PDBlib Class. More...

#include <geant4/tree/geant4-10.6-release/examples/extended/medical/dna/pdb4dna/include/PDBlib.hh>

Public Member Functions
	PDBlib ()
	First constructor.

	~PDBlib ()
	Destructor.

Molecule *	Load (const std::string &filename, unsigned short int &isDNA, unsigned short int verbose)
	Load PDB file into memory.

Barycenter *	ComputeNucleotideBarycenters (Molecule *moleculeListTemp)
	Compute nucleotide barycenter from memory.

void	ComputeBoundingVolumeParams (Molecule *moleculeListTemp, double &dX, double &dY, double &dZ, double &tX, double &tY, double &tZ)
	Compute the corresponding bounding volume parameters.

void	ComputeNbNucleotidsPerStrand (Molecule *moleculeListTemp)
	Compute number of nucleotide per strand.

unsigned short int	ComputeMatchEdepDNA (Barycenter , Molecule , double x, double y, double z, int &numStrand, int &numNucleotid, int &codeResidue)
	Compute if energy is deposited in per atom.

Private Member Functions
double	DistanceTwo3Dpoints (double xA, double xB, double yA, double yB, double zA, double zB)
	return distance between two 3D points

Private Attributes
int	fNbNucleotidsPerStrand
	Number of nucleotid per strand.

Detailed Description

PDBlib Class.

This Class define Molecule model ...

Definition at line 56 of file PDBlib.hh.

View newest version in sPHENIX GitHub at line 56 of file PDBlib.hh

Constructor & Destructor Documentation

PDBlib::PDBlib ( )

First constructor.

Definition at line 65 of file PDBlib.cc.

View newest version in sPHENIX GitHub at line 65 of file PDBlib.cc

PDBlib::~PDBlib ( )

inline

Destructor.

Definition at line 62 of file PDBlib.hh.

View newest version in sPHENIX GitHub at line 62 of file PDBlib.hh

Member Function Documentation

void PDBlib::ComputeBoundingVolumeParams	(	Molecule *	moleculeListTemp,
		double &	dX,
		double &	dY,
		double &	dZ,
		double &	tX,
		double &	tY,
		double &	tZ
	)

Compute the corresponding bounding volume parameters.

the corresponding bounding volume parameters

the corresponding bounding volume parameters to build a box from atoms coordinates

Definition at line 661 of file PDBlib.cc.

View newest version in sPHENIX GitHub at line 661 of file PDBlib.cc

References DBL_MAX, Molecule::fMaxGlobX, Molecule::fMaxGlobY, Molecule::fMaxGlobZ, Molecule::fMinGlobX, Molecule::fMinGlobY, Molecule::fMinGlobZ, and Molecule::GetNext().

Referenced by DetectorConstruction::DrawBoundingVolume().

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unsigned short int PDBlib::ComputeMatchEdepDNA	(	Barycenter *	BarycenterList,
		Molecule *	moleculeListTemp,
		double	x,
		double	y,
		double	z,
		int &	numStrand,
		int &	numNucleotid,
		int &	codeResidue
	)

Compute if energy is deposited in per atom.

Compute barycenters.

Compute barycenters and its coordinate for nucleotides

Definition at line 759 of file PDBlib.cc.

View newest version in sPHENIX GitHub at line 759 of file PDBlib.cc

References DistanceTwo3Dpoints(), Barycenter::fCenterX, Barycenter::fCenterY, Barycenter::fCenterZ, Residue::fNbAtom, fNbNucleotidsPerStrand, Residue::fResName, Residue::fResSeq, Residue::GetFirst(), Molecule::GetFirst(), Barycenter::GetNext(), Molecule::GetNext(), Residue::GetNext(), Atom::GetNext(), Atom::GetX(), Atom::GetY(), Atom::GetZ(), INT_MAX, k, y, and z.

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void PDBlib::ComputeNbNucleotidsPerStrand ( Molecule * moleculeListTemp )

Compute number of nucleotide per strand.

Compute number of nucleotide per strand for DNA

Definition at line 725 of file PDBlib.cc.

View newest version in sPHENIX GitHub at line 725 of file PDBlib.cc

References fNbNucleotidsPerStrand, Molecule::GetFirst(), Molecule::GetNext(), Residue::GetNext(), and k.

Referenced by DetectorConstruction::DefineVolumes().

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Barycenter * PDBlib::ComputeNucleotideBarycenters ( Molecule * moleculeListTemp )

Compute nucleotide barycenter from memory.

Compute barycenters.

Compute barycenters and its coordinate for nucleotides

Parameters

moleculeListTemp * moleculeList

Returns: Barycenter *

molecs->push_back(*moleculeListTemp);

Definition at line 451 of file PDBlib.cc.

View newest version in sPHENIX GitHub at line 451 of file PDBlib.cc

References DistanceTwo3Dpoints(), Barycenter::fCenterX, Barycenter::fCenterY, Barycenter::fCenterZ, Atom::fElement, Residue::fNbAtom, Residue::fResSeq, Atom::fX, Atom::fY, Atom::fZ, Residue::GetFirst(), Molecule::GetFirst(), Molecule::GetNext(), Residue::GetNext(), Atom::GetNext(), k, max, Barycenter::SetDistance(), Barycenter::SetNext(), and Barycenter::SetRadius().

Referenced by DetectorConstruction::DefineVolumes().

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double PDBlib::DistanceTwo3Dpoints	(	double	xA,
		double	xB,
		double	yA,
		double	yB,
		double	zA,
		double	zB
	)

private

return distance between two 3D points

Definition at line 883 of file PDBlib.cc.

View newest version in sPHENIX GitHub at line 883 of file PDBlib.cc

Referenced by ComputeMatchEdepDNA(), and ComputeNucleotideBarycenters().

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Molecule * PDBlib::Load	(	const std::string &	filename,
		unsigned short int &	isDNA,
		unsigned short int	verbose = `0`
	)

Load PDB file into memory.

Load a PDB file into memory.

molecule (polymer,?), read line, key words

Parameters

filename	G4String for filename
isDNA
verbose

Returns: List of molecules

Definition at line 82 of file PDBlib.cc.

View newest version in sPHENIX GitHub at line 82 of file PDBlib.cc

References compare(), DBL_MAX, g4zmq::exit(), FatalException, Molecule::fCenterX, Molecule::fCenterY, Molecule::fCenterZ, INPUTHEPMC::filename, Molecule::fMaxGlobX, Molecule::fMaxGlobY, Molecule::fMaxGlobZ, Molecule::fMinGlobX, Molecule::fMinGlobY, Molecule::fMinGlobZ, Residue::fNbAtom, Molecule::fNbResidue, Atom::fNumInRes, G4cerr, G4cout, G4endl, G4Exception(), int(), INT_MAX, maxY, maxZ, minY, Residue::SetFirst(), Molecule::SetFirst(), Molecule::SetNext(), Residue::SetNext(), Atom::SetNext(), x, y, and z.

Referenced by DetectorConstruction::DefineVolumes().

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Member Data Documentation

int PDBlib::fNbNucleotidsPerStrand

private

Number of nucleotid per strand.

Definition at line 95 of file PDBlib.hh.

View newest version in sPHENIX GitHub at line 95 of file PDBlib.hh

Referenced by ComputeMatchEdepDNA(), and ComputeNbNucleotidsPerStrand().

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

geant4/tree/geant4-10.6-release/examples/extended/medical/dna/pdb4dna/include/PDBlib.hh
geant4/tree/geant4-10.6-release/examples/extended/medical/dna/pdb4dna/src/PDBlib.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation