#include <PDBatom.hh>

Collaboration diagram for Atom:

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...

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...

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
Atom *	fpNext
	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:

source/examples/extended/medical/dna/pdb4dna/include/PDBatom.hh
source/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