Geant4  10.02.p02
Atom Class Reference

Atom Class. More...

#include <PDBatom.hh>

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Public Member Functions

 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 More...
 
 ~Atom ()
 Empty destructor. More...
 
AtomGetNext ()
 Returns the next Atom. More...
 
double GetX ()
 Return the X position for the Atom. More...
 
double GetY ()
 Return the Y position for the Atom. More...
 
double GetZ ()
 Return the Z position for the Atom. More...
 
int GetID ()
 Return the Atom's ID. More...
 
string GetName ()
 Return name of the atom. More...
 
string GetElementName ()
 Return name of the element. More...
 
double GetVanDerWaalsRadius ()
 Return name of the atom. More...
 
void SetNext (Atom *)
 Set the next atom. More...
 

Public Attributes

int fSerial
 its serial number More...
 
int fNumInRes
 its number in residue sequence More...
 
string fName
 Atom name. More...
 
string fResName
 Residue name. More...
 
int fResSeq
 Residue sequence number. More...
 
double fX
 X orthogonal coordinates in Angstroms. More...
 
double fY
 Y orthogonal coordinates in Angstroms. More...
 
double fZ
 Z orthogonal coordinates in Angstroms. More...
 
double fVdwRadius
 
double fOccupancy
 Occupancy for the Atom. More...
 
string fElement
 Element symbol extracted from 'atom name'. More...
 
double fTempFactor
 Temperature factor for the Atom. More...
 

Private Attributes

AtomfpNext
 Pointer to the next Atom. More...
 

Detailed Description

Atom Class.

This Class define Atom model ...

Definition at line 57 of file PDBatom.hh.

Constructor & Destructor Documentation

Atom::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

< Atom name

< Residue name

< Residue sequence number

< occupancy

Definition at line 44 of file PDBatom.cc.

References fElement, fName, fNumInRes, fOccupancy, fpNext, fResName, fResSeq, fSerial, fTempFactor, fVdwRadius, fX, fY, fZ, n, and s.

Atom::~Atom ( )
inline

Empty destructor.

Definition at line 66 of file PDBatom.hh.

Member Function Documentation

string Atom::GetElementName ( )

Return name of the element.

Definition at line 108 of file PDBatom.cc.

References fElement.

int Atom::GetID ( )

Return the Atom's ID.

Definition at line 94 of file PDBatom.cc.

References fSerial.

string Atom::GetName ( void  )

Return name of the atom.

Definition at line 101 of file PDBatom.cc.

References fName.

Atom * Atom::GetNext ( )

Returns the next Atom.

Definition at line 66 of file PDBatom.cc.

References fpNext.

Referenced by DetectorConstruction::AtomisticView(), PDBlib::ComputeMatchEdepDNA(), and PDBlib::ComputeNucleotideBarycenters().

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double Atom::GetVanDerWaalsRadius ( )

Return name of the atom.

Definition at line 115 of file PDBatom.cc.

References fVdwRadius.

double Atom::GetX ( )

Return the X position for the Atom.

Definition at line 73 of file PDBatom.cc.

References fX.

Referenced by PDBlib::ComputeMatchEdepDNA().

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double Atom::GetY ( )

Return the Y position for the Atom.

Definition at line 80 of file PDBatom.cc.

References fY.

Referenced by PDBlib::ComputeMatchEdepDNA().

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double Atom::GetZ ( )

Return the Z position for the Atom.

Definition at line 87 of file PDBatom.cc.

References fZ.

Referenced by PDBlib::ComputeMatchEdepDNA().

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void Atom::SetNext ( Atom AtomNext)

Set the next atom.

Definition at line 122 of file PDBatom.cc.

References fpNext.

Referenced by PDBlib::Load().

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Member Data Documentation

string Atom::fElement

Element symbol extracted from 'atom name'.

Definition at line 99 of file PDBatom.hh.

Referenced by Atom(), DetectorConstruction::AtomisticView(), PDBlib::ComputeNucleotideBarycenters(), and GetElementName().

string Atom::fName

Atom name.

Definition at line 91 of file PDBatom.hh.

Referenced by Atom(), and GetName().

int Atom::fNumInRes

its number in residue sequence

Definition at line 90 of file PDBatom.hh.

Referenced by Atom(), and PDBlib::Load().

double Atom::fOccupancy

Occupancy for the Atom.

Definition at line 98 of file PDBatom.hh.

Referenced by Atom().

Atom* Atom::fpNext
private

Pointer to the next Atom.

Definition at line 103 of file PDBatom.hh.

Referenced by Atom(), GetNext(), and SetNext().

string Atom::fResName

Residue name.

Definition at line 92 of file PDBatom.hh.

Referenced by Atom().

int Atom::fResSeq

Residue sequence number.

Definition at line 93 of file PDBatom.hh.

Referenced by Atom().

int Atom::fSerial

its serial number

Definition at line 89 of file PDBatom.hh.

Referenced by Atom(), and GetID().

double Atom::fTempFactor

Temperature factor for the Atom.

Definition at line 100 of file PDBatom.hh.

Referenced by Atom().

double Atom::fVdwRadius

Definition at line 97 of file PDBatom.hh.

Referenced by Atom(), and GetVanDerWaalsRadius().

double Atom::fX

X orthogonal coordinates in Angstroms.

Definition at line 94 of file PDBatom.hh.

Referenced by Atom(), DetectorConstruction::AtomisticView(), PDBlib::ComputeNucleotideBarycenters(), and GetX().

double Atom::fY

Y orthogonal coordinates in Angstroms.

Definition at line 95 of file PDBatom.hh.

Referenced by Atom(), DetectorConstruction::AtomisticView(), PDBlib::ComputeNucleotideBarycenters(), and GetY().

double Atom::fZ

Z orthogonal coordinates in Angstroms.

Definition at line 96 of file PDBatom.hh.

Referenced by Atom(), DetectorConstruction::AtomisticView(), PDBlib::ComputeNucleotideBarycenters(), and GetZ().


The documentation for this class was generated from the following files: