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/**********************************************************************
example.cpp - example of interfacing of OpenBabel with Boost Graph Library
Copyright (C) 2007 by Gerde Menche
This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/
#include "babelconfig.h"
#include "openbabel/mol.h"
#include "openbabel/obconversion.h"
#include <iostream>
//#include <unistd.h>
#include "mol_graph.h"
#include "verbose_visitors.h"
#include <boost/graph/breadth_first_search.hpp>
#include <boost/graph/undirected_dfs.hpp>
#include <boost/pending/queue.hpp>
using namespace std;
using OpenBabel::OBMol;
using OpenBabel::OBAtom;
using OpenBabel::OBBond;
using OpenBabel::OBConversion;
using OpenBabel::OBFormat;
int main(int argc,char **argv)
{
int c;
char *FileIn = NULL;
if (argc != 2)
{
cout << "give file name\n";
return 1;
}
FileIn = argv[1];
// Find Input filetype
OBConversion conv;
OBFormat *format = conv.FormatFromExt(FileIn);
if (!format || !conv.SetInAndOutFormats(format, format))
{
cerr << argv[0] << ": cannot read input format!" << endl;
exit (-1);
}
ifstream ifs;
// Read the file
ifs.open(FileIn);
if (!ifs)
{
cerr << argv[0] << ": cannot read input file!" << endl;
exit (-1);
}
OBMol mol;
for (c=0;;)
{
mol.Clear();
conv.Read(&mol, &ifs);
if (mol.Empty())
break;
OBAtom* atom = *(mol.BeginAtoms());
// Examples using breadth first search
std::cout << "\nBREADTH FIRST SEARCH\n";
boost::queue< OBAtom* > buffer;
boost::breadth_first_search( mol,atom,buffer, OpenBabel::OBVerboseBFSVisitor(cout),
OBAtomMap< boost::default_color_type >(mol) );
OBAtomMap< OBAtom* >predecessor_map_bfs(mol,(OBAtom*)0);
OBAtomMap< int >distance_map_bfs(mol, 0);
boost::breadth_first_search( mol,atom,buffer,
boost::make_bfs_visitor( std::make_pair (
boost::record_predecessors(predecessor_map_bfs,boost::on_tree_edge()),
boost::record_distances(distance_map_bfs,boost::on_tree_edge()) )),
OBAtomMap< boost::default_color_type >(mol) );
for ( OpenBabel::OBAtomIterator beg = mol.BeginAtoms();
beg != mol.EndAtoms(); ++beg )
{
OBAtom* parent = predecessor_map_bfs[*beg];
if ( parent )
{
std::cout << (*beg)->GetIdx() - 1 << " has parent : "
<< parent->GetIdx() - 1 << "\t";
}
else
{
std::cout << (*beg)->GetIdx() - 1 << " has no parent\t\t";
}
std::cout << " graph theoretical distance : " << distance_map_bfs[*beg] << "\n";
}
std::vector< boost::graph_traits<OpenBabel::OBMol>::edge_descriptor > bv;
boost::breadth_first_search( mol,atom,buffer,
boost::make_bfs_visitor(
boost::record( std::back_inserter(bv), boost::on_gray_target() )),
OBAtomMap< boost::default_color_type >(mol) );
std::cout << "\nBACK EDGES\n";
for ( std::vector< boost::graph_traits<OpenBabel::OBMol>::edge_descriptor >::iterator
beg = bv.begin(), end = bv.end();
beg != end; ++beg )
{
std::cout << '(' << (*beg)->GetBeginAtom()->GetIdx() << ")--";
std::cout << (*beg)->GetIdx() << "--(";
std::cout << (*beg)->GetEndAtom()->GetIdx() << ")\n";
}
// Examples using depth first search
std::cout << "\nDEPTH FIRST SEARCH\n";
boost::undirected_dfs( mol, OpenBabel::OBVerboseDFSVisitor(cout),
OBAtomMap< boost::default_color_type >(mol),
OBBondMap< boost::default_color_type >(mol),
atom );
OBAtomMap< OBAtom* >predecessor_map_dfs(mol,(OBAtom*)0);
OBAtomMap< int >distance_map_dfs(mol,0);
boost::undirected_dfs( mol,
boost::make_dfs_visitor( std::make_pair (
boost::record_predecessors(predecessor_map_dfs,boost::on_tree_edge()),
boost::record_distances(distance_map_dfs,boost::on_tree_edge()) )),
OBAtomMap< boost::default_color_type >(mol),
OBBondMap< boost::default_color_type >(mol),
atom );
for ( OpenBabel::OBAtomIterator beg = mol.BeginAtoms();
beg != mol.EndAtoms(); ++beg )
{
OBAtom* parent = predecessor_map_dfs[*beg];
if ( parent )
{
std::cout << (*beg)->GetIdx() - 1 << " has parent : "
<< parent->GetIdx() - 1 << "\t";
}
else
{
std::cout << (*beg)->GetIdx() - 1 << " has no parent\t\t";
}
std::cout << " graph theoretical distance : " << distance_map_dfs[*beg] << "\n";
}
} // end for loop
return(1);
}
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