pdb4dna/include/PDBatom.hh

0001 //
0002 // ********************************************************************
0003 // * License and Disclaimer                                           *
0004 // *                                                                  *
0005 // * The  Geant4 software  is  copyright of the Copyright Holders  of *
0006 // * the Geant4 Collaboration.  It is provided  under  the terms  and *
0007 // * conditions of the Geant4 Software License,  included in the file *
0008 // * LICENSE and available at  http://cern.ch/geant4/license .  These *
0009 // * include a list of copyright holders.                             *
0010 // *                                                                  *
0011 // * Neither the authors of this software system, nor their employing *
0012 // * institutes,nor the agencies providing financial support for this *
0013 // * work  make  any representation or  warranty, express or implied, *
0014 // * regarding  this  software system or assume any liability for its *
0015 // * use.  Please see the license in the file  LICENSE  and URL above *
0016 // * for the full disclaimer and the limitation of liability.         *
0017 // *                                                                  *
0018 // * This  code  implementation is the result of  the  scientific and *
0019 // * technical work of the GEANT4 collaboration.                      *
0020 // * By using,  copying,  modifying or  distributing the software (or *
0021 // * any work based  on the software)  you  agree  to acknowledge its *
0022 // * use  in  resulting  scientific  publications,  and indicate your *
0023 // * acceptance of all terms of the Geant4 Software license.          *
0024 // ********************************************************************
0025 //
0026 // This example is provided by the Geant4-DNA collaboration
0027 // Any report or published results obtained using the Geant4-DNA software
0028 // shall cite the following Geant4-DNA collaboration publication:
0029 // Med. Phys. 37 (2010) 4692-4708
0030 // Delage et al. PDB4DNA: implementation of DNA geometry from the Protein Data
0031 //                  Bank (PDB) description for Geant4-DNA Monte-Carlo
0032 //                  simulations (submitted to Comput. Phys. Commun.)
0033 // The Geant4-DNA web site is available at http://geant4-dna.org
0034 //
0035 // --------------------------------------------------------------
0036 // Authors: E. Delage
0037 // november 2013
0038 // --------------------------------------------------------------
0039 //
0040 //
0041 /// \file PDBatom.hh
0042 /// \brief Definition of the Atom class
0043
0044 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0045
0046 #ifndef ATOM_H
0047 #  define ATOM_H
0048
0049 #  include <string>
0050
0051 //! Atom Class
0052 /*!
0053  * This Class define Atom model ...
0054  */
0055 class Atom
0056 {
0057   public:
0058     //! constructor with initialization
0059     Atom(int serial, const std::string& name, const std::string& resName, int numInRes, int resSeq,
0060          double xInit, double yInit, double zInit, double radius, double occupancy,
0061          double tempFactor, const std::string& element);
0062
0063     //! Empty destructor
0064     ~Atom() {};
0065
0066     //! Returns the next Atom
0067     Atom* GetNext();
0068     //! Return the X position for the Atom
0069     double GetX();
0070     //! Return the Y position for the Atom
0071     double GetY();
0072     //! Return the Z position for the Atom
0073     double GetZ();
0074     //! Return the Atom's ID
0075     int GetID();
0076     //! Return name of the atom
0077     const std::string& GetName();
0078     //! Return name of the element
0079     const std::string& GetElementName();
0080     //! Return name of the atom
0081     double GetVanDerWaalsRadius();
0082     //! Set the next atom
0083     void SetNext(Atom*);
0084
0085     int fSerial;  //!< its serial number
0086     int fNumInRes;  //!< its number in residue sequence
0087     std::string fName;  //!< Atom name
0088     std::string fResName;  //!< Residue name
0089     int fResSeq;  //!< Residue sequence number
0090     double fX;  //!< X orthogonal coordinates in Angstroms
0091     double fY;  //!< Y orthogonal coordinates in Angstroms
0092     double fZ;  //!< Z orthogonal coordinates in Angstroms
0093     double fVdwRadius;  // Vand der Waals Radius in Angstrom
0094     double fOccupancy;  //!< Occupancy for the Atom
0095     std::string fElement;  //!< Element symbol extracted from 'atom name'
0096     double fTempFactor;  //!< Temperature factor for the Atom
0097
0098   private:
0099     Atom* fpNext;  //!< Pointer to the next Atom
0100 };
0101 #endif
0102
0103 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......