chain.h

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// -*- C++ -*-

/*
 * Gnome Chemistry Utils
 * libs/gcu/chain.h
 *
 * Copyright (C) 2001-2011 Jean Bréfort <jean.brefort@normalesup.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; either version 3 of the
 * License, or (at your option) any later version.
 *
 * 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.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301
 * USA
 */

#ifndef GCU_CHAIN_H
#define GCU_CHAIN_H

#include "object.h"
#include <map>

namespace gcu {

class Atom;
class Bond;
class Molecule;

typedef struct
{
        Bond *fwd;
        Bond *rev;
} ChainElt;

class Chain: public Object
{
public:
        Chain (Bond* pBond, Atom* pAtom = NULL, TypeId Type = ChainType);
        Chain (Molecule* molecule, Bond* pBond, TypeId Type = ChainType);
        Chain (Molecule* molecule, Atom* pAtom, TypeId Type = ChainType);
        virtual ~Chain();

        void FindCycles (Atom* pAtom);
        bool FindCycle (Atom* pAtom, Bond* pBond);
        virtual void Erase (Atom* pAtom1, Atom* pAtom2);
        virtual void Insert (Atom* pAtom1, Atom* pAtom2, Chain& chain);
        void Extract (Atom* pAtom1, Atom* pAtom2, Chain& chain);
        void Reverse ();
        void Append (Chain& chain);
        void AddBond (Atom* start, Atom* end);
        unsigned GetUnsaturations ();
        unsigned GetHeteroatoms ();
        bool Contains (Atom* pAtom);
        bool Contains (Bond* pBond);
        unsigned GetLength ();
        double GetMeanBondLength ();
        Atom* GetNextAtom (Atom* pAtom);

        std::string Name ();

        unsigned BuildLength (unsigned *cycle_size = NULL, unsigned *cycle_pos = NULL);

protected:
        std::map<Atom*, ChainElt> m_Bonds;
        Molecule* m_Molecule;
};

}       //      namespace gcu

#endif // GCHEMPAINT_CHAIN_H