false);
    TEST_ASSERT(smiles == "C(C(C(O)C)C(C)C)C");
    delete frag;
    delete mol;
  }

  std::cout << "Finished" << std::endl;
}

void testGithubIssue103() {
  std::cout << "-----------------------\n Testing github Issue103: "
               "stereochemistry and pathToSubmol"
            << std::endl;
  {
    std::string smiles = "O=C(O)C(=O)C[C@@]1(C(=O)O)C=C[C@H](O)C=C1";
    RWMol *mol = SmilesToMol(smiles);
    TEST_ASSERT(mol);

    PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mol, 2, 12);
    TEST_ASSERT(pth.size() == 5);
    ROMol *frag = Subgraphs::pathToSubmol(*mol, pth, false);
    smiles = MolToSmiles(*frag, true);
    TEST_ASSERT(smiles == "C=CC(O)C=C");
    delete frag;
    delete mol;
  }
  {
    std::string smiles = "O=C(O)C(=O)C[C@@]1(C(=O)O)C=C[C@H](O)C=C1";
    RWMol *mol = SmilesToMol(smiles);
    TEST_ASSERT(mol);

    PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mol, 2, 12);
    TEST_ASSERT(pth.size() == 5);
    ROMol *frag = Subgraphs::pathToSubmol(*mol, pth, false);
    smiles = MolToSmarts(*frag);
    TEST_ASSERT(smiles == "[#6](-[#6@H](-[#8])-[#6]=[#6])=[#6]");
    delete frag;
    delete mol;
  }
  {
    std::string smiles = "O=C(O)C(=O)C[C@@]1(C(=O)O)C=C[C@H](O)C=C1";
    RWMol *mol = SmilesToMol(smiles);
    TEST_ASSERT(mol);

    PATH_TYPE pth = findAtomEnvironmentOfRadiusN(*mol, 2, 12);
    TEST_ASSERT(pth.size() == 5);
    ROMol *frag = Subgraphs::pathToSubmol(*mol, pth, true);
    smiles = MolToSmarts(*frag);
    TEST_ASSERT(smiles == "[#6](-[#6@](-[#8])-[#6]=[#6])=[#6]");
    delete frag;
    delete mol;
  }

  std::cout << "Finished" << std::endl;
}

// -------------------------------------------------------------------
int main() {
  test1();
  test2();
  testGithubIssue103();
  return 0;
}

don't need this anymore. `useStereo=true` is the default now.