// $Id$
//
//  Copyright (C) 2004-2008 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.
//

#define NO_IMPORT_ARRAY
#include <boost/python.hpp>
#include <string>
#include "rdchem.h"
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/types.h>
#include <Geometry/point.h>
#include <GraphMol/Conformer.h>
#include <RDBoost/PySequenceHolder.h>
//#include "seqs.hpp"

namespace python = boost::python;

namespace RDKit{
  RDGeom::Point3D GetAtomPos(const Conformer *conf, unsigned int aid) {
    RDGeom::Point3D res=conf->getAtomPos(aid);
    return res;
  }

  void SetAtomPos(Conformer *conf, unsigned int aid, python::object loc) { 
    //const std::vector<double> &loc) {
    int dim = python::extract<int>(loc.attr("__len__")());
    CHECK_INVARIANT(dim == 3, "");
    PySequenceHolder<double> pdata(loc);
    RDGeom::Point3D pt(pdata[0], pdata[1], pdata[2]);
    conf->setAtomPos(aid, pt);
  }


  std::string confClassDoc="The class to store 2D or 3D conformation of a molecule\n";

  struct conformer_wrapper {
    static void wrap() {
      python::class_<Conformer, CONFORMER_SPTR>("Conformer",confClassDoc.c_str(),python::init<>())
        .def(python::init<unsigned int>("Constructor with the number of atoms specified"))
        
        .def("GetNumAtoms", &Conformer::getNumAtoms,
             "Get the number of atoms in the conformer\n")

        .def("GetOwningMol", &Conformer::getOwningMol,
             "Get the owning molecule\n",
             python::return_value_policy<python::reference_existing_object>())
        
        .def("GetId", &Conformer::getId,
             "Get the ID of the conformer")
        .def("SetId", &Conformer::setId,
             "Set the ID of the conformer\n")
        
        .def("GetAtomPosition", GetAtomPos,
             "Get the posistion of an atom\n")
        
        .def("SetAtomPosition", SetAtomPos,
             "Set the position of the specified atom\n")
        .def("SetAtomPosition", &Conformer::setAtomPos,
             "Set the position of the specified atom\n")

        .def("Set3D", &Conformer::set3D,
             "Set the 3D flag of the conformer\n")
        .def("Is3D", &Conformer::is3D,
             "returns the 3D flag of the conformer\n")
        ;

    };
  };
}

void wrap_conformer() {
  RDKit::conformer_wrapper::wrap();
}