molecule.h

/***************************************************************************
                          molecule.h  -  description
                             -------------------
    author               : Armando Navarro-Vazquez
    email                : armando.deus@gmail.com
 ***************************************************************************/

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

#ifndef MAGNES_MOLECULE_H
#define MAGNES_MOLECULE_H

#include <string>
#include <vector>
#include <list>



#include "atom.h"
#include "pdbtools.h"
#include "energy.h"
#include "mathtools.h"
#include "coreexport.h"
#include "frame.h"
namespace magnes
{
typedef std::vector<size_t> Ring;
class MoleculePrivate;
class FramePrivate;

class MAGNES_CORE_API Molecule
{
public:
    Molecule();
    Molecule ( const Molecule& mol );
    Molecule& operator= ( const Molecule& mol );
    ~Molecule();
    Molecule At ( size_t frame ) const;
    const std::vector<Frame>& Frames() const;
    std::vector<Frame>& Frames();
    const Frame& CurrentFrame() const;
    Frame& CurrentFrame();
    size_t CurrentFrameIndex() const;
    void SetCurrentFrame ( size_t i ) ;
    const std::vector<Atom>& Atoms() const;
    std::vector<Atom>& Atoms() ;
    const std::vector<Bond>& Bonds() const;
    std::vector<Bond>& Bonds();
    size_t NBonds(size_t i, size_t j) const;
    const std::vector<double>& Populations() const;
    std::vector<double>& Populations();
    double Weight() const { return CalculateWeight(); }
    void MoveToCentroid();
    std::vector < std::vector<size_t> > Rings ( size_t size=0 ) const;
    std::vector< std::vector<size_t> > EssentialRings(size_t size=0 ) const;
    bool IsRingTied(const std::vector<size_t>& ring) const;
    std::vector<size_t> ShortestPath(size_t i, size_t j) const;
    std::vector<int>  FindAtomByName ( const std::string& name ) const;
    double CalculateWeight() const;
    Atom::hybridization Hybridization ( size_t atom ) const;
    void SetBonds ( bool eachframe=false );
    const std::vector<PDBResidue*>& Residues() const;
    std::vector<PDBResidue*>& Residues();
    std::list<int> Elements() const;
    std::list<std::string> ElementSymbols() const;
    std::vector<size_t> Neighbours ( size_t i ) const;
    size_t IndexFromPDB(const std::string& pdbname,const std::string& resname,const std::string& resindex) const;
    std::vector< std::vector<double> > SuperImposeMackay(size_t reframe, const std::vector<size_t>& atoms);
    std::vector< std::vector<double> > SuperImpose(size_t reframe, const std::vector<size_t>& atoms, bool massweighted=false);
    std::vector< std::vector< double > > EckartTransform(size_t reframe, const std::vector<size_t>& atoms);
    bool CheckConformersSanity() const;
    void ReparentFrames();
    const std::string& FileName() const;
    void SetFileName(const std::string& filename);
private:
    bool FindInShell(std::vector<size_t>& searched,size_t j) const;
private:
    MoleculePrivate* m_private;

};

MAGNES_CORE_API std::ostream& operator << ( std::ostream& s,const magnes::Molecule& m );
MAGNES_CORE_API bool CompareMolecules(const magnes::Molecule& mol1,const magnes::Molecule& mol2);

}


#endif // MAGNES_MOLECULE_H