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//
// 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;
}
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