#include <Atoms.h>
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 |
atomElement & | getElement (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 () |
atomElement & | setElement (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 |
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Definition at line 18 of file Atoms.cpp. References _atoms, and _numberOfAtoms. |
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Definition at line 60 of file Atoms.h. References _atoms, and atomElement::_name. |
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Definition at line 49 of file Atoms.cpp. References _atoms, _numberOfAtoms, and atomElement::_xyz. Referenced by setOfFragments::buildFromAtoms(), and BoxPartition::innerReperOfMolecule(). |
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Definition at line 379 of file Atoms.cpp. References _atoms, _numberOfAtoms, atomElement::copy(), and getElement(). Referenced by FragmentElement::setAtoms(). Here is the call graph for this function: ![]() |
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Definition at line 35 of file Atoms.cpp. References _numberOfAtoms. Referenced by setOfFragments::buildFromAtoms(), and BoxPartition::partitionate(). |
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Definition at line 65 of file Atoms.cpp. References numberOfAtoms(). Referenced by readQCIFile(). Here is the call graph for this function: ![]() |
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Definition at line 417 of file Atoms.cpp. References _atoms, atomElement::_connect, and _numberOfAtoms. Referenced by sortInFirstDimension(). |
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Definition at line 54 of file Atoms.h. References _atoms, and atomElement::_fragName. |
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Definition at line 51 of file Atoms.h. References _atoms, and atomElement::_fragName. |
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Definition at line 48 of file Atoms.h. References _atoms, and atomElement::_name. |
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Definition at line 66 of file Atoms.h. References _atoms. |
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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(). |
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Definition at line 45 of file Atoms.h. References _atoms, and atomElement::_name. Referenced by FragmentElement::setLoad(), FragmentElement::writeQCIFile(), and setOfFragments::writeToFile(). |
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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(). |
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Definition at line 363 of file Atoms.cpp. References _atoms, _numberOfAtoms, _numberOfFragments, and atomElement::getFragmentName(). Referenced by setOfFragments::buildFromAtoms(), and readQCIFile(). Here is the call graph for this function: ![]() |
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Definition at line 77 of file Atoms.h. References _numberOfAA. |
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Definition at line 41 of file Atoms.h. References _numberOfAtoms. Referenced by findNumberOfAtoms(), main(), and sortInFirstDimension(). |
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Definition at line 80 of file Atoms.h. References _numberOfFragments. |
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Definition at line 74 of file Atoms.h. References _numberOfFragments. |
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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(). Here is the call graph for this function: ![]() |
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Definition at line 146 of file Atoms.cpp. References _atoms, atomElement::_name, atomElement::_num, _numberOfAtoms, and atomElement::_xyz. Referenced by main(). |
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Definition at line 25 of file Atoms.cpp. References _atoms, and _numberOfAtoms. |
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Definition at line 69 of file Atoms.h. References _atoms. |
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Definition at line 31 of file Atoms.cpp. References _atoms, and _numberOfAtoms. Referenced by setOfFragments::buildFromAtoms(). |
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Definition at line 391 of file Atoms.cpp. References _atoms, _numberOfAtoms, and atomElement::copy(). Referenced by sortInFirstDimension(), and BoxPartition::sortInFirstDimension(). Here is the call graph for this function: ![]() |
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Definition at line 254 of file Atoms.cpp. References _atoms, atomElement::_connect, atomElement::_fragName, atomElement::_name, atomElement::_num, _numberOfAtoms, and atomElement::_xyz. |
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Definition at line 278 of file Atoms.cpp. Referenced by main(). |
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Definition at line 183 of file Atoms.cpp. References _atoms, atomElement::_connect, _numberOfAtoms, and atomElement::_xyz. |
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Definition at line 318 of file Atoms.cpp. References _atoms, atomElement::_name, and atomElement::_xyz. |
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Definition at line 347 of file Atoms.cpp. References _atoms, atomElement::_name, _numberOfAtoms, and atomElement::_xyz. |
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Definition at line 312 of file Atoms.cpp. References writeXYZFile(). Here is the call graph for this function: ![]() |
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Definition at line 306 of file Atoms.cpp. Referenced by main(), and writeXYZFile(). |
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Definition at line 335 of file Atoms.cpp. References _atoms, atomElement::_name, _numberOfAtoms, and atomElement::_xyz. |
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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(). |
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Definition at line 115 of file Atoms.h. Referenced by numberOfAA(), and readQCIFile(). |
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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(). |
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Definition at line 116 of file Atoms.h. Referenced by getNumberOfFragments(), numberOfFragements(), and numberOfFragments(). |