pdb4dna/include/PDBatom.hh

0001 //
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0025 //
0026 /// \file PDBatom.hh
0027 /// \brief Definition of the PDBatom class
0028
0029 // This example is provided by the Geant4-DNA collaboration
0030 // Any report or published results obtained using the Geant4-DNA software
0031 // shall cite the following Geant4-DNA collaboration publication:
0032 // Med. Phys. 37 (2010) 4692-4708
0033 // Delage et al. PDB4DNA: implementation of DNA geometry from the Protein Data
0034 //                  Bank (PDB) description for Geant4-DNA Monte-Carlo
0035 //                  simulations (submitted to Comput. Phys. Commun.)
0036 // The Geant4-DNA web site is available at http://geant4-dna.org
0037 //
0038 // --------------------------------------------------------------
0039 // Authors: E. Delage
0040 // november 2013
0041 // --------------------------------------------------------------
0042 //
0043 //
0044
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0046
0047 #ifndef ATOM_H
0048 #  define ATOM_H
0049
0050 #  include <string>
0051
0052 //! Atom Class
0053 /*!
0054  * This Class define Atom model ...
0055  */
0056 class Atom
0057 {
0058   public:
0059     //! constructor with initialization
0060     Atom(int serial, const std::string& name, const std::string& resName, int numInRes, int resSeq,
0061          double xInit, double yInit, double zInit, double radius, double occupancy,
0062          double tempFactor, const std::string& element);
0063
0064     //! Empty destructor
0065     ~Atom() {};
0066
0067     //! Returns the next Atom
0068     Atom* GetNext();
0069     //! Return the X position for the Atom
0070     double GetX();
0071     //! Return the Y position for the Atom
0072     double GetY();
0073     //! Return the Z position for the Atom
0074     double GetZ();
0075     //! Return the Atom's ID
0076     int GetID();
0077     //! Return name of the atom
0078     const std::string& GetName();
0079     //! Return name of the element
0080     const std::string& GetElementName();
0081     //! Return name of the atom
0082     double GetVanDerWaalsRadius();
0083     //! Set the next atom
0084     void SetNext(Atom*);
0085
0086     int fSerial;  //!< its serial number
0087     int fNumInRes;  //!< its number in residue sequence
0088     std::string fName;  //!< Atom name
0089     std::string fResName;  //!< Residue name
0090     int fResSeq;  //!< Residue sequence number
0091     double fX;  //!< X orthogonal coordinates in Angstroms
0092     double fY;  //!< Y orthogonal coordinates in Angstroms
0093     double fZ;  //!< Z orthogonal coordinates in Angstroms
0094     double fVdwRadius;  // Vand der Waals Radius in Angstrom
0095     double fOccupancy;  //!< Occupancy for the Atom
0096     std::string fElement;  //!< Element symbol extracted from 'atom name'
0097     double fTempFactor;  //!< Temperature factor for the Atom
0098
0099   private:
0100     Atom* fpNext;  //!< Pointer to the next Atom
0101 };
0102 #endif
0103
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