/home/kitware/dashboards/avogadro/libavogadro/src/atom.h

/**********************************************************************
  Atom - Atom class derived from the base Primitive class

  Copyright (C) 2007 Donald Ephraim Curtis
  Copyright (c) 2008-2009 Geoff Hutchison
  Copyright (c) 2008-2009 Marcus D. Hanwell
  Copyright (c) 2010 Konstantin Tokarev

  This file is part of the Avogadro molecular editor project.
  For more information, see <http://avogadro.openmolecules.net/>

  Avogadro 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 2 of the License, or
  (at your option) any later version.

  Avogadro 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 Street, Fifth Floor, Boston, MA
  02110-1301, USA.
 **********************************************************************/

#ifndef ATOM_H
#define ATOM_H

#include <avogadro/primitive.h>
#include <QtCore/QList>

namespace OpenBabel {
  class OBAtom;
}

namespace Avogadro {

  class Molecule;
  class Bond;
  class Residue;
  class AtomPrivate;
  class A_EXPORT Atom : public Primitive
  {
  Q_OBJECT

  public:
    Atom(QObject *parent=0);

    ~Atom();

    void setPos(const Eigen::Vector3d &vec);

    void setPos(const Eigen::Vector3d *vec) { setPos(*vec); }

    void setAtomicNumber(int num);

    void setPartialCharge(double charge) const;

    void setFormalCharge(int charge);

    void setGroupIndex(unsigned int index);

    void setForceVector(const Eigen::Vector3d &force);

    void setCustomLabel(const QString &label);

    void setCustomColorName(const QString &name);

    void setCustomRadius(const double radius);
    Molecule * molecule() const { return m_molecule; }

    const Eigen::Vector3d * pos() const;

    int atomicNumber() const { return m_atomicNumber; }

    QList<unsigned long> bonds() const { return m_bonds; }

    QList<unsigned long> neighbors() const;

    Bond * bond(const Atom *other) const;

    double valence() const { return static_cast<double>(m_bonds.size()); }

    unsigned int groupIndex() const;
    
    bool isHydrogen() const { return m_atomicNumber == 1; }

    double partialCharge() const;

    int formalCharge() const;

    QString customLabel() const;

    QString customColorName() const;

    double customRadius() const;

    const Eigen::Vector3d forceVector() const;

    unsigned long residueId() const;

    Residue * residue() const;
    OpenBabel::OBAtom OBAtom();
    //const OpenBabel::OBAtom OBAtom() const;

    bool setOBAtom(OpenBabel::OBAtom *obatom);
    Atom& operator=(const Atom& other);
    friend class Molecule;
    friend class Bond;
    friend class Residue;

  protected:
    void addBond(unsigned long bond);

    void addBond(Bond* bond);

    void removeBond(Bond* bond);

    void removeBond(unsigned long bond);

    void setResidue(unsigned long id);

    void setResidue(const Residue *residue);

    AtomPrivate * const d_ptr;
    Molecule *m_molecule; 
    int m_atomicNumber;
    QList<unsigned long> m_bonds;

    Q_DECLARE_PRIVATE(Atom)
  };

} // End namespace Avoagdro

#endif