AvogadroLibs 1.97.0
Molecule Member List

This is the complete list of members for Molecule, including all inherited members.

addAtom(unsigned char atomicNumber) overrideMoleculevirtual
addAtom(unsigned char atomicNumber, Index uniqueId)Moleculevirtual
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) overrideMoleculevirtual
addBond(Index atomId1, Index atomId2, unsigned char bondOrder=1) overrideMoleculevirtual
addBond(const AtomType &a, const AtomType &b, unsigned char bondOrder, Index uniqueId)Moleculevirtual
addBond(Index atomId1, Index atomId2, unsigned char bondOrder, Index uniqueId)Moleculevirtual
addBonds(const Core::Array< std::pair< Index, Index > > &bonds, const Core::Array< unsigned char > &orders) (defined in Molecule)Molecule
addCube()Molecule
Added enum valueMolecule
addMesh()Molecule
addResidue(std::string &name, Index &number, char &id) (defined in Molecule)Molecule
addResidue(Residue &residue) (defined in Molecule)Molecule
atom(Index index) constMolecule
atomByUniqueId(Index uniqueId)Molecule
atomCount() constMolecule
atomCount(unsigned char atomicNumber) constMolecule
atomicNumber(Index atomId) constMolecule
atomicNumbers() constMolecule
atomPosition2d(Index atomId) constMolecule
atomPosition3d(Index atomId) constMolecule
atomPositions2d() constMolecule
atomPositions2d()Molecule
atomPositions3d() constMolecule
atomPositions3d()Molecule
Atoms enum valueMolecule
atomSelected(Index atomId) constMolecule
AtomType typedefMolecule
atomUniqueId(const AtomType &atom) constMolecule
atomUniqueId(Index atom) constMolecule
atomUniqueIds() (defined in Molecule)Molecule
basisSet()Molecule
basisSet() const (defined in Molecule)Molecule
bestFitPlane() constMolecule
bestFitPlane(const Array< Vector3 > &pos)Moleculestatic
bond(Index index) constMolecule
bond(const AtomType &a, const AtomType &b) constMolecule
bond(Index atomId1, Index atomId2) constMolecule
bondByUniqueId(Index uniqueId)Molecule
bondCount() constMolecule
bondOrder(Index bondId) constMolecule
bondOrders() constMolecule
bondPair(Index bondId) constMolecule
bondPairs() constMolecule
Bonds enum value (defined in Molecule)Molecule
bonds(const AtomType &a)Molecule
bonds(Index a)Molecule
bonds(Index a) constMolecule
BondType typedefMolecule
bondUniqueId(const BondType &bond) constMolecule
bondUniqueId(Index bond) constMolecule
bondUniqueIds() (defined in Molecule)Molecule
centerOfGeometry() constMolecule
centerOfMass() constMolecule
changed(unsigned int change)Moleculesignal
clearAtoms()Moleculevirtual
clearBonds()Moleculevirtual
clearCubes() (defined in Molecule)Molecule
clearMeshes() (defined in Molecule)Molecule
color(Index atomId) constMolecule
colors()Molecule
colors() constMolecule
composition() constMolecule
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 typedefMolecule
customElementMap() constMolecule
data(const std::string &name) constMolecule
dataMap() constMolecule
dataMap()Molecule
ElementMask typedefMolecule
elements() constMolecule
emitChanged(unsigned int change)Moleculeslot
findAtomUniqueId(Index index) const (defined in Molecule)Molecule
findBondUniqueId(Index index) const (defined in Molecule)Molecule
forceVector(Index atomId) constMolecule
forceVectors() constMolecule
forceVectors()Molecule
formalCharge(Index atomId) constMolecule
formalCharges()Molecule
formalCharges() constMolecule
formula(const std::string &delimiter="", int showCountsOver=1) constMolecule
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() constMolecule
hallNumber() constMolecule
hasCustomElements() constMolecule
hasData(const std::string &name) constMolecule
hybridization(Index atomId) constMolecule
hybridizations()Molecule
hybridizations() constMolecule
isSelectionEmpty() constMolecule
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)Moleculeprotected
m_colors (defined in Molecule)Moleculeprotected
m_coordinates3dMoleculeprotected
m_cubes (defined in Molecule)Moleculeprotected
m_customElementMap (defined in Molecule)Moleculeprotected
m_data (defined in Molecule)Moleculeprotected
m_elementsMoleculeprotected
m_forceVectors (defined in Molecule)Moleculeprotected
m_formalCharges (defined in Molecule)Moleculeprotected
m_hallNumber (defined in Molecule)Moleculeprotected
m_hybridizations (defined in Molecule)Moleculeprotected
m_label (defined in Molecule)Moleculeprotected
m_meshes (defined in Molecule)Moleculeprotected
m_partialChargesMoleculeprotected
m_positions2d (defined in Molecule)Moleculeprotected
m_positions3d (defined in Molecule)Moleculeprotected
m_residues (defined in Molecule)Moleculeprotected
m_selectedAtoms (defined in Molecule)Moleculeprotected
m_timesteps (defined in Molecule)Moleculeprotected
m_unitCell (defined in Molecule)Moleculeprotected
m_vibrationFrequencies (defined in Molecule)Moleculeprotected
m_vibrationIRIntensities (defined in Molecule)Moleculeprotected
m_vibrationLx (defined in Molecule)Moleculeprotected
m_vibrationRamanIntensities (defined in Molecule)Moleculeprotected
makeBondPair(const Index &a, const Index &b) (defined in Molecule)Moleculestatic
mass() constMolecule
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) noexceptMolecule
MoleculeChange enum nameMolecule
NoChange enum valueMolecule
operator=(const Molecule &other)Molecule
operator=(const Core::Molecule &other)Molecule
Avogadro::Core::Molecule::operator=(Molecule &&other) noexceptMolecule
partialCharges(const std::string &type) constMolecule
partialChargeTypes() constMolecule
perceiveBondsFromResidueData()Molecule
perceiveBondsSimple(const double tolerance=0.45, const double minDistance=0.32)Molecule
perceiveSubstitutedCations()Molecule
PersistentAtomType typedefMolecule
PersistentBondType typedefMolecule
radius() constMolecule
removeAtom(Index index) overrideMoleculevirtual
removeAtom(const AtomType &atom) overrideMoleculevirtual
removeBond(Index index) overrideMoleculevirtual
removeBond(const BondType &bond) overrideMoleculevirtual
removeBond(const AtomType &atom1, const AtomType &atom2) overrideMoleculevirtual
removeBond(Index atom1, Index atom2) overrideMoleculevirtual
removeBonds(Index atom) (defined in Molecule)Molecule
Removed enum value (defined in Molecule)Molecule
residue(Index index) (defined in Molecule)Molecule
residueCount() constMolecule
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
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
undoMolecule() (defined in Molecule)Molecule
unitCell()Molecule
unitCell() constMolecule
UnitCell enum value (defined in Molecule)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() overrideMoleculevirtual