pdb4dna/src/PDBatom.cc

0001 //
0002 // ********************************************************************
0003 // * License and Disclaimer                                           *
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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 /// \file PDBatom.cc
0037 /// \brief Implementation of the PDBatom class
0038
0039 #include "PDBatom.hh"
0040
0041 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0042
0043 Atom::Atom(int s, const std::string& n, const std::string& rN, int numInRes, int rS, double xInit,
0044            double yInit, double zInit, double radius, double o, double tF, const std::string& e)
0045 {
0046   fSerial = s;
0047   fName = n;  //!< Atom name
0048   fResName = rN;  //!< Residue name
0049   fNumInRes = numInRes;
0050   fResSeq = rS;  //!< Residue sequence number
0051   fX = xInit;
0052   fY = yInit;
0053   fZ = zInit;
0054   fVdwRadius = radius;
0055   fOccupancy = o;  //!< occupancy
0056   fTempFactor = tF;
0057   fElement = e;
0058   fpNext = 0;
0059 }
0060
0061 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0062
0063 Atom* Atom::GetNext()
0064 {
0065   return fpNext;
0066 }
0067
0068 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0069
0070 double Atom::GetX()
0071 {
0072   return fX;
0073 }
0074
0075 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0076
0077 double Atom::GetY()
0078 {
0079   return fY;
0080 }
0081
0082 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0083
0084 double Atom::GetZ()
0085 {
0086   return fZ;
0087 }
0088
0089 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0090
0091 int Atom::GetID()
0092 {
0093   return fSerial;
0094 }
0095
0096 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0097
0098 const std::string& Atom::GetName()
0099 {
0100   return fName;
0101 }
0102
0103 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0104
0105 const std::string& Atom::GetElementName()
0106 {
0107   return fElement;
0108 }
0109
0110 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0111
0112 double Atom::GetVanDerWaalsRadius()
0113 {
0114   return fVdwRadius;
0115 }
0116
0117 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0118
0119 void Atom::SetNext(Atom* AtomNext)
0120 {
0121   fpNext = AtomNext;
0122 }