#include <PDBatom.hh>

Collaboration diagram for Atom:

Public Member Functions
	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 More...

	~Atom ()
	Empty destructor. More...

Atom *	GetNext ()
	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...

const std::string &	GetName ()
	Return name of the atom. More...

const std::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...

std::string	fName
	Atom name. More...

std::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...

std::string	fElement
	Element symbol extracted from 'atom name'. More...

double	fTempFactor
	Temperature factor for the Atom. More...

Private Attributes
Atom *	fpNext
	Pointer to the next Atom. More...

Detailed Description

Atom Class.

This Class define Atom model ...

Definition at line 56 of file PDBatom.hh.

Constructor & Destructor Documentation

Atom::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

< 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 74 of file PDBatom.hh.

Member Function Documentation

const std::string & Atom::GetElementName ( )

Return name of the element.

Definition at line 109 of file PDBatom.cc.

References fElement.

int Atom::GetID ( )

Return the Atom's ID.

Definition at line 95 of file PDBatom.cc.

References fSerial.

const std::string & Atom::GetName ( void )

Return name of the atom.

Definition at line 102 of file PDBatom.cc.

References fName.

Atom * Atom::GetNext ( )

Returns the next Atom.

Definition at line 67 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 116 of file PDBatom.cc.

References fVdwRadius.

double Atom::GetX ( )

Return the X position for the Atom.

Definition at line 74 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 81 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 88 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 123 of file PDBatom.cc.

References fpNext.

Referenced by PDBlib::Load().

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Member Data Documentation

std::string Atom::fElement

Element symbol extracted from 'atom name'.

Definition at line 107 of file PDBatom.hh.

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

std::string Atom::fName

Atom name.

Definition at line 99 of file PDBatom.hh.

Referenced by Atom(), and GetName().

int Atom::fNumInRes

its number in residue sequence

Definition at line 98 of file PDBatom.hh.

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

double Atom::fOccupancy

Occupancy for the Atom.

Definition at line 106 of file PDBatom.hh.

Referenced by Atom().

Atom* Atom::fpNext

private

Pointer to the next Atom.

Definition at line 111 of file PDBatom.hh.

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

std::string Atom::fResName

Residue name.

Definition at line 100 of file PDBatom.hh.

Referenced by Atom().

int Atom::fResSeq

Residue sequence number.

Definition at line 101 of file PDBatom.hh.

Referenced by Atom().

int Atom::fSerial

its serial number

Definition at line 97 of file PDBatom.hh.

Referenced by Atom(), and GetID().

double Atom::fTempFactor

Temperature factor for the Atom.

Definition at line 108 of file PDBatom.hh.

Referenced by Atom().

double Atom::fVdwRadius

Definition at line 105 of file PDBatom.hh.

Referenced by Atom(), and GetVanDerWaalsRadius().

double Atom::fX

X orthogonal coordinates in Angstroms.

Definition at line 102 of file PDBatom.hh.

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

double Atom::fY

Y orthogonal coordinates in Angstroms.

Definition at line 103 of file PDBatom.hh.

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

double Atom::fZ

Z orthogonal coordinates in Angstroms.

Definition at line 104 of file PDBatom.hh.

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

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

geant4.10.03/examples/extended/medical/dna/pdb4dna/include/PDBatom.hh
geant4.10.03/examples/extended/medical/dna/pdb4dna/src/PDBatom.cc

Public Member Functions

Public Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation