PDBstructure Class Reference

#include <pdbstruct.h>

List of all members.


Detailed Description

Definition at line 97 of file pdbstruct.h.

Public Types

typedef PDBelement TelementBase

Public Member Functions

void buildGravityCenter (double *G)
void findMinMax (double *atomMin, double *atomMax)
std::string & fragmentName (const int i)
std::string fragmentName (const int i) const
std::string getAtomName (const int i) const
PDBelementgetElement (const int i)
PDBelement getElement (const int i) const
std::string getNumberInString (const int numResiduInMolecule)
int & numberOfAtoms ()
int numberOfAtoms () const
int & numberOfFragments ()
int numberOfFragments () const
int & numberOfResidus ()
int numberOfResidus () const
 PDBstructure (const int size)
 PDBstructure ()
bool readPDBFile (std::ifstream &data)
bool setFragName (FragmentsDataBase &base, const std::string &type)
bool setFragName (FragmentsDataBase &base)
void swap (const int i, const int j)
void writePDBFileForAtoms (std::ofstream &out, std::vector< int > &index)
void writeQCIFile (std::ofstream &out)
void writeXYZFile (std::ofstream &out)
void writeXYZFileForAtoms (std::ofstream &out, std::vector< int > &index)
 ~PDBstructure ()

Protected Attributes

PDBelement_atoms
int _numberOfAtoms
int _numberOfFragments
int _numberOfResidus
int _spinMultiplicity
int _systemCharge


Member Typedef Documentation

typedef PDBelement PDBstructure::TelementBase
 

Definition at line 101 of file pdbstruct.h.


Constructor & Destructor Documentation

PDBstructure::PDBstructure  ) 
 

Definition at line 94 of file pdbstruct.cpp.

PDBstructure::PDBstructure const int  size  ) 
 

Definition at line 98 of file pdbstruct.cpp.

PDBstructure::~PDBstructure  ) 
 

Definition at line 103 of file pdbstruct.cpp.

References _atoms, _numberOfAtoms, _numberOfFragments, _numberOfResidus, _spinMultiplicity, and _systemCharge.


Member Function Documentation

void PDBstructure::buildGravityCenter double *  G  ) 
 

Definition at line 441 of file pdbstruct.cpp.

References _atoms, _numberOfAtoms, and PDBelement::_xyz.

void PDBstructure::findMinMax double *  atomMin,
double *  atomMax
 

Definition at line 427 of file pdbstruct.cpp.

References _numberOfAtoms.

Referenced by AAPartition::partitionate().

std::string& PDBstructure::fragmentName const int  i  )  [inline]
 

Definition at line 150 of file pdbstruct.h.

References _atoms, and PDBelement::_fragName.

std::string PDBstructure::fragmentName const int  i  )  const [inline]
 

Definition at line 147 of file pdbstruct.h.

References _atoms, and PDBelement::_fragName.

std::string PDBstructure::getAtomName const int  i  )  const [inline]
 

Definition at line 125 of file pdbstruct.h.

References PDBelement::_atomName, and _atoms.

Referenced by setFragName().

PDBelement& PDBstructure::getElement const int  i  )  [inline]
 

Definition at line 156 of file pdbstruct.h.

References _atoms.

PDBelement PDBstructure::getElement const int  i  )  const [inline]
 

Definition at line 153 of file pdbstruct.h.

References _atoms.

Referenced by AAPartition::setAtomsInKernel(), AAPartition::setNeigboors(), AAPartition::sortInFirstDimension(), and AAPartition::statistiques().

std::string PDBstructure::getNumberInString const int  numResiduInMolecule  ) 
 

Definition at line 273 of file pdbstruct.cpp.

Referenced by setFragName().

int& PDBstructure::numberOfAtoms  )  [inline]
 

Definition at line 132 of file pdbstruct.h.

References _numberOfAtoms.

int PDBstructure::numberOfAtoms  )  const [inline]
 

Definition at line 129 of file pdbstruct.h.

References _numberOfAtoms.

Referenced by AAPartition::attachAtoms(), AAPartition::setAtomsInKernel(), and AAPartition::sortInFirstDimension().

int& PDBstructure::numberOfFragments  )  [inline]
 

Definition at line 144 of file pdbstruct.h.

References _numberOfFragments.

int PDBstructure::numberOfFragments  )  const [inline]
 

Definition at line 141 of file pdbstruct.h.

References _numberOfFragments.

int& PDBstructure::numberOfResidus  )  [inline]
 

Definition at line 138 of file pdbstruct.h.

References _numberOfResidus.

int PDBstructure::numberOfResidus  )  const [inline]
 

Definition at line 135 of file pdbstruct.h.

References _numberOfResidus.

Referenced by main().

bool PDBstructure::readPDBFile std::ifstream &  data  ) 
 

Definition at line 111 of file pdbstruct.cpp.

References _atoms, _numberOfAtoms, _numberOfFragments, _numberOfResidus, PDBelement::numberOfResidu(), PDBelement::readAtom(), and PDBelement::readConnection().

Referenced by main().

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bool PDBstructure::setFragName FragmentsDataBase base,
const std::string &  type
 

Definition at line 286 of file pdbstruct.cpp.

References _atoms, PDBelement::_fragName, _numberOfAtoms, _numberOfFragments, _numberOfResidus, PDBelement::_residuName, AA(), PDBelement::getAtomName(), getAtomName(), FragmentsDataBase::getFragmentNameFrom(), getNumberInString(), PDBelement::getResiduName(), and FragmentsDataBase::nameOfDataBase().

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bool PDBstructure::setFragName FragmentsDataBase base  ) 
 

Definition at line 281 of file pdbstruct.cpp.

References FRAG().

Referenced by main().

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void PDBstructure::swap const int  i,
const int  j
 

Definition at line 416 of file pdbstruct.cpp.

References _atoms, _numberOfAtoms, and PDBelement::copy().

Referenced by AAPartition::sortInFirstDimension().

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void PDBstructure::writePDBFileForAtoms std::ofstream &  out,
std::vector< int > &  index
 

Definition at line 241 of file pdbstruct.cpp.

References PDBelement::_atomName, _atoms, PDBelement::_numResiduInMolecule, PDBelement::_residuName, and PDBelement::_xyz.

void PDBstructure::writeQCIFile std::ofstream &  out  ) 
 

Definition at line 178 of file pdbstruct.cpp.

References PDBelement::_atomName, _atoms, PDBelement::_connection, PDBelement::_fragName, _numberOfAtoms, _spinMultiplicity, _systemCharge, PDBelement::_xyz, and posAtomInString().

Referenced by main().

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void PDBstructure::writeXYZFile std::ofstream &  out  ) 
 

Definition at line 206 of file pdbstruct.cpp.

References PDBelement::_atomName, _atoms, _numberOfAtoms, PDBelement::_xyz, and posAtomInString().

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void PDBstructure::writeXYZFileForAtoms std::ofstream &  out,
std::vector< int > &  index
 

Definition at line 223 of file pdbstruct.cpp.

References PDBelement::_atomName, _atoms, _numberOfAtoms, PDBelement::_xyz, and posAtomInString().

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Member Data Documentation

PDBelement* PDBstructure::_atoms [protected]
 

Definition at line 171 of file pdbstruct.h.

Referenced by buildGravityCenter(), fragmentName(), getAtomName(), getElement(), readPDBFile(), setFragName(), swap(), writePDBFileForAtoms(), writeQCIFile(), writeXYZFile(), writeXYZFileForAtoms(), and ~PDBstructure().

int PDBstructure::_numberOfAtoms [protected]
 

Definition at line 168 of file pdbstruct.h.

Referenced by buildGravityCenter(), findMinMax(), numberOfAtoms(), readPDBFile(), setFragName(), swap(), writeQCIFile(), writeXYZFile(), writeXYZFileForAtoms(), and ~PDBstructure().

int PDBstructure::_numberOfFragments [protected]
 

Definition at line 170 of file pdbstruct.h.

Referenced by numberOfFragments(), readPDBFile(), setFragName(), and ~PDBstructure().

int PDBstructure::_numberOfResidus [protected]
 

Definition at line 169 of file pdbstruct.h.

Referenced by numberOfResidus(), readPDBFile(), setFragName(), and ~PDBstructure().

int PDBstructure::_spinMultiplicity [protected]
 

Definition at line 166 of file pdbstruct.h.

Referenced by writeQCIFile(), and ~PDBstructure().

int PDBstructure::_systemCharge [protected]
 

Definition at line 165 of file pdbstruct.h.

Referenced by writeQCIFile(), and ~PDBstructure().


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