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Molecule Member List

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

activeCube() | Molecule |
activeCube() const (defined in Molecule) | Molecule |
activeCubeIndex() const | Molecule |
addAtom(unsigned char atomicNumber) | Molecule | virtual
addAtom(unsigned char atomicNumber, Vector3 position3d) (defined in Molecule) | Molecule |
addBond(Index atom1, Index atom2, unsigned char order=1) | Molecule | virtual
addBond(const AtomType &atom1, const AtomType &atom2, unsigned char order=1) | Molecule | virtual
addBonds(const Array< std::pair< Index, Index > > &bonds, const Array< unsigned char > &orders) (defined in Molecule) | Molecule |
addConstraint(Real Value, Index a, Index b, Index c=MaxIndex, Index d=MaxIndex) | Molecule |
addConstraint(Constraint &c) | 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) const | Molecule |
atomCount() const | Molecule |
atomCount(unsigned char atomicNumber) const | Molecule |
atomicNumber(Index atomId) const | Molecule |
atomicNumbers() const | Molecule |
atomLabel(Index atomId) const | Molecule |
atomLabels() const (defined in Molecule) | Molecule |
atomPosition2d(Index atomId) const | Molecule |
atomPosition3d(Index atomId) const | Molecule |
atomPositions2d() const | Molecule |
atomPositions2d() | Molecule |
atomPositions3d() const | Molecule |
atomPositions3d() | Molecule |
atomSelected(Index atomId) const | Molecule |
AtomType typedef | 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 |
bondCount() const | Molecule |
bondLabel(Index bondIndex) const | Molecule |
bondLabels() const (defined in Molecule) | 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 |
BondType typedef | Molecule |
boundingBox(Vector3 &boxMin, Vector3 &boxMax, const double radius=1.0) const | Molecule |
centerOfGeometry() const | Molecule |
centerOfMass() const | Molecule |
clearAtoms() | Molecule | virtual
clearBonds() | Molecule | virtual
clearConstraints() | Molecule |
clearCoordinate3d() | Molecule |
clearCubes() (defined in Molecule) | Molecule |
clearMeshes() (defined in Molecule) | Molecule |
clearVelocities() | Molecule |
color(Index atomId) const | Molecule |
colors() | Molecule |
colors() const | Molecule |
composition() const | Molecule |
constraints() | Molecule |
constraints() const | Molecule |
coordinate3d(size_t index) const (defined in Molecule) | Molecule |
coordinate3dCount() const (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 |
estimateVelocities() | 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 |
formulaComposition() const | Molecule |
frozenAtom(Index atomId) const | Molecule |
frozenAtomAxis(Index atomId, int axis) const | Molecule |
frozenAtomMask() const | Molecule |
getAtomBonds(Index index) const | Molecule |
getAtomOrders(Index index) const | 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 |
isotope(Index atomId) const | Molecule |
isotopes() | Molecule |
isotopes() const | Molecule |
isSelectionEmpty() const | Molecule |
layer(Index atomId) const (defined in Molecule) | Molecule |
layer() (defined in Molecule) | Molecule |
layer() const (defined in Molecule) | Molecule |
m_activeCubeIndex (defined in Molecule) | Molecule | protected
m_atomLabels (defined in Molecule) | Molecule | protected
m_basisSet (defined in Molecule) | Molecule | protected
m_bondLabels (defined in Molecule) | Molecule | protected
m_colors (defined in Molecule) | Molecule | protected
m_constraints (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_isotopes | 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_residueLabels (defined in Molecule) | Molecule | protected
m_residues (defined in Molecule) | Molecule | protected
m_selectedAtoms (defined in Molecule) | Molecule | protected
m_spectra | Molecule | protected
m_timesteps (defined in Molecule) | Molecule | protected
m_unitCell (defined in Molecule) | Molecule | protected
m_velocities | 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 |
Molecule() | Molecule |
Molecule(const Molecule &other) | Molecule |
Molecule(Molecule &&other) noexcept | Molecule |
monoisotopicMass() const | Molecule |
operator=(const Molecule &other) | 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 |
radius() const | Molecule |
readProperties(const Molecule &other) | Molecule |
removeAtom(Index index) | Molecule | virtual
removeAtom(const AtomType &atom) | Molecule | virtual
removeBond(Index index) | Molecule | virtual
removeBond(const BondType &bond) | Molecule | virtual
removeBond(Index atom1, Index atom2) | Molecule | virtual
removeBond(const AtomType &atom1, const AtomType &atom2) | Molecule | virtual
removeBonds(Index atom) | Molecule |
removeConstraint(Index a, Index b, Index c=MaxIndex, Index d=MaxIndex) | Molecule |
residue(Index index) (defined in Molecule) | Molecule |
residue(Index index) const (defined in Molecule) | Molecule |
residueCount() const | Molecule |
residueLabel(Index residueIndex) const | Molecule |
residueLabels() const (defined in Molecule) | Molecule |
residues() (defined in Molecule) | Molecule |
residues() const (defined in Molecule) | Molecule |
setActiveCubeIndex(Index index) | Molecule |
setAtomicNumber(Index atomId, unsigned char atomicNumber) | Molecule |
setAtomicNumbers(const Core::Array< unsigned char > &nums) | Molecule |
setAtomLabel(Index atomId, const std::string &label) | Molecule |
setAtomLabels(const Core::Array< std::string > &label) | 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 |
setBondLabel(Index bondIndex, const std::string &label) | Molecule |
setBondLabels(const Core::Array< std::string > &label) | 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 |
setConstraints(const std::vector< Core::Constraint > &constraints) | Molecule |
setCoordinate3d(int coord) (defined in Molecule) | Molecule |
setCoordinate3d(const Array< Vector3 > &coords, size_t 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 |
setIsotope(Index atomId, unsigned short isotope) | Molecule |
setIsotopes(const Core::Array< unsigned short > &isotopes) | Molecule |
setLayer(Index atomId, size_t layer) (defined in Molecule) | Molecule |
setPartialCharges(const std::string &type, const MatrixX &value) | Molecule |
setResidueLabel(Index residueIndex, const std::string &label) | Molecule |
setResidueLabels(const Core::Array< std::string > &label) | Molecule |
setSpectra(const std::string &name, const MatrixX &value) | Molecule |
setTimeStep(double timestep, int index) | Molecule |
setUnitCell(UnitCell *uc) | Molecule |
setVelocities(const Array< Vector3 > &velocities, int index) | 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 |
spectra(const std::string &name) const | Molecule |
spectraTypes() const | 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 |
unitCell() | Molecule |
unitCell() const | Molecule |
velocities(int index) 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() | Molecule | virtual