| _atoms | setOfAtoms | [protected] |
| _numberOfAA | setOfAtoms | [protected] |
| _numberOfAtoms | setOfAtoms | [protected] |
| _numberOfFragments | setOfAtoms | [protected] |
| atomName(const int i) | setOfAtoms | [inline] |
| buildGravityCenter(double *G) | setOfAtoms | |
| buildIinertialMatrix(double *coordG) | setOfAtoms | |
| copyFrom(const int beginAtom, const int EndAtom, const setOfAtoms &atoms) | setOfAtoms | |
| findMinMax(double *atomMin, double *atomMax) | setOfAtoms | |
| findNumberOfAtoms(std::ifstream &data) | setOfAtoms | |
| fixConnectivity(const std::vector< int > &reOrder) | setOfAtoms | |
| fragmentName(const int i) const | setOfAtoms | [inline] |
| fragmentName(const int i) | setOfAtoms | [inline] |
| getAtomName(const int i) const | setOfAtoms | [inline] |
| getElement(const int i) const | setOfAtoms | [inline] |
| getElement(const int i) | setOfAtoms | [inline] |
| getName(const int i) const | setOfAtoms | [inline] |
| getNumberOfAtoms() const | setOfAtoms | [inline] |
| getNumberOfFragments() | setOfAtoms | |
| numberOfAA() const | setOfAtoms | [inline] |
| numberOfAtoms() const | setOfAtoms | [inline] |
| numberOfFragements() const | setOfAtoms | [inline] |
| numberOfFragments() const | setOfAtoms | [inline] |
| readQCIFile(std::ifstream &data) | setOfAtoms | |
| readXYZFile(std::ifstream &data) | setOfAtoms | |
| reset() | setOfAtoms | |
| setElement(const int i) | setOfAtoms | [inline] |
| setNumberOfAtoms(const int size) | setOfAtoms | |
| setOfAtoms() | setOfAtoms | |
| setOfAtoms(const int size) | setOfAtoms | |
| swap(const int i, const int j) | setOfAtoms | |
| TelementBase typedef | setOfAtoms | |
| writeQCIFile(std::ofstream &out, std::vector< int > &index) | setOfAtoms | |
| writeQCIFile(std::ofstream &out) | setOfAtoms | |
| writeVMDFile(std::ofstream &out, const std::vector< std::string > &color) | setOfAtoms | |
| writeXYZFile(std::ofstream &out, std::vector< int > &index) | setOfAtoms | |
| writeXYZFile(std::ofstream &out) | setOfAtoms | |
| writeXYZFile(std::ofstream &out, double *H) | setOfAtoms | |
| writeXYZFile(std::ofstream &out, double *H, const std::vector< int > &index) | setOfAtoms | |
| writeXYZPosition(std::ofstream &out, double *H) | setOfAtoms | |
| ~setOfAtoms() | setOfAtoms | |