Geant4  10.02.p01
PDBatom.cc
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26 // This example is provided by the Geant4-DNA collaboration
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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 // $Id$
36 //
39 
40 #include "PDBatom.hh"
41 
42 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
43 
44 Atom::Atom(int s,string n,string rN,int numInRes,int rS,
45  double xInit,double yInit,double zInit,
46  double radius,
47  double o, double tF, string e)
48 {
49  fSerial=s;
50  fName=n;
51  fResName=rN;
52  fNumInRes=numInRes;
53  fResSeq=rS;
54  fX=xInit;
55  fY=yInit;
56  fZ=zInit;
57  fVdwRadius=radius;
58  fOccupancy=o;
59  fTempFactor=tF;
60  fElement=e;
61  fpNext=0;
62 }
63 
64 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
65 
67 {
68  return fpNext;
69 }
70 
71 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
72 
73 double Atom::GetX()
74 {
75  return fX;
76 }
77 
78 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
79 
80 double Atom::GetY()
81 {
82  return fY;
83 }
84 
85 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
86 
87 double Atom::GetZ()
88 {
89  return fZ;
90 }
91 
92 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
93 
95 {
96  return fSerial;
97 }
98 
99 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
100 
102 {
103  return fName;
104 }
105 
106 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
107 
109 {
110  return fElement;
111 }
112 
113 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
114 
116 {
117  return fVdwRadius;
118 }
119 
120 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
121 
122 void Atom::SetNext(Atom *AtomNext)
123 {
124  fpNext=AtomNext;
125 }
string GetName()
Return name of the atom.
Definition: PDBatom.cc:101
string fResName
Residue name.
Definition: PDBatom.hh:92
int fSerial
its serial number
Definition: PDBatom.hh:89
double GetVanDerWaalsRadius()
Return name of the atom.
Definition: PDBatom.cc:115
double fZ
Z orthogonal coordinates in Angstroms.
Definition: PDBatom.hh:96
double GetX()
Return the X position for the Atom.
Definition: PDBatom.cc:73
void SetNext(Atom *)
Set the next atom.
Definition: PDBatom.cc:122
static const double s
Definition: G4SIunits.hh:168
int fNumInRes
its number in residue sequence
Definition: PDBatom.hh:90
double GetZ()
Return the Z position for the Atom.
Definition: PDBatom.cc:87
Atom Class.
Definition: PDBatom.hh:57
string fName
Atom name.
Definition: PDBatom.hh:91
string fElement
Element symbol extracted from 'atom name'.
Definition: PDBatom.hh:99
Atom(int serial, string name, string resName, int numInRes, int resSeq, double xInit, double yInit, double zInit, double radius, double occupancy, double tempFactor, string element)
constructor with initialization
Definition: PDBatom.cc:44
const G4int n
int fResSeq
Residue sequence number.
Definition: PDBatom.hh:93
double fVdwRadius
Definition: PDBatom.hh:97
double fTempFactor
Temperature factor for the Atom.
Definition: PDBatom.hh:100
double fOccupancy
Occupancy for the Atom.
Definition: PDBatom.hh:98
double fX
X orthogonal coordinates in Angstroms.
Definition: PDBatom.hh:94
Atom * GetNext()
Returns the next Atom.
Definition: PDBatom.cc:66
Definition of the Atom class.
double fY
Y orthogonal coordinates in Angstroms.
Definition: PDBatom.hh:95
string GetElementName()
Return name of the element.
Definition: PDBatom.cc:108
int GetID()
Return the Atom's ID.
Definition: PDBatom.cc:94
Atom * fpNext
Pointer to the next Atom.
Definition: PDBatom.hh:103
double GetY()
Return the Y position for the Atom.
Definition: PDBatom.cc:80