setOfAtoms Class Reference

#include <Atoms.h>

List of all members.


Detailed Description

Definition at line 28 of file Atoms.h.

Public Types

typedef atomElement TelementBase

Public Member Functions

std::string & atomName (const int i)
void buildGravityCenter (double *G)
bool buildIinertialMatrix (double *coordG)
void copyFrom (const int beginAtom, const int EndAtom, const setOfAtoms &atoms)
void findMinMax (double *atomMin, double *atomMax)
int findNumberOfAtoms (std::ifstream &data)
void fixConnectivity (const std::vector< int > &reOrder)
std::string & fragmentName (const int i)
std::string fragmentName (const int i) const
std::string getAtomName (const int i) const
atomElementgetElement (const int i)
atomElement getElement (const int i) const
std::string getName (const int i) const
int getNumberOfAtoms () const
int getNumberOfFragments ()
int numberOfAA () const
int numberOfAtoms () const
int numberOfFragements () const
int numberOfFragments () const
bool readQCIFile (std::ifstream &data)
void readXYZFile (std::ifstream &data)
void reset ()
atomElementsetElement (const int i)
void setNumberOfAtoms (const int size)
 setOfAtoms (const int size)
 setOfAtoms ()
void swap (const int i, const int j)
void writeQCIFile (std::ofstream &out)
void writeQCIFile (std::ofstream &out, std::vector< int > &index)
void writeVMDFile (std::ofstream &out, const std::vector< std::string > &color)
void writeXYZFile (std::ofstream &out, double *H, const std::vector< int > &index)
void writeXYZFile (std::ofstream &out, double *H)
void writeXYZFile (std::ofstream &out)
void writeXYZFile (std::ofstream &out, std::vector< int > &index)
void writeXYZPosition (std::ofstream &out, double *H)
 ~setOfAtoms ()

Protected Attributes

atomElement_atoms
int _numberOfAA
int _numberOfAtoms
int _numberOfFragments


Member Typedef Documentation

typedef atomElement setOfAtoms::TelementBase
 

Definition at line 31 of file Atoms.h.


Constructor & Destructor Documentation

setOfAtoms::setOfAtoms  ) 
 

Definition at line 12 of file Atoms.cpp.

setOfAtoms::setOfAtoms const int  size  ) 
 

Definition at line 15 of file Atoms.cpp.

setOfAtoms::~setOfAtoms  ) 
 

Definition at line 18 of file Atoms.cpp.

References _atoms, and _numberOfAtoms.


Member Function Documentation

std::string& setOfAtoms::atomName const int  i  )  [inline]
 

Definition at line 60 of file Atoms.h.

References _atoms, and atomElement::_name.

void setOfAtoms::buildGravityCenter double *  G  ) 
 

Definition at line 49 of file Atoms.cpp.

References _atoms, _numberOfAtoms, and atomElement::_xyz.

Referenced by setOfFragments::buildFromAtoms(), and BoxPartition::innerReperOfMolecule().

bool setOfAtoms::buildIinertialMatrix double *  coordG  ) 
 

Definition at line 410 of file Atoms.cpp.

void setOfAtoms::copyFrom const int  beginAtom,
const int  EndAtom,
const setOfAtoms atoms
 

Definition at line 379 of file Atoms.cpp.

References _atoms, _numberOfAtoms, atomElement::copy(), and getElement().

Referenced by FragmentElement::setAtoms().

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

Definition at line 35 of file Atoms.cpp.

References _numberOfAtoms.

Referenced by setOfFragments::buildFromAtoms(), and BoxPartition::partitionate().

int setOfAtoms::findNumberOfAtoms std::ifstream &  data  ) 
 

Definition at line 65 of file Atoms.cpp.

References numberOfAtoms().

Referenced by readQCIFile().

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void setOfAtoms::fixConnectivity const std::vector< int > &  reOrder  ) 
 

Definition at line 417 of file Atoms.cpp.

References _atoms, atomElement::_connect, and _numberOfAtoms.

Referenced by sortInFirstDimension().

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

Definition at line 54 of file Atoms.h.

References _atoms, and atomElement::_fragName.

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

Definition at line 51 of file Atoms.h.

References _atoms, and atomElement::_fragName.

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

Definition at line 48 of file Atoms.h.

References _atoms, and atomElement::_name.

atomElement& setOfAtoms::getElement const int  i  )  [inline]
 

Definition at line 66 of file Atoms.h.

References _atoms.

atomElement setOfAtoms::getElement const int  i  )  const [inline]
 

Definition at line 63 of file Atoms.h.

References _atoms.

Referenced by setOfFragments::buildFromAtoms(), copyFrom(), BoxPartition::innerReperOfMolecule(), BoxPartition::projectOnInnerReper(), BoxPartition::setAtomsInKernel(), sortInFirstDimension(), and BoxPartition::sortInFirstDimension().

std::string setOfAtoms::getName const int  i  )  const [inline]
 

Definition at line 45 of file Atoms.h.

References _atoms, and atomElement::_name.

Referenced by FragmentElement::setLoad(), FragmentElement::writeQCIFile(), and setOfFragments::writeToFile().

int setOfAtoms::getNumberOfAtoms  )  const [inline]
 

Definition at line 38 of file Atoms.h.

References _numberOfAtoms.

Referenced by setOfFragments::buildFromAtoms(), BoxPartition::innerReperOfMolecule(), main(), FragmentElement::numberOfAtoms(), BoxPartition::partitionate(), BoxPartition::projectOnInnerReper(), BoxPartition::setAtomsInKernel(), FragmentElement::setLoad(), and BoxPartition::sortInFirstDimension().

int setOfAtoms::getNumberOfFragments  ) 
 

Definition at line 363 of file Atoms.cpp.

References _atoms, _numberOfAtoms, _numberOfFragments, and atomElement::getFragmentName().

Referenced by setOfFragments::buildFromAtoms(), and readQCIFile().

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int setOfAtoms::numberOfAA  )  const [inline]
 

Definition at line 77 of file Atoms.h.

References _numberOfAA.

int setOfAtoms::numberOfAtoms  )  const [inline]
 

Definition at line 41 of file Atoms.h.

References _numberOfAtoms.

Referenced by findNumberOfAtoms(), main(), and sortInFirstDimension().

int setOfAtoms::numberOfFragements  )  const [inline]
 

Definition at line 80 of file Atoms.h.

References _numberOfFragments.

int setOfAtoms::numberOfFragments  )  const [inline]
 

Definition at line 74 of file Atoms.h.

References _numberOfFragments.

bool setOfAtoms::readQCIFile std::ifstream &  data  ) 
 

Definition at line 80 of file Atoms.cpp.

References _atoms, atomElement::_num, _numberOfAA, _numberOfAtoms, AA(), findNumberOfAtoms(), atomElement::fragmentName(), getNumberOfFragments(), atomElement::number(), and atomElement::read().

Referenced by main().

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void setOfAtoms::readXYZFile std::ifstream &  data  ) 
 

Definition at line 146 of file Atoms.cpp.

References _atoms, atomElement::_name, atomElement::_num, _numberOfAtoms, and atomElement::_xyz.

Referenced by main().

void setOfAtoms::reset  ) 
 

Definition at line 25 of file Atoms.cpp.

References _atoms, and _numberOfAtoms.

atomElement& setOfAtoms::setElement const int  i  )  [inline]
 

Definition at line 69 of file Atoms.h.

References _atoms.

void setOfAtoms::setNumberOfAtoms const int  size  ) 
 

Definition at line 31 of file Atoms.cpp.

References _atoms, and _numberOfAtoms.

Referenced by setOfFragments::buildFromAtoms().

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

Definition at line 391 of file Atoms.cpp.

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

Referenced by sortInFirstDimension(), and BoxPartition::sortInFirstDimension().

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

Definition at line 254 of file Atoms.cpp.

References _atoms, atomElement::_connect, atomElement::_fragName, atomElement::_name, atomElement::_num, _numberOfAtoms, and atomElement::_xyz.

void setOfAtoms::writeQCIFile std::ofstream &  out,
std::vector< int > &  index
 

Definition at line 278 of file Atoms.cpp.

Referenced by main().

void setOfAtoms::writeVMDFile std::ofstream &  out,
const std::vector< std::string > &  color
 

Definition at line 183 of file Atoms.cpp.

References _atoms, atomElement::_connect, _numberOfAtoms, and atomElement::_xyz.

void setOfAtoms::writeXYZFile std::ofstream &  out,
double *  H,
const std::vector< int > &  index
 

Definition at line 318 of file Atoms.cpp.

References _atoms, atomElement::_name, and atomElement::_xyz.

void setOfAtoms::writeXYZFile std::ofstream &  out,
double *  H
 

Definition at line 347 of file Atoms.cpp.

References _atoms, atomElement::_name, _numberOfAtoms, and atomElement::_xyz.

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

Definition at line 312 of file Atoms.cpp.

References writeXYZFile().

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void setOfAtoms::writeXYZFile std::ofstream &  out,
std::vector< int > &  index
 

Definition at line 306 of file Atoms.cpp.

Referenced by main(), and writeXYZFile().

void setOfAtoms::writeXYZPosition std::ofstream &  out,
double *  H
 

Definition at line 335 of file Atoms.cpp.

References _atoms, atomElement::_name, _numberOfAtoms, and atomElement::_xyz.


Member Data Documentation

atomElement* setOfAtoms::_atoms [protected]
 

Definition at line 117 of file Atoms.h.

Referenced by atomName(), buildGravityCenter(), copyFrom(), fixConnectivity(), fragmentName(), getAtomName(), getElement(), getName(), getNumberOfFragments(), readQCIFile(), readXYZFile(), reset(), setElement(), setNumberOfAtoms(), swap(), writeQCIFile(), writeVMDFile(), writeXYZFile(), writeXYZPosition(), and ~setOfAtoms().

int setOfAtoms::_numberOfAA [protected]
 

Definition at line 115 of file Atoms.h.

Referenced by numberOfAA(), and readQCIFile().

int setOfAtoms::_numberOfAtoms [protected]
 

Definition at line 114 of file Atoms.h.

Referenced by buildGravityCenter(), copyFrom(), findMinMax(), fixConnectivity(), getNumberOfAtoms(), getNumberOfFragments(), numberOfAtoms(), readQCIFile(), readXYZFile(), reset(), setNumberOfAtoms(), swap(), writeQCIFile(), writeVMDFile(), writeXYZFile(), writeXYZPosition(), and ~setOfAtoms().

int setOfAtoms::_numberOfFragments [protected]
 

Definition at line 116 of file Atoms.h.

Referenced by getNumberOfFragments(), numberOfFragements(), and numberOfFragments().


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