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

/**********************************************************************
  Protein - Protein class

  Copyright (C) 2009 Tim Vandermeersch

  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 PROTEIN_H
#define PROTEIN_H

#include <avogadro/global.h>

#include <QObject>
#include <QVector>

namespace Avogadro {

  class Atom;
  class Residue;
  class Molecule;

  class ProteinPrivate;
  class A_EXPORT Protein : public QObject
  {
    Q_OBJECT

    public:
      Protein(Molecule *molecule);
      virtual ~Protein();



      const QVector<QVector<Residue*> >& chains() const;
      int numChains() const;
      QList<unsigned long> chainAtoms(int index) const;
      QList<unsigned long> chainResidues(int index) const;



      QByteArray secondaryStructure() const;
      bool isHelix(Residue *residue) const;
      bool isSheet(Residue *residue) const;

    private:
      bool extractFromPDB();
      
      void sortResiduesByChain();
      void iterateForward(Atom *prevCA, Atom *currN, QVector<bool> &visited);
      void iterateBackward(Atom *prevN, Atom *currCA, QVector<bool> &visited);

      void detectHBonds();

      void detectStructure();
      void extendHelix(char c, int turn, Residue *residue, const QVector<Residue*> &residues);
      void extendSheet(int delta, Residue *residue, const QVector<Residue*> &residues);
      void clearShortPatterns();
      void clearShortPatterns(char c, int min);

      int residueIndex(Residue *residue) const;

      int numHelixes(char c) const;
      QList<unsigned long> helixBackboneAtoms(char c, int index);

      ProteinPrivate * const d;
  };

} // End namespace Avogadro

#endif