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// $Id$
//
// Copyright (C) 2005-2006 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 <RDGeneral/RDLog.h>
#include <boost/log/functions.hpp>
#include <GraphMol/RDKitBase.h>
#include <string>
#include <iostream>
#include <GraphMol/FeatTrees/FeatTree.h>
#include <GraphMol/FeatTrees/FeatTreeUtils.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <boost/graph/graph_utility.hpp>
using namespace RDKit;
using namespace FeatTrees;
void showFeatTree(FeatTreeGraph &featGraph) {
typedef boost::property_map<FeatTreeGraph, FeatTreeNode_t>::type
FeatTreeNodePMap;
FeatTreeNodePMap nodes = boost::get(FeatTreeNode_t(), featGraph);
boost::graph_traits<FeatTreeGraph>::vertex_iterator vtx, endVtx;
unsigned int i;
for (boost::tie(vtx, endVtx) = boost::vertices(featGraph), i = 0;
vtx != endVtx; ++vtx, ++i) {
UINT_SET s = nodes[*vtx];
std::cout << "\t" << i << ": [";
std::copy(s.begin(), s.end(), std::ostream_iterator<int>(std::cout, ","));
std::cout << "]" << std::endl;
}
}
void test1() {
BOOST_LOG(rdInfoLog) << "\t---------------------------------\n";
BOOST_LOG(rdInfoLog) << "\t test1: building FeatTreeGraphs \n\n";
std::string smi;
ROMol *m;
FeatTreeGraphSPtr fGraph;
std::vector<unsigned int> atomIndices;
smi = "CCC";
std::cout << smi << std::endl;
m = SmilesToMol(smi);
TEST_ASSERT(m);
fGraph.reset(new FeatTreeGraph());
addRingsAndConnectors(*m, *fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 0);
TEST_ASSERT(boost::num_edges(*fGraph) == 0);
replaceCycles(*fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 0);
TEST_ASSERT(boost::num_edges(*fGraph) == 0);
addRingRingBonds(*m, *fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 0);
TEST_ASSERT(boost::num_edges(*fGraph) == 0);
atomIndices = addNonringAtoms(*m, *fGraph);
TEST_ASSERT(atomIndices.size() == 3);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 0);
addBondsFromNonringAtoms(*m, *fGraph, atomIndices);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 2);
addZeroNodes(*fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 2);
fGraph = molToBaseTree(*m);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 2);
smi = "C1CC1OOC1CCC1";
std::cout << smi << std::endl;
m = SmilesToMol(smi);
TEST_ASSERT(m);
fGraph.reset(new FeatTreeGraph());
addRingsAndConnectors(*m, *fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 2);
TEST_ASSERT(boost::num_edges(*fGraph) == 0);
replaceCycles(*fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 2);
TEST_ASSERT(boost::num_edges(*fGraph) == 0);
addRingRingBonds(*m, *fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 2);
TEST_ASSERT(boost::num_edges(*fGraph) == 0);
atomIndices = addNonringAtoms(*m, *fGraph);
TEST_ASSERT(atomIndices.size() == 9);
TEST_ASSERT(boost::num_vertices(*fGraph) == 4);
TEST_ASSERT(boost::num_edges(*fGraph) == 0);
addBondsFromNonringAtoms(*m, *fGraph, atomIndices);
TEST_ASSERT(boost::num_vertices(*fGraph) == 4);
TEST_ASSERT(boost::num_edges(*fGraph) == 3);
addZeroNodes(*fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 4);
TEST_ASSERT(boost::num_edges(*fGraph) == 3);
fGraph = molToBaseTree(*m);
TEST_ASSERT(boost::num_vertices(*fGraph) == 4);
TEST_ASSERT(boost::num_edges(*fGraph) == 3);
delete m;
smi = "C1CC2C1CCC2C(=O)";
std::cout << smi << std::endl;
m = SmilesToMol(smi);
TEST_ASSERT(m);
fGraph.reset(new FeatTreeGraph());
addRingsAndConnectors(*m, *fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 2);
TEST_ASSERT(boost::num_edges(*fGraph) == 1);
replaceCycles(*fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 2);
TEST_ASSERT(boost::num_edges(*fGraph) == 1);
addRingRingBonds(*m, *fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 2);
TEST_ASSERT(boost::num_edges(*fGraph) == 1);
atomIndices = addNonringAtoms(*m, *fGraph);
TEST_ASSERT(atomIndices.size() == 9);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 1);
addBondsFromNonringAtoms(*m, *fGraph, atomIndices);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 2);
addZeroNodes(*fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 2);
fGraph = molToBaseTree(*m);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 2);
delete m;
smi = "CC12CCCCC1CCCC2";
std::cout << smi << std::endl;
m = SmilesToMol(smi);
TEST_ASSERT(m);
fGraph.reset(new FeatTreeGraph());
addRingsAndConnectors(*m, *fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 2);
TEST_ASSERT(boost::num_edges(*fGraph) == 1);
replaceCycles(*fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 2);
TEST_ASSERT(boost::num_edges(*fGraph) == 1);
addRingRingBonds(*m, *fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 2);
TEST_ASSERT(boost::num_edges(*fGraph) == 1);
atomIndices = addNonringAtoms(*m, *fGraph);
TEST_ASSERT(atomIndices.size() == 11);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 1);
addBondsFromNonringAtoms(*m, *fGraph, atomIndices);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 3);
addZeroNodes(*fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 4);
TEST_ASSERT(boost::num_edges(*fGraph) == 3);
fGraph = molToBaseTree(*m);
TEST_ASSERT(boost::num_vertices(*fGraph) == 4);
TEST_ASSERT(boost::num_edges(*fGraph) == 3);
delete m;
smi = "C1CC2CCCCC2CC1C1CC(CC2)CCC21";
std::cout << smi << std::endl;
m = SmilesToMol(smi);
TEST_ASSERT(m);
fGraph.reset(new FeatTreeGraph());
addRingsAndConnectors(*m, *fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 5);
TEST_ASSERT(boost::num_edges(*fGraph) == 4);
replaceCycles(*fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 1);
addRingRingBonds(*m, *fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 2);
atomIndices = addNonringAtoms(*m, *fGraph);
TEST_ASSERT(atomIndices.size() == 18);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 2);
addBondsFromNonringAtoms(*m, *fGraph, atomIndices);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 2);
addZeroNodes(*fGraph);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 2);
fGraph = molToBaseTree(*m);
TEST_ASSERT(boost::num_vertices(*fGraph) == 3);
TEST_ASSERT(boost::num_edges(*fGraph) == 2);
BOOST_LOG(rdInfoLog) << "\tDone\n";
}
int main() {
RDLog::InitLogs();
// boost::logging::disable_logs("rdApp.info");
// BOOST_LOG(rdInfoLog) <<
// "********************************************************\n";
// BOOST_LOG(rdInfoLog) << "Testing FeatTrees\n";
test1();
// BOOST_LOG(rdInfoLog) <<
// "*******************************************************\n";
return (0);
}
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