Geant4
10.01.p02
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#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... | |
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 669 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().
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
Molecule | * moleculeList |
Definition at line 775 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.
void PDBlib::ComputeNbNucleotidsPerStrand | ( | Molecule * | moleculeListTemp | ) |
Compute number of nucleotide per strand.
Compute number of nucleotide per strand for DNA
Definition at line 739 of file PDBlib.cc.
References fNbNucleotidsPerStrand, Molecule::GetFirst(), Residue::GetNext(), and Molecule::GetNext().
Referenced by DetectorConstruction::DefineVolumes().
Barycenter * PDBlib::ComputeNucleotideBarycenters | ( | Molecule * | moleculeListTemp | ) |
Compute nucleotide barycenter from memory.
Compute barycenters.
Compute barycenters and its coordinate for nucleotides
Molecule | * moleculeList |
molecs->push_back(*moleculeListTemp);
Definition at line 481 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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private |
return distance between two 3D points
Definition at line 895 of file PDBlib.cc.
Referenced by ComputeMatchEdepDNA(), and ComputeNucleotideBarycenters().
Molecule * PDBlib::Load | ( | const string & | filename, |
unsigned short int & | isDNA, | ||
unsigned short int | verbose = 0 |
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) |
Load PDB file into memory.
Load a PDB file into memory.
molecule (polymer,?), read line, key words
filename | string for filename |
verbosity |
Definition at line 74 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(), and z.
Referenced by DetectorConstruction::DefineVolumes().
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private |
Number of nucleotid per strand.
Definition at line 97 of file PDBlib.hh.
Referenced by ComputeMatchEdepDNA(), and ComputeNbNucleotidsPerStrand().