#include <PDBlib.hh>
Public Member Functions | |
| PDBlib () | |
| First constructor. More... | |
| ~PDBlib () | |
| Destructor. More... | |
| Molecule * | Load (const std::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
Constructor & Destructor Documentation
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 662 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().
Here is the call graph for this function: Here is the caller graph for this function:| 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 760 of file PDBlib.cc.
References DistanceTwo3Dpoints(), Barycenter::fCenterX, Barycenter::fCenterY, Barycenter::fCenterZ, Residue::fNbAtom, fNbNucleotidsPerStrand, Residue::fResName, Residue::fResSeq, Molecule::GetFirst(), Residue::GetFirst(), Barycenter::GetNext(), Molecule::GetNext(), Residue::GetNext(), Atom::GetNext(), Atom::GetX(), Atom::GetY(), Atom::GetZ(), and INT_MAX.
Here is the call graph for this function:| void PDBlib::ComputeNbNucleotidsPerStrand | ( | Molecule * | moleculeListTemp | ) |
Compute number of nucleotide per strand.
Compute number of nucleotide per strand for DNA
Definition at line 726 of file PDBlib.cc.
References fNbNucleotidsPerStrand, Molecule::GetFirst(), Molecule::GetNext(), and Residue::GetNext().
Referenced by DetectorConstruction::DefineVolumes().
Here is the call graph for this function: Here is the caller graph for this function:| 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 452 of file PDBlib.cc.
References DistanceTwo3Dpoints(), Barycenter::fCenterX, Barycenter::fCenterY, Barycenter::fCenterZ, Atom::fElement, Residue::fNbAtom, Residue::fResSeq, Atom::fX, Atom::fY, Atom::fZ, Molecule::GetFirst(), Residue::GetFirst(), Molecule::GetNext(), Residue::GetNext(), Atom::GetNext(), G4INCL::Math::max(), Barycenter::SetDistance(), Barycenter::SetNext(), and Barycenter::SetRadius().
Referenced by DetectorConstruction::DefineVolumes().
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private |
return distance between two 3D points
Definition at line 884 of file PDBlib.cc.
Referenced by ComputeMatchEdepDNA(), and ComputeNucleotideBarycenters().
Here is the caller graph for this function:| 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 83 of file PDBlib.cc.
References DBL_MAX, FatalException, Molecule::fCenterX, Molecule::fCenterY, Molecule::fCenterZ, Molecule::fMaxGlobX, Molecule::fMaxGlobY, Molecule::fMaxGlobZ, Molecule::fMinGlobX, Molecule::fMinGlobY, Molecule::fMinGlobZ, Residue::fNbAtom, Molecule::fNbResidue, Atom::fNumInRes, G4cerr, G4cout, G4endl, G4Exception(), INT_MAX, Molecule::SetFirst(), Residue::SetFirst(), Residue::SetNext(), Molecule::SetNext(), and Atom::SetNext().
Referenced by DetectorConstruction::DefineVolumes().
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private |
Number of nucleotid per strand.
Definition at line 96 of file PDBlib.hh.
Referenced by ComputeMatchEdepDNA(), and ComputeNbNucleotidsPerStrand().
The documentation for this class was generated from the following files:
