Geant4  10.03.p03
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
PDBatom.hh
Go to the documentation of this file.
1 //
2 // ********************************************************************
3 // * License and Disclaimer *
4 // * *
5 // * The Geant4 software is copyright of the Copyright Holders of *
6 // * the Geant4 Collaboration. It is provided under the terms and *
7 // * conditions of the Geant4 Software License, included in the file *
8 // * LICENSE and available at http://cern.ch/geant4/license . These *
9 // * include a list of copyright holders. *
10 // * *
11 // * Neither the authors of this software system, nor their employing *
12 // * institutes,nor the agencies providing financial support for this *
13 // * work make any representation or warranty, express or implied, *
14 // * regarding this software system or assume any liability for its *
15 // * use. Please see the license in the file LICENSE and URL above *
16 // * for the full disclaimer and the limitation of liability. *
17 // * *
18 // * This code implementation is the result of the scientific and *
19 // * technical work of the GEANT4 collaboration. *
20 // * By using, copying, modifying or distributing the software (or *
21 // * any work based on the software) you agree to acknowledge its *
22 // * use in resulting scientific publications, and indicate your *
23 // * acceptance of all terms of the Geant4 Software license. *
24 // ********************************************************************
25 //
26 // This example is provided by the Geant4-DNA collaboration
27 // Any report or published results obtained using the Geant4-DNA software
28 // shall cite the following Geant4-DNA collaboration publication:
29 // Med. Phys. 37 (2010) 4692-4708
30 // Delage et al. PDB4DNA: implementation of DNA geometry from the Protein Data
31 // Bank (PDB) description for Geant4-DNA Monte-Carlo
32 // simulations (submitted to Comput. Phys. Commun.)
33 // The Geant4-DNA web site is available at http://geant4-dna.org
34 //
35 // --------------------------------------------------------------
36 // Authors: E. Delage
37 // november 2013
38 // --------------------------------------------------------------
39 //
40 // $Id$
41 //
44 
45 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
46 
47 #ifndef ATOM_H
48 #define ATOM_H
49 
50 #include <string>
51 
53 
56 class Atom
57 {
58 public:
60  Atom(int serial,
61  const std::string& name,
62  const std::string& resName,
63  int numInRes,
64  int resSeq,
65  double xInit,
66  double yInit,
67  double zInit,
68  double radius,
69  double occupancy,
70  double tempFactor,
71  const std::string& element);
72 
75  {
76  };
77 
79  Atom *GetNext();
81  double GetX();
83  double GetY();
85  double GetZ();
87  int GetID();
89  const std::string& GetName();
91  const std::string& GetElementName();
93  double GetVanDerWaalsRadius();
95  void SetNext(Atom *);
96 
97  int fSerial;
98  int fNumInRes;
99  std::string fName;
100  std::string fResName;
101  int fResSeq;
102  double fX;
103  double fY;
104  double fZ;
105  double fVdwRadius; // Vand der Waals Radius in Angstrom
106  double fOccupancy;
107  std::string fElement;
108  double fTempFactor;
109 
110 private:
111  Atom * fpNext;
112 };
113 #endif
114 
115 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
std::string fResName
Residue name.
Definition: PDBatom.hh:100
Atom(int serial, const std::string &name, const std::string &resName, int numInRes, int resSeq, double xInit, double yInit, double zInit, double radius, double occupancy, double tempFactor, const std::string &element)
constructor with initialization
Definition: PDBatom.cc:44
const XML_Char * name
Definition: expat.h:151
const std::string & GetName()
Return name of the atom.
Definition: PDBatom.cc:102
~Atom()
Empty destructor.
Definition: PDBatom.hh:74
int fSerial
its serial number
Definition: PDBatom.hh:97
double GetVanDerWaalsRadius()
Return name of the atom.
Definition: PDBatom.cc:116
double fZ
Z orthogonal coordinates in Angstroms.
Definition: PDBatom.hh:104
double GetX()
Return the X position for the Atom.
Definition: PDBatom.cc:74
void SetNext(Atom *)
Set the next atom.
Definition: PDBatom.cc:123
std::string fName
Atom name.
Definition: PDBatom.hh:99
int fNumInRes
its number in residue sequence
Definition: PDBatom.hh:98
double GetZ()
Return the Z position for the Atom.
Definition: PDBatom.cc:88
Atom Class.
Definition: PDBatom.hh:56
int fResSeq
Residue sequence number.
Definition: PDBatom.hh:101
double fVdwRadius
Definition: PDBatom.hh:105
double fTempFactor
Temperature factor for the Atom.
Definition: PDBatom.hh:108
double fOccupancy
Occupancy for the Atom.
Definition: PDBatom.hh:106
double fX
X orthogonal coordinates in Angstroms.
Definition: PDBatom.hh:102
Atom * GetNext()
Returns the next Atom.
Definition: PDBatom.cc:67
double fY
Y orthogonal coordinates in Angstroms.
Definition: PDBatom.hh:103
const std::string & GetElementName()
Return name of the element.
Definition: PDBatom.cc:109
std::string fElement
Element symbol extracted from &#39;atom name&#39;.
Definition: PDBatom.hh:107
int GetID()
Return the Atom&#39;s ID.
Definition: PDBatom.cc:95
double GetY()
Return the Y position for the Atom.
Definition: PDBatom.cc:81