AvogadroLibs  1.96.0
Molecule Member List

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

addAtom(unsigned char atomicNumber)Moleculevirtual
addAtom(unsigned char atomicNumber, Vector3 position3d) (defined in Molecule)Molecule
addBond(Index atom1, Index atom2, unsigned char order=1)Moleculevirtual
addBond(const AtomType &atom1, const AtomType &atom2, unsigned char order=1)Moleculevirtual
addBonds(const Array< std::pair< Index, Index >> &bonds, const Array< unsigned char > &orders) (defined in Molecule)Molecule
addCube()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) constMolecule
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
atomSelected(Index atomId) constMolecule
AtomType typedefMolecule
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
bondCount() constMolecule
bondOrder(Index bondId) constMolecule
bondOrders() constMolecule
bondPair(Index bondId) constMolecule
bondPairs() constMolecule
bonds(const AtomType &a)Molecule
bonds(Index a)Molecule
bonds(Index a) constMolecule
BondType typedefMolecule
centerOfGeometry() constMolecule
centerOfMass() constMolecule
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() constMolecule
CustomElementMap typedefMolecule
data(const std::string &name) constMolecule
dataMap() constMolecule
dataMap()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
m_basisSet (defined in Molecule)Moleculeprotected
m_colors (defined in Molecule)Moleculeprotected
m_coordinates3d (defined in Molecule)Moleculeprotected
m_cubes (defined in Molecule)Moleculeprotected
m_customElementMap (defined in Molecule)Moleculeprotected
m_data (defined in Molecule)Moleculeprotected
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_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_vibrationIntensities (defined in Molecule)Moleculeprotected
m_vibrationLx (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
Molecule()Molecule
Molecule(const Molecule &other)Molecule
Molecule(Molecule &&other) noexceptMolecule
operator=(const Molecule &other)Molecule
operator=(Molecule &&other) noexceptMolecule
perceiveBondsFromResidueData()Molecule
perceiveBondsSimple(const double tolerance=0.45, const double minDistance=0.32)Molecule
perceiveSubstitutedCations()Molecule
radius() constMolecule
removeAtom(Index index)Moleculevirtual
removeAtom(const AtomType &atom)Moleculevirtual
removeBond(Index index)Moleculevirtual
removeBond(const BondType &bond)Moleculevirtual
removeBond(Index atom1, Index atom2)Moleculevirtual
removeBond(const AtomType &atom1, const AtomType &atom2)Moleculevirtual
removeBonds(Index atom) (defined in Molecule)Molecule
residue(Index index) (defined in Molecule)Molecule
residueCount() constMolecule
residues() (defined in Molecule)Molecule
residues() const (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
setTimeStep(double timestep, int index)Molecule
setUnitCell(UnitCell *uc)Molecule
setVibrationFrequencies(const Array< double > &freq) (defined in Molecule)Molecule
setVibrationIntensities(const Array< double > &intensities) (defined in Molecule)Molecule
setVibrationLx(const Array< Array< Vector3 >> &lx) (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
unitCell()Molecule
unitCell() constMolecule
vibrationFrequencies() const (defined in Molecule)Molecule
vibrationIntensities() const (defined in Molecule)Molecule
vibrationLx(int mode) const (defined in Molecule)Molecule
~Molecule()Moleculevirtual