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Public Member Functions | Private Member Functions | Private Attributes | List of all members
PDBlib Class Reference

PDBlib Class. More...

#include <PDBlib.hh>

Public Member Functions

 PDBlib ()
 First constructor. More...
 
 ~PDBlib ()
 Destructor. More...
 
Molecule * Load (const string &filename, unsigned short int &isDNA, unsigned short int verbose)
 Load PDB file into memory. More...
 
Barycenter * ComputeNucleotideBarycenters (Molecule *moleculeListTemp)
 Compute nucleotide barycenter from memory. More...
 
void ComputeBoundingVolumeParams (Molecule *moleculeListTemp, double &dX, double &dY, double &dZ, double &tX, double &tY, double &tZ)
 Compute the corresponding bounding volume parameters. More...
 
void ComputeNbNucleotidsPerStrand (Molecule *moleculeListTemp)
 Compute number of nucleotide per strand. More...
 
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. More...
 

Private Member Functions

double DistanceTwo3Dpoints (double xA, double xB, double yA, double yB, double zA, double zB)
 return distance between two 3D points More...
 

Private Attributes

int fNbNucleotidsPerStrand
 Number of nucleotid per strand. More...
 

Detailed Description

PDBlib Class.

This Class define Molecule model ...

Definition at line 58 of file PDBlib.hh.

Constructor & Destructor Documentation

PDBlib::PDBlib ( )

First constructor.

Definition at line 58 of file PDBlib.cc.

PDBlib::~PDBlib ( )
inline

Destructor.

Definition at line 64 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 667 of file PDBlib.cc.

References Molecule::fMaxGlobX, Molecule::fMaxGlobY, Molecule::fMaxGlobZ, Molecule::fMinGlobX, Molecule::fMinGlobY, Molecule::fMinGlobZ, Molecule::GetNext(), G4INCL::Math::max(), and G4INCL::Math::min().

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

Parameters
Molecule* moleculeList
Returns
Barycenter *

Definition at line 772 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(), Atom::GetNext(), Residue::GetNext(), Molecule::GetNext(), Atom::GetX(), Atom::GetY(), Atom::GetZ(), G4INCL::Math::max(), 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 736 of file PDBlib.cc.

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

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
Molecule* moleculeList
Returns
Barycenter *

molecs->push_back(*moleculeListTemp);

Definition at line 480 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(), Residue::GetNext(), Atom::GetNext(), Molecule::GetNext(), G4INCL::Math::max(), Barycenter::SetDistance(), 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 892 of file PDBlib.cc.

Referenced by ComputeMatchEdepDNA(), and ComputeNucleotideBarycenters().

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Molecule * PDBlib::Load ( const 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
filenamestring for filename
verbosity
Returns
List of molecules

Definition at line 73 of file PDBlib.cc.

References Molecule::fCenterX, Molecule::fCenterY, Molecule::fCenterZ, Molecule::fMaxGlobX, Molecule::fMaxGlobY, Molecule::fMaxGlobZ, Molecule::fMinGlobX, Molecule::fMinGlobY, Molecule::fMinGlobZ, Residue::fNbAtom, Molecule::fNbResidue, Atom::fNumInRes, G4cout, G4endl, G4INCL::Math::max(), G4INCL::Math::min(), Residue::SetFirst(), Molecule::SetFirst(), Residue::SetNext(), Molecule::SetNext(), Atom::SetNext(), x, 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 97 of file PDBlib.hh.

Referenced by ComputeMatchEdepDNA(), and ComputeNbNucleotidsPerStrand().

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