gcp/molecule.h

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// -*- C++ -*-

/*
 * GChemPaint library
 * molecule.h
 *
 * Copyright (C) 2001-2012 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 GCHEMPAINT_MOLECULE_H
#define GCHEMPAINT_MOLECULE_H

#include "fragment.h"
#include <list>
#include <gcugtk/molecule.h>

namespace gcu {
class UIManager;
}

namespace gcp {

class Bond;

class Molecule: public gcugtk::Molecule
{
friend class MoleculePrivate;
public:
        Molecule (gcu::TypeId Type = gcu::MoleculeType);
        Molecule (Atom* pAtom);
        virtual ~Molecule ();
        void AddChild (gcu::Object* object);
        void AddAtom (gcu::Atom* pAtom);
        void AddFragment (Fragment* pFragment);
        void AddBond (gcu::Bond* pBond);
        void Remove (gcu::Object* pObject);
        bool Merge (Molecule* pMolecule, bool RemoveDuplicates = false);
        bool Load (xmlNodePtr node);
        xmlNodePtr Save (xmlDocPtr xml) const;
        void Clear ();
        void Transform2D (gcu::Matrix2D& m, double x, double y);
        Object* GetAtomAt (double x, double y, double z = 0.);
        double GetYAlign ();
        bool BuildContextualMenu (gcu::UIManager *UIManager, gcu::Object *object, double x, double y);
        bool OnSignal (gcu::SignalId Signal, gcu::Object *Child);
        void SelectAlignmentItem (gcu::Object *child);
        std::string GetAlignmentId () {return (m_Alignment)? m_Alignment->GetId (): "";}
        void OpenCalc ();
        void CheckCrossings (Bond *pBond);
        std::string GetRawFormula () const;
        void OnLoaded ();
        unsigned GetAtomsNumber () const;

        double GetMeanBondLength () const;

        void AddChiralAtom (Atom *atom) {m_ChiralAtoms.insert (atom);}

        bool AtomIsChiral (Atom *atom) const;

private:
        std::list< Fragment * > m_Fragments;
        std::set < Atom * > m_ChiralAtoms;
        gcu::Object *m_Alignment;
        bool m_IsResidue;
};

}       //      namespace gcp

#endif // GCHEMPAINT_MOLECULE_H