atom.h

/***************************************************************************
                          atom.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_ATOM_H
#define MAGNES_ATOM_H


#include <string>
#include <vector>
#include <list>
#include <map>
#include "coordinate.h"
#include "coreexport.h"

namespace magnes
{
  class PDBResidue;

  class MAGNES_CORE_API Atom
  {
    public:
      class MAGNES_CORE_API IsotopeData
      {
        public:
        IsotopeData(double mass, double abundance, int mult, double lambda, double q) : _mass(mass), _abundance(abundance), _mult(mult), _lambda(lambda), _q(q) {}
        double Mass() const { return _mass; }
        double Abundance() const { return _abundance; }
        int Multiplicity() const { return _mult; }
        double MagnetoGyricRatio() const { return _lambda; }
        double Quadrupole() const { return _q; }
        private:
        double _mass;
        double _abundance;
        int _mult;
        double _lambda;
        double _q;
      };
      
      class MAGNES_CORE_API AtomData
      {
        public:

          class rgb
          {
            public:
              rgb ( int lr, int lg, int lb ) : r ( lr ) , g ( lg ) ,b ( lb ) {}
              int r; int g; int b;
          };
          AtomData ( int z, double m, double w, double r, double el, rgb c,const std::map<const int,const IsotopeData>* idata=NULL ) :
              _Z ( z ), _mass ( m ), _vdw ( w ), _cr ( r ), _Pel ( el ), _color ( c ) , _idata(idata)     {}

          int _Z;
          double _mass;
          double _vdw;
          double _cr;
          double _Pel;
          rgb _color;
          const std::map<const int, const IsotopeData>* _idata;
      };

      enum hybridization { UNKNOWN=0, SP, SP2, SP3 };
      Atom();
      ~Atom();

      Atom ( const std::string& symbol ) { SetSymbol ( symbol ); m_residue=NULL; }
      Atom ( int z ) { SetZ ( z ); m_residue=NULL; }
      double AtomicMass() const { return m_data->second._mass; }
      void Color ( float* r, float* g, float* b ) const;
      int Z() const { return m_data->second._Z; }
      double VdW() const { return m_data->second._vdw; }
      double CovalentRadius() const { return m_data->second._cr; }
      double PaulingElectronegativity() const { return m_data->second._Pel; }
      const std::string& Symbol() const { return m_data->first; }
      void SetSymbol ( const std::string& symbol );
      void SetZ ( int z );
      void SetPDBResidue(PDBResidue* r) { m_residue=r; }
      PDBResidue* Residue() { return m_residue; }
      const PDBResidue* Residue() const { return m_residue; }
      void SetPDBName(const std::string& name) { m_pdbname=name; }
      const std::string& PDBName() const { return m_pdbname; } 
      const std::pair<const int,const IsotopeData>* NMRIsotope() const;
      void SetCurrentNMRIsotope(int m);
      const std::map<const int,const IsotopeData>& NMRIsotopes() const { return *m_data->second._idata; }
      size_t MMType() const { return m_mmtype; }
      void SetMMType(size_t mmtype) { m_mmtype=mmtype; }
    private:
      double GetAtomicMass() const;
      const std::pair<const std::string,const AtomData>* m_data;
      const std::pair<const int,const IsotopeData>* m_isotope;
      PDBResidue* m_residue;
      std::string m_pdbname;
      size_t m_mmtype;

  };

  MAGNES_CORE_API typedef std::map<const std::string, const magnes::Atom::AtomData> PeriodicTable;

  MAGNES_CORE_API const PeriodicTable& GetPeriodicTable();

  MAGNES_CORE_API void BuildPeriodicTable();
  
  MAGNES_CORE_API int ZFromSymbol(const std::string& symbol);
  
   MAGNES_CORE_API std::string SymbolFromZ(int z);

   MAGNES_CORE_API const std::pair<const int,const Atom::IsotopeData>* DefaultNMRProperties(const std::string& symbol);
}

#endif // MAGNES_ATOM_H