AvogadroLibs 1.98.1
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This is the complete list of members for Molecule, including all inherited members.
addAtom(unsigned char atomicNumber) override | Molecule | virtual |
addAtom(unsigned char atomicNumber, Index uniqueId) | Molecule | virtual |
addAtom(unsigned char number, Vector3 position3d, Index uniqueId=MaxIndex) (defined in Molecule) | Molecule | |
addAtom(unsigned char atomicNumber, Vector3 position3d) (defined in Molecule) | Molecule | |
addBond(const AtomType &a, const AtomType &b, unsigned char bondOrder=1) override | Molecule | virtual |
addBond(Index atomId1, Index atomId2, unsigned char bondOrder=1) override | Molecule | virtual |
addBond(const AtomType &a, const AtomType &b, unsigned char bondOrder, Index uniqueId) | Molecule | virtual |
addBond(Index atomId1, Index atomId2, unsigned char bondOrder, Index uniqueId) | Molecule | virtual |
addBonds(const Core::Array< std::pair< Index, Index > > &bonds, const Core::Array< unsigned char > &orders) (defined in Molecule) | Molecule | |
addCube() | Molecule | |
Added enum value | Molecule | |
addMesh() | Molecule | |
addResidue(std::string &name, Index &number, char &id) (defined in Molecule) | Molecule | |
addResidue(Residue &residue) (defined in Molecule) | Molecule | |
atom(Index index) const | Molecule | |
atomByUniqueId(Index uniqueId) | Molecule | |
atomCount() const | Molecule | |
atomCount(unsigned char atomicNumber) const | Molecule | |
atomicNumber(Index atomId) const | Molecule | |
atomicNumbers() const | Molecule | |
atomPosition2d(Index atomId) const | Molecule | |
atomPosition3d(Index atomId) const | Molecule | |
atomPositions2d() const | Molecule | |
atomPositions2d() | Molecule | |
atomPositions3d() const | Molecule | |
atomPositions3d() | Molecule | |
Atoms enum value | Molecule | |
atomSelected(Index atomId) const | Molecule | |
AtomType typedef | Molecule | |
atomUniqueId(const AtomType &atom) const | Molecule | |
atomUniqueId(Index atom) const | Molecule | |
atomUniqueIds() (defined in Molecule) | Molecule | |
basisSet() | Molecule | |
basisSet() const (defined in Molecule) | Molecule | |
bestFitPlane() const | Molecule | |
bestFitPlane(const Array< Vector3 > &pos) | Molecule | static |
bond(Index index) const | Molecule | |
bond(const AtomType &a, const AtomType &b) const | Molecule | |
bond(Index atomId1, Index atomId2) const | Molecule | |
bondByUniqueId(Index uniqueId) | Molecule | |
bondCount() const | Molecule | |
bondOrder(Index bondId) const | Molecule | |
bondOrders() const | Molecule | |
bondPair(Index bondId) const | Molecule | |
bondPairs() const | Molecule | |
bonds(const AtomType &a) | Molecule | |
bonds(Index a) | Molecule | |
bonds(Index a) const | Molecule | |
Bonds enum value (defined in Molecule) | Molecule | |
BondType typedef | Molecule | |
bondUniqueId(const BondType &bond) const | Molecule | |
bondUniqueId(Index bond) const | Molecule | |
bondUniqueIds() (defined in Molecule) | Molecule | |
boundingBox(Vector3 &boxMin, Vector3 &boxMax, const double radius=1.0) const | Molecule | |
centerOfGeometry() const | Molecule | |
centerOfMass() const | Molecule | |
changed(unsigned int change) | Molecule | signal |
clearAtoms() | Molecule | virtual |
clearBonds() | Molecule | virtual |
clearCubes() (defined in Molecule) | Molecule | |
clearMeshes() (defined in Molecule) | Molecule | |
color(Index atomId) const | Molecule | |
colors() | Molecule | |
colors() const | Molecule | |
composition() const | Molecule | |
coordinate3d(int index) const (defined in Molecule) | Molecule | |
coordinate3dCount() (defined in Molecule) | Molecule | |
cube(Index index) (defined in Molecule) | Molecule | |
cube(Index index) const (defined in Molecule) | Molecule | |
cubeCount() const (defined in Molecule) | Molecule | |
cubes() | Molecule | |
cubes() const (defined in Molecule) | Molecule | |
CustomElementMap typedef | Molecule | |
customElementMap() const | Molecule | |
data(const std::string &name) const | Molecule | |
dataMap() const | Molecule | |
dataMap() | Molecule | |
ElementMask typedef | Molecule | |
elements() const | Molecule | |
emitChanged(unsigned int change) | Molecule | slot |
findAtomUniqueId(Index index) const (defined in Molecule) | Molecule | |
findBondUniqueId(Index index) const (defined in Molecule) | Molecule | |
forceVector(Index atomId) const | Molecule | |
forceVectors() const | Molecule | |
forceVectors() | Molecule | |
formalCharge(Index atomId) const | Molecule | |
formalCharges() | Molecule | |
formalCharges() const | Molecule | |
formula(const std::string &delimiter="", int showCountsOver=1) const | Molecule | |
frozenAtom(Index atomId) const | Molecule | |
frozenAtomMask() const (defined in Molecule) | Molecule | |
getAtomBonds(Index index) const (defined in Molecule) | Molecule | |
getAtomOrders(Index index) const (defined in Molecule) | Molecule | |
getAtomsAtLayer(size_t layer) (defined in Molecule) | Molecule | |
graph() const | Molecule | |
hallNumber() const | Molecule | |
hasCustomElements() const | Molecule | |
hasData(const std::string &name) const | Molecule | |
hybridization(Index atomId) const | Molecule | |
hybridizations() | Molecule | |
hybridizations() const | Molecule | |
isSelectionEmpty() const | Molecule | |
label(Index atomId) const (defined in Molecule) | Molecule | |
layer(Index atomId) const (defined in Molecule) | Molecule | |
layer() (defined in Molecule) | Molecule | |
layer() const (defined in Molecule) | Molecule | |
Layers enum value (defined in Molecule) | Molecule | |
m_basisSet (defined in Molecule) | Molecule | protected |
m_colors (defined in Molecule) | Molecule | protected |
m_coordinates3d | Molecule | protected |
m_cubes (defined in Molecule) | Molecule | protected |
m_customElementMap (defined in Molecule) | Molecule | protected |
m_data (defined in Molecule) | Molecule | protected |
m_elements | Molecule | protected |
m_forceVectors (defined in Molecule) | Molecule | protected |
m_formalCharges (defined in Molecule) | Molecule | protected |
m_frozenAtomMask (defined in Molecule) | Molecule | protected |
m_hallNumber (defined in Molecule) | Molecule | protected |
m_hybridizations (defined in Molecule) | Molecule | protected |
m_label (defined in Molecule) | Molecule | protected |
m_meshes (defined in Molecule) | Molecule | protected |
m_partialCharges | Molecule | protected |
m_positions2d (defined in Molecule) | Molecule | protected |
m_positions3d (defined in Molecule) | Molecule | protected |
m_residues (defined in Molecule) | Molecule | protected |
m_selectedAtoms (defined in Molecule) | Molecule | protected |
m_timesteps (defined in Molecule) | Molecule | protected |
m_unitCell (defined in Molecule) | Molecule | protected |
m_vibrationFrequencies (defined in Molecule) | Molecule | protected |
m_vibrationIRIntensities (defined in Molecule) | Molecule | protected |
m_vibrationLx (defined in Molecule) | Molecule | protected |
m_vibrationRamanIntensities (defined in Molecule) | Molecule | protected |
makeBondPair(const Index &a, const Index &b) (defined in Molecule) | Molecule | static |
mass() const | Molecule | |
mesh(Index index) (defined in Molecule) | Molecule | |
mesh(Index index) const (defined in Molecule) | Molecule | |
meshCount() const (defined in Molecule) | Molecule | |
Modified enum value (defined in Molecule) | Molecule | |
Molecule(QObject *parent_=nullptr) (defined in Molecule) | Molecule | |
Molecule(const Molecule &other) | Molecule | |
Molecule(const Core::Molecule &other) | Molecule | |
Avogadro::Core::Molecule::Molecule() | Molecule | |
Avogadro::Core::Molecule::Molecule(Molecule &&other) noexcept | Molecule | |
MoleculeChange enum name | Molecule | |
NoChange enum value | Molecule | |
operator=(const Molecule &other) | Molecule | |
operator=(const Core::Molecule &other) | Molecule | |
Avogadro::Core::Molecule::operator=(Molecule &&other) noexcept | Molecule | |
partialCharges(const std::string &type) const | Molecule | |
partialChargeTypes() const | Molecule | |
perceiveBondOrders() (defined in Molecule) | Molecule | |
perceiveBondsFromResidueData() | Molecule | |
perceiveBondsSimple(const double tolerance=0.45, const double minDistance=0.32) | Molecule | |
perceiveSubstitutedCations() | Molecule | |
PersistentAtomType typedef | Molecule | |
PersistentBondType typedef | Molecule | |
radius() const | Molecule | |
removeAtom(Index index) override | Molecule | virtual |
removeAtom(const AtomType &atom) override | Molecule | virtual |
removeBond(Index index) override | Molecule | virtual |
removeBond(const BondType &bond) override | Molecule | virtual |
removeBond(const AtomType &atom1, const AtomType &atom2) override | Molecule | virtual |
removeBond(Index atom1, Index atom2) override | Molecule | virtual |
removeBonds(Index atom) (defined in Molecule) | Molecule | |
Removed enum value (defined in Molecule) | Molecule | |
residue(Index index) (defined in Molecule) | Molecule | |
residueCount() const | Molecule | |
residues() (defined in Molecule) | Molecule | |
residues() const (defined in Molecule) | Molecule | |
Selection enum value (defined in Molecule) | Molecule | |
setAtomicNumber(Index atomId, unsigned char atomicNumber) | Molecule | |
setAtomicNumbers(const Core::Array< unsigned char > &nums) | Molecule | |
setAtomPosition2d(Index atomId, const Vector2 &pos) | Molecule | |
setAtomPosition3d(Index atomId, const Vector3 &pos) | Molecule | |
setAtomPositions2d(const Core::Array< Vector2 > &pos) | Molecule | |
setAtomPositions3d(const Core::Array< Vector3 > &pos) | Molecule | |
setAtomSelected(Index atomId, bool selected) | Molecule | |
setBasisSet(BasisSet *basis) | Molecule | |
setBondOrder(Index bondId, unsigned char order) | Molecule | |
setBondOrders(const Array< unsigned char > &orders) | Molecule | |
setBondPair(Index bondId, const std::pair< Index, Index > &pair) | Molecule | |
setBondPairs(const Array< std::pair< Index, Index > > &pairs) | Molecule | |
setColor(Index atomId, Vector3ub color) | Molecule | |
setColors(const Core::Array< Vector3ub > &colors) | Molecule | |
setCoordinate3d(int coord) (defined in Molecule) | Molecule | |
setCoordinate3d(const Array< Vector3 > &coords, int index) (defined in Molecule) | Molecule | |
setCustomElementMap(const CustomElementMap &map) | Molecule | |
setData(const std::string &name, const Variant &value) | Molecule | |
setDataMap(const VariantMap &map) | Molecule | |
setForceVector(Index atomId, const Vector3 &force) | Molecule | |
setForceVectors(const Core::Array< Vector3 > &forces) | Molecule | |
setFormalCharge(Index atomId, signed char charge) | Molecule | |
setFormalCharges(const Core::Array< signed char > &charges) | Molecule | |
setFrozenAtom(Index atomId, bool frozen) | Molecule | |
setFrozenAtomAxis(Index atomId, int axis, bool frozen) | Molecule | |
setHallNumber(unsigned short hallNumber) | Molecule | |
setHybridization(Index atomId, AtomHybridization hybridization) | Molecule | |
setHybridizations(const Core::Array< AtomHybridization > &hybs) | Molecule | |
setLabel(const Core::Array< std::string > &label) (defined in Molecule) | Molecule | |
setLabel(Index atomId, const std::string &label) (defined in Molecule) | Molecule | |
setLayer(Index atomId, size_t layer) (defined in Molecule) | Molecule | |
setPartialCharges(const std::string &type, const MatrixX &value) | Molecule | |
setTimeStep(double timestep, int index) | Molecule | |
setUnitCell(UnitCell *uc) | Molecule | |
setVibrationFrequencies(const Array< double > &freq) (defined in Molecule) | Molecule | |
setVibrationIRIntensities(const Array< double > &intensities) (defined in Molecule) | Molecule | |
setVibrationLx(const Array< Array< Vector3 > > &lx) (defined in Molecule) | Molecule | |
setVibrationRamanIntensities(const Array< double > &intensities) (defined in Molecule) | Molecule | |
swapAtom(Index a, Index b) (defined in Molecule) | Molecule | |
swapBond(Index a, Index b) (defined in Molecule) | Molecule | |
timeStep(int index, bool &status) (defined in Molecule) | Molecule | |
totalCharge() const | Molecule | |
totalSpinMultiplicity() const | Molecule | |
undoMolecule() (defined in Molecule) | Molecule | |
UnitCell enum value (defined in Molecule) | Molecule | |
unitCell() | Molecule | |
unitCell() const | Molecule | |
vibrationFrequencies() const (defined in Molecule) | Molecule | |
vibrationIRIntensities() const (defined in Molecule) | Molecule | |
vibrationLx(int mode) const (defined in Molecule) | Molecule | |
vibrationRamanIntensities() const (defined in Molecule) | Molecule | |
~Molecule() override | Molecule | virtual |