/*
 *            Copyright 2009-2018 The VOTCA Development Team
 *                       (http://www.votca.org)
 *
 *      Licensed under the Apache License, Version 2.0 (the "License")
 *
 * You may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *              http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */
/// For earlier commit history see ctp commit 77795ea591b29e664153f9404c8655ba28dc14e9

#include <stdio.h>
#include <vector>
#include <iostream>
#include <fstream>
#include <votca/tools/vec.h>
#include <votca/xtp/molecule.h>
#include <votca/xtp/segment.h>
#include <votca/xtp/fragment.h>
#include <votca/xtp/atom.h>

using namespace std;
using namespace votca::tools;

namespace votca { namespace xtp {

/// Destructor
Molecule::~Molecule() {

    _segments.clear();
    _fragments.clear();
    _atoms.clear();
    
}

/// Returns ID of the molecule
const int &Molecule::getId() {
        return _id;
}

/// Returns the name of the molecule
const string &Molecule::getName() {
        return _name;
}

void Molecule::AddSegment( Segment* segment ) {
    _segments.push_back( segment );
    segment->setMolecule(this);
}

void Molecule::AddFragment(Fragment* fragment ) {
    _fragments.push_back( fragment );
    fragment->setMolecule(this);
}

void Molecule::AddAtom(Atom *atom ) {
    _atoms.push_back(atom);
    atom->setMolecule(this);
}

/// Returns a pointer to the atom
Atom *Molecule::getAtom(const int &id) {
    throw runtime_error( string("Not implemented") ); 
}

/// Returns atom type
const string &Molecule::getAtomType(const int &id) {
    throw runtime_error( string("Not implemented") ); 
}

/// Returns atom position
const vec Molecule::getAtomPosition(const int &id) {
    throw runtime_error( string("Not implemented") ); 
}

/// Returns number of atoms in the molecule
int Molecule::NumberOfAtoms() {
    return _atoms.size(); 
}

}}