/* 
* $Id$
*
*  Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
*  All rights reserved.
* 
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met: 
*
*     * Redistributions of source code must retain the above copyright 
*       notice, this list of conditions and the following disclaimer.
*     * Redistributions in binary form must reproduce the above
*       copyright notice, this list of conditions and the following 
*       disclaimer in the documentation and/or other materials provided 
*       with the distribution.
*     * Neither the name of Novartis Institutes for BioMedical Research Inc. 
*       nor the names of its contributors may be used to endorse or promote 
*       products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/

%include "std_string.i"
%include "std_vector.i"
%include "std_map.i"
%include "std_pair.i"

%{
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/MolSupplier.v1API.h>
#include <GraphMol/Resonance.h>
#include <GraphMol/Substruct/SubstructMatch.h>
%}

%include "Streams.i"
%ignore RDKit::v2;
%newobject RDKit::ForwardSDMolSupplier::next;
%newobject RDKit::ResonanceMolSupplier::next;
%newobject RDKit::SDMolSupplier::next;
%newobject RDKit::SmilesMolSupplier::next;
%newobject RDKit::TDTMolSupplier::next;
%newobject RDKit::PDBMolSupplier::next;


%include <GraphMol/FileParsers/MolSupplier.h>
%include <GraphMol/FileParsers/MolSupplier.v1API.h>

#ifdef RDK_USE_BOOST_IOSTREAMS
%extend RDKit::v1::ForwardSDMolSupplier {
    ForwardSDMolSupplier(RDKit::gzstream *strm, bool sanitize=true, bool removeHs = true,
                  bool strictParsing = true) {
    const bool takeOwnership = false;
    RDKit::ForwardSDMolSupplier*foo = new RDKit::ForwardSDMolSupplier(
                                     (std::istream*)strm,
                                     takeOwnership,
                                     sanitize, removeHs, strictParsing);
    PRECONDITION(!foo->atEnd(), "LDJKLJF");
    return foo;
  }
};
#endif

%include <GraphMol/Resonance.h>

%extend RDKit::ResonanceMolSupplier {
  std::vector< std::vector<std::pair<int, int> > > getSubstructMatches(RDKit::ROMol &query,bool uniquify=false, bool useChirality=false, int numThreads=1){
    std::vector<RDKit::MatchVectType> mv;
    SubstructMatch(*($self),query,mv,uniquify,true,useChirality,false,1000,numThreads);
    return mv;
  }
}

