ECCE @ EIC Software
Reference for
ECCE @ EIC
simulation and reconstruction software on GitHub
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#include <geant4/tree/geant4-10.6-release/examples/extended/medical/dna/pdb4dna/include/PDBatom.hh>
Public Member Functions | |
Atom (int serial, const std::string &name, const std::string &resName, int numInRes, int resSeq, double xInit, double yInit, double zInit, double radius, double occupancy, double tempFactor, const std::string &element) | |
constructor with initialization | |
~Atom () | |
Empty destructor. | |
Atom * | GetNext () |
Returns the next Atom. | |
double | GetX () |
Return the X position for the Atom. | |
double | GetY () |
Return the Y position for the Atom. | |
double | GetZ () |
Return the Z position for the Atom. | |
int | GetID () |
Return the Atom's ID. | |
const std::string & | GetName () |
Return name of the atom. | |
const std::string & | GetElementName () |
Return name of the element. | |
double | GetVanDerWaalsRadius () |
Return name of the atom. | |
void | SetNext (Atom *) |
Set the next atom. | |
Public Attributes | |
int | fSerial |
its serial number | |
int | fNumInRes |
its number in residue sequence | |
std::string | fName |
Atom name. | |
std::string | fResName |
Residue name. | |
int | fResSeq |
Residue sequence number. | |
double | fX |
X orthogonal coordinates in Angstroms. | |
double | fY |
Y orthogonal coordinates in Angstroms. | |
double | fZ |
Z orthogonal coordinates in Angstroms. | |
double | fVdwRadius |
double | fOccupancy |
Occupancy for the Atom. | |
std::string | fElement |
Element symbol extracted from 'atom name'. | |
double | fTempFactor |
Temperature factor for the Atom. | |
Private Attributes | |
Atom * | fpNext |
Pointer to the next Atom. | |
Atom Class.
This Class define Atom model ...
Definition at line 55 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 55 of file PDBatom.hh
Atom::Atom | ( | int | serial, |
const std::string & | name, | ||
const std::string & | resName, | ||
int | numInRes, | ||
int | resSeq, | ||
double | xInit, | ||
double | yInit, | ||
double | zInit, | ||
double | radius, | ||
double | occupancy, | ||
double | tempFactor, | ||
const std::string & | element | ||
) |
constructor with initialization
< Atom name
< Residue name
< Residue sequence number
< occupancy
Definition at line 43 of file PDBatom.cc.
View newest version in sPHENIX GitHub at line 43 of file PDBatom.cc
References e, fElement, fName, fNumInRes, fOccupancy, fpNext, fResName, fResSeq, fSerial, fTempFactor, fVdwRadius, fX, fY, fZ, n, and radius.
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inline |
Empty destructor.
Definition at line 73 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 73 of file PDBatom.hh
const std::string & Atom::GetElementName | ( | ) |
Return name of the element.
Definition at line 108 of file PDBatom.cc.
View newest version in sPHENIX GitHub 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.
View newest version in sPHENIX GitHub at line 94 of file PDBatom.cc
References fSerial.
const std::string & Atom::GetName | ( | void | ) |
Return name of the atom.
Definition at line 101 of file PDBatom.cc.
View newest version in sPHENIX GitHub at line 101 of file PDBatom.cc
References fName.
Atom * Atom::GetNext | ( | ) |
Returns the next Atom.
Definition at line 66 of file PDBatom.cc.
View newest version in sPHENIX GitHub at line 66 of file PDBatom.cc
References fpNext.
Referenced by DetectorConstruction::AtomisticView(), PDBlib::ComputeMatchEdepDNA(), and PDBlib::ComputeNucleotideBarycenters().
double Atom::GetVanDerWaalsRadius | ( | ) |
Return name of the atom.
Definition at line 115 of file PDBatom.cc.
View newest version in sPHENIX GitHub 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.
View newest version in sPHENIX GitHub at line 73 of file PDBatom.cc
References fX.
Referenced by PDBlib::ComputeMatchEdepDNA().
double Atom::GetY | ( | ) |
Return the Y position for the Atom.
Definition at line 80 of file PDBatom.cc.
View newest version in sPHENIX GitHub at line 80 of file PDBatom.cc
References fY.
Referenced by PDBlib::ComputeMatchEdepDNA().
double Atom::GetZ | ( | ) |
Return the Z position for the Atom.
Definition at line 87 of file PDBatom.cc.
View newest version in sPHENIX GitHub at line 87 of file PDBatom.cc
References fZ.
Referenced by PDBlib::ComputeMatchEdepDNA().
Set the next atom.
Definition at line 122 of file PDBatom.cc.
View newest version in sPHENIX GitHub at line 122 of file PDBatom.cc
References fpNext.
Referenced by PDBlib::Load().
std::string Atom::fElement |
Element symbol extracted from 'atom name'.
Definition at line 106 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 106 of file PDBatom.hh
Referenced by Atom(), DetectorConstruction::AtomisticView(), PDBlib::ComputeNucleotideBarycenters(), and GetElementName().
std::string Atom::fName |
Atom name.
Definition at line 98 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 98 of file PDBatom.hh
int Atom::fNumInRes |
its number in residue sequence
Definition at line 97 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 97 of file PDBatom.hh
Referenced by Atom(), and PDBlib::Load().
double Atom::fOccupancy |
Occupancy for the Atom.
Definition at line 105 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 105 of file PDBatom.hh
Referenced by Atom().
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private |
Pointer to the next Atom.
Definition at line 110 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 110 of file PDBatom.hh
std::string Atom::fResName |
Residue name.
Definition at line 99 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 99 of file PDBatom.hh
Referenced by Atom().
int Atom::fResSeq |
Residue sequence number.
Definition at line 100 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 100 of file PDBatom.hh
Referenced by Atom().
int Atom::fSerial |
its serial number
Definition at line 96 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 96 of file PDBatom.hh
double Atom::fTempFactor |
Temperature factor for the Atom.
Definition at line 107 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 107 of file PDBatom.hh
Referenced by Atom().
double Atom::fVdwRadius |
Definition at line 104 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 104 of file PDBatom.hh
Referenced by Atom(), and GetVanDerWaalsRadius().
double Atom::fX |
X orthogonal coordinates in Angstroms.
Definition at line 101 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 101 of file PDBatom.hh
Referenced by Atom(), DetectorConstruction::AtomisticView(), PDBlib::ComputeNucleotideBarycenters(), and GetX().
double Atom::fY |
Y orthogonal coordinates in Angstroms.
Definition at line 102 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 102 of file PDBatom.hh
Referenced by Atom(), DetectorConstruction::AtomisticView(), PDBlib::ComputeNucleotideBarycenters(), and GetY().
double Atom::fZ |
Z orthogonal coordinates in Angstroms.
Definition at line 103 of file PDBatom.hh.
View newest version in sPHENIX GitHub at line 103 of file PDBatom.hh
Referenced by Atom(), DetectorConstruction::AtomisticView(), PDBlib::ComputeNucleotideBarycenters(), and GetZ().