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 | |
| 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 | |
| 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_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 | |
| 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 | |
| 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 |
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