Core Classes

• Class Avogadro::Core::Array
  • Array
    • Array::value_type
    • Array::allocator_type
    • Array::reference
    • Array::const_reference
    • Array::pointer
    • Array::const_pointer
    • Array::iterator
    • Array::const_iterator
    • Array::reverse_iterator
    • Array::const_reverse_iterator
    • Array::difference_type
    • Array::size_type
    • Array::Container
    • Array::ValueType
    • Array::Array()
    • Array::Array()
    • Array::Array()
    • Array::Array()
    • Array::~Array()
    • Array::detachWithCopy()
    • Array::detach()
    • Array::data()
    • Array::data()
    • Array::constData()
    • Array::size()
    • Array::max_size()
    • Array::empty()
    • Array::capacity()
    • Array::reserve()
    • Array::resize()
    • Array::clear()
    • Array::begin()
    • Array::end()
    • Array::begin()
    • Array::end()
    • Array::rbegin()
    • Array::rend()
    • Array::rbegin()
    • Array::rend()
    • Array::front()
    • Array::front()
    • Array::back()
    • Array::back()
    • Array::assign()
    • Array::assign()
    • Array::push_back()
    • Array::pop_back()
    • Array::insert()
    • Array::insert()
    • Array::insert()
    • Array::erase()
    • Array::erase()
    • Array::operator[]()
    • Array::operator[]()
    • Array::at()
    • Array::operator=()
    • Array::operator=()
    • Array::operator=()
    • Array::swap()
    • Array::swapAndPop()
    • Array::d
• Class Avogadro::Core::ArraySet
  • ArraySet
    • ArraySet::ArraySet()
    • ArraySet::~ArraySet()
    • ArraySet::isType()
    • ArraySet::m_content
    • ArraySet::m_data
    • ArraySet::Holder
      • ArraySet::Holder::Holder()
      • ArraySet::Holder::type()
      • ArraySet::Holder::clone()
      • ArraySet::Holder::m_content
    • ArraySet::PlaceHolder
      • ArraySet::PlaceHolder::~PlaceHolder()
      • ArraySet::PlaceHolder::type()
      • ArraySet::PlaceHolder::clone()
• Class Avogadro::Core::ArraySet::Holder
  • Holder
    • Holder::Holder()
    • Holder::type()
    • Holder::clone()
    • Holder::m_content
• Class Avogadro::Core::ArraySet::PlaceHolder
  • PlaceHolder
    • PlaceHolder::~PlaceHolder()
    • PlaceHolder::type()
    • PlaceHolder::clone()
• Class Avogadro::Core::Atom
  • Atom
    • Atom::Atom()
    • Atom::Atom()
• Class Avogadro::Core::AtomTemplate
  • AtomTemplate
    • AtomTemplate::setAtomicNumber()
    • AtomTemplate::atomicNumber()
    • AtomTemplate::setPosition2d()
    • AtomTemplate::position2d()
    • AtomTemplate::setPosition3d()
    • AtomTemplate::position3d()
    • AtomTemplate::setHybridization()
    • AtomTemplate::hybridization()
    • AtomTemplate::setFormalCharge()
    • AtomTemplate::formalCharge()
    • AtomTemplate::setColor()
    • AtomTemplate::color()
    • AtomTemplate::setLayer()
    • AtomTemplate::layer()
    • AtomTemplate::MoleculeType
    • AtomTemplate::AtomTemplate()
    • AtomTemplate::AtomTemplate()
    • AtomTemplate::operator==()
    • AtomTemplate::operator!=()
    • AtomTemplate::operator++()
    • AtomTemplate::operator++()
    • AtomTemplate::operator--()
    • AtomTemplate::operator--()
    • AtomTemplate::isValid()
    • AtomTemplate::molecule()
    • AtomTemplate::index()
    • AtomTemplate::setSelected()
    • AtomTemplate::selected()
    • AtomTemplate::setForceVector()
    • AtomTemplate::forceVector()
    • AtomTemplate::setLabel()
    • AtomTemplate::label()
• Class Avogadro::Core::AtomTyper
  • AtomTyper
    • AtomTyper::ValueType
    • AtomTyper::AtomTyper()
    • AtomTyper::~AtomTyper()
    • AtomTyper::setMolecule()
    • AtomTyper::run()
    • AtomTyper::atomType()
    • AtomTyper::types()
    • AtomTyper::reset()
    • AtomTyper::initialize()
    • AtomTyper::type()
    • AtomTyper::m_molecule
    • AtomTyper::m_types
• Class Avogadro::Core::AvoSpglib
  • AvoSpglib
    • AvoSpglib::AvoSpglib()
    • AvoSpglib::~AvoSpglib()
    • AvoSpglib::getHallNumber()
    • AvoSpglib::reduceToPrimitive()
    • AvoSpglib::conventionalizeCell()
    • AvoSpglib::symmetrize()
• Class Avogadro::Core::BasisSet
  • BasisSet
    • BasisSet::ElectronType
      • BasisSet::ElectronType::Paired
      • BasisSet::ElectronType::Alpha
      • BasisSet::ElectronType::Beta
    • BasisSet::BasisSet()
    • BasisSet::~BasisSet()
    • BasisSet::clone()
    • BasisSet::setElectronCount()
    • BasisSet::electronCount()
    • BasisSet::setMolecule()
    • BasisSet::molecule()
    • BasisSet::molecule()
    • BasisSet::setName()
    • BasisSet::name()
    • BasisSet::setTheoryName()
    • BasisSet::theoryName()
    • BasisSet::molecularOrbitalCount()
    • BasisSet::homo()
    • BasisSet::homo()
    • BasisSet::lumo()
    • BasisSet::lumo()
    • BasisSet::isValid()
    • BasisSet::m_electrons
    • BasisSet::m_molecule
    • BasisSet::m_name
    • BasisSet::m_theoryName
• Class Avogadro::Core::Bond
  • Bond
    • Bond::Bond()
    • Bond::Bond()
• Class Avogadro::Core::BondTemplate
  • BondTemplate
    • BondTemplate::atom1()
    • BondTemplate::atom2()
    • BondTemplate::setOrder()
    • BondTemplate::order()
    • BondTemplate::MoleculeType
    • BondTemplate::AtomType
    • BondTemplate::BondTemplate()
    • BondTemplate::BondTemplate()
    • BondTemplate::operator==()
    • BondTemplate::operator!=()
    • BondTemplate::operator++()
    • BondTemplate::operator++()
    • BondTemplate::operator--()
    • BondTemplate::operator--()
    • BondTemplate::isValid()
    • BondTemplate::molecule()
    • BondTemplate::index()
    • BondTemplate::getOtherAtom()
    • BondTemplate::getOtherAtom()
• Class Avogadro::Core::Color3f
  • Color3f
    • Color3f::Color3f()
    • Color3f::Color3f()
    • Color3f::set()
    • Color3f::red()
    • Color3f::green()
    • Color3f::blue()
    • Color3f::data()
    • Color3f::data()
    • Color3f::m_data
• Class Avogadro::Core::CoordinateBlockGenerator
  • CoordinateBlockGenerator
    • CoordinateBlockGenerator::DistanceUnit
      • CoordinateBlockGenerator::DistanceUnit::Angstrom
      • CoordinateBlockGenerator::DistanceUnit::Bohr
    • CoordinateBlockGenerator::setDistanceUnit()
    • CoordinateBlockGenerator::distanceUnit()
    • CoordinateBlockGenerator::CoordinateBlockGenerator()
    • CoordinateBlockGenerator::setMolecule()
    • CoordinateBlockGenerator::molecule()
    • CoordinateBlockGenerator::setSpecification()
    • CoordinateBlockGenerator::specification()
    • CoordinateBlockGenerator::generateCoordinateBlock()
• Class Avogadro::Core::CoordinateSet
  • CoordinateSet
    • CoordinateSet::CoordinateSet()
    • CoordinateSet::~CoordinateSet()
    • CoordinateSet::resize()
    • CoordinateSet::size()
    • CoordinateSet::coordinates()
    • CoordinateSet::coordinates()
    • CoordinateSet::operator()()
    • CoordinateSet::operator[]()
    • CoordinateSet::operator[]()
• Class Avogadro::Core::CrystalTools
  • CrystalTools
    • CrystalTools::Option
      • CrystalTools::Option::None
      • CrystalTools::Option::TransformAtoms
    • CrystalTools::Options
    • CrystalTools::wrapAtomsToUnitCell()
    • CrystalTools::rotateToStandardOrientation()
    • CrystalTools::setVolume()
    • CrystalTools::niggliReduce()
    • CrystalTools::isNiggliReduced()
    • CrystalTools::buildSupercell()
    • CrystalTools::setCellMatrix()
    • CrystalTools::fractionalCoordinates()
    • CrystalTools::fractionalCoordinates()
    • CrystalTools::setFractionalCoordinates()
• Class Avogadro::Core::Cube
  • Cube
    • Cube::Type
      • Cube::Type::VdW
      • Cube::Type::SolventAccessible
      • Cube::Type::SolventExcluded
      • Cube::Type::ESP
      • Cube::Type::ElectronDensity
      • Cube::Type::SpinDensity
      • Cube::Type::MO
      • Cube::Type::FromFile
      • Cube::Type::None
    • Cube::Cube()
    • Cube::~Cube()
    • Cube::min()
    • Cube::max()
    • Cube::spacing()
    • Cube::dimensions()
    • Cube::setLimits()
    • Cube::setLimits()
    • Cube::setLimits()
    • Cube::setLimits()
    • Cube::setLimits()
    • Cube::setLimits()
    • Cube::data()
    • Cube::data()
    • Cube::setData()
    • Cube::addData()
    • Cube::closestIndex()
    • Cube::indexVector()
    • Cube::position()
    • Cube::value()
    • Cube::value()
    • Cube::valuef()
    • Cube::value()
    • Cube::setValue()
    • Cube::setValue()
    • Cube::fill()
    • Cube::fillStripe()
    • Cube::minValue()
    • Cube::maxValue()
    • Cube::setName()
    • Cube::name()
    • Cube::setCubeType()
    • Cube::cubeType()
    • Cube::lock()
    • Cube::m_data
    • Cube::m_min
    • Cube::m_max
    • Cube::m_spacing
    • Cube::m_points
    • Cube::m_minValue
    • Cube::m_maxValue
    • Cube::m_name
    • Cube::m_cubeType
    • Cube::m_lock
• Class Avogadro::Core::Elements
  • Elements
    • Elements::Elements()
    • Elements::~Elements()
    • Elements::elementCount()
    • Elements::atomicNumberFromName()
    • Elements::atomicNumberFromSymbol()
    • Elements::guessAtomicNumber()
    • Elements::name()
    • Elements::symbol()
    • Elements::mass()
    • Elements::radiusVDW()
    • Elements::radiusCovalent()
    • Elements::color()
    • Elements::valenceElectrons()
• Class Avogadro::Core::GaussianSet
  • GaussianSet
    • GaussianSet::orbital
      • GaussianSet::orbital::S
      • GaussianSet::orbital::SP
      • GaussianSet::orbital::P
      • GaussianSet::orbital::D
      • GaussianSet::orbital::D5
      • GaussianSet::orbital::F
      • GaussianSet::orbital::F7
      • GaussianSet::orbital::G
      • GaussianSet::orbital::G9
      • GaussianSet::orbital::H
      • GaussianSet::orbital::H11
      • GaussianSet::orbital::I
      • GaussianSet::orbital::I13
      • GaussianSet::orbital::UU
    • GaussianSet::GaussianSet()
    • GaussianSet::~GaussianSet()
    • GaussianSet::clone()
    • GaussianSet::addBasis()
    • GaussianSet::addGto()
    • GaussianSet::setMolecularOrbitals()
    • GaussianSet::setMolecularOrbitals()
    • GaussianSet::setCount()
    • GaussianSet::setActiveSetStep()
    • GaussianSet::setMolecularOrbitalEnergy()
    • GaussianSet::setMolecularOrbitalOccupancy()
    • GaussianSet::setMolecularOrbitalNumber()
    • GaussianSet::setDensityMatrix()
    • GaussianSet::setSpinDensityMatrix()
    • GaussianSet::generateDensityMatrix()
    • GaussianSet::generateSpinDensityMatrix()
    • GaussianSet::molecularOrbitalCount()
    • GaussianSet::outputAll()
    • GaussianSet::isValid()
    • GaussianSet::setScfType()
    • GaussianSet::scfType()
    • GaussianSet::setFunctionalName()
    • GaussianSet::functionalName()
    • GaussianSet::initCalculation()
    • GaussianSet::symmetry()
    • GaussianSet::symmetry()
    • GaussianSet::atomIndices()
    • GaussianSet::atomIndices()
    • GaussianSet::moIndices()
    • GaussianSet::moIndices()
    • GaussianSet::gtoIndices()
    • GaussianSet::gtoIndices()
    • GaussianSet::cIndices()
    • GaussianSet::cIndices()
    • GaussianSet::gtoA()
    • GaussianSet::gtoA()
    • GaussianSet::gtoC()
    • GaussianSet::gtoC()
    • GaussianSet::gtoCN()
    • GaussianSet::moMatrix()
    • GaussianSet::moMatrix()
    • GaussianSet::moEnergy()
    • GaussianSet::moEnergy()
    • GaussianSet::moOccupancy()
    • GaussianSet::moOccupancy()
    • GaussianSet::moNumber()
    • GaussianSet::moNumber()
    • GaussianSet::densityMatrix()
    • GaussianSet::spinDensityMatrix()
• Class Avogadro::Core::GaussianSetTools
  • GaussianSetTools
    • GaussianSetTools::GaussianSetTools()
    • GaussianSetTools::~GaussianSetTools()
    • GaussianSetTools::setElectronType()
    • GaussianSetTools::calculateMolecularOrbital()
    • GaussianSetTools::calculateMolecularOrbital()
    • GaussianSetTools::calculateElectronDensity()
    • GaussianSetTools::calculateElectronDensity()
    • GaussianSetTools::calculateSpinDensity()
    • GaussianSetTools::calculateSpinDensity()
    • GaussianSetTools::isValid()
• Class Avogadro::Core::Graph
  • Graph
    • Graph::Graph()
    • Graph::Graph()
    • Graph::~Graph()
    • Graph::setSize()
    • Graph::size()
    • Graph::isEmpty()
    • Graph::clear()
    • Graph::addVertex()
    • Graph::removeVertex()
    • Graph::swapVertexIndices()
    • Graph::vertexCount()
    • Graph::addEdge()
    • Graph::removeEdge()
    • Graph::removeEdge()
    • Graph::removeEdges()
    • Graph::removeEdges()
    • Graph::editEdgeInPlace()
    • Graph::swapEdgeIndices()
    • Graph::edgeCount()
    • Graph::neighbors()
    • Graph::edges()
    • Graph::endpoints()
    • Graph::degree()
    • Graph::containsEdge()
    • Graph::edgePairs()
    • Graph::connectedComponents()
    • Graph::connectedComponent()
    • Graph::subgraphsCount()
    • Graph::subgraph()
    • Graph::subgraphCount()
    • Graph::getConnectedID()
• Class Avogadro::Core::Mesh
  • Mesh
    • Mesh::Mesh()
    • Mesh::Mesh()
    • Mesh::~Mesh()
    • Mesh::reserve()
    • Mesh::setStable()
    • Mesh::stable()
    • Mesh::setIsoValue()
    • Mesh::isoValue()
    • Mesh::setOtherMesh()
    • Mesh::otherMesh()
    • Mesh::setCube()
    • Mesh::cube()
    • Mesh::vertices()
    • Mesh::numVertices()
    • Mesh::vertex()
    • Mesh::setVertices()
    • Mesh::addVertices()
    • Mesh::normals()
    • Mesh::numNormals()
    • Mesh::normal()
    • Mesh::setNormals()
    • Mesh::addNormals()
    • Mesh::colors()
    • Mesh::color()
    • Mesh::setColors()
    • Mesh::addColors()
    • Mesh::valid()
    • Mesh::clear()
    • Mesh::operator=()
    • Mesh::setName()
    • Mesh::name()
    • Mesh::lock()
    • Mesh::smooth()
• Class Avogadro::Core::Molecule
  • Molecule
    • Molecule::customElementMap()
    • Molecule::setCustomElementMap()
    • Molecule::addBond()
    • Molecule::addBond()
    • Molecule::removeBond()
    • Molecule::removeBond()
    • Molecule::bonds()
    • Molecule::bonds()
    • Molecule::bonds()
    • Molecule::setUnitCell()
    • Molecule::unitCell()
    • Molecule::unitCell()
    • Molecule::setHallNumber()
    • Molecule::hallNumber()
    • Molecule::AtomType
    • Molecule::BondType
    • Molecule::CustomElementMap
    • Molecule::ElementMask
    • Molecule::Molecule()
    • Molecule::Molecule()
    • Molecule::Molecule()
    • Molecule::operator=()
    • Molecule::operator=()
    • Molecule::~Molecule()
    • Molecule::readProperties()
    • Molecule::setData()
    • Molecule::data()
    • Molecule::hasData()
    • Molecule::setDataMap()
    • Molecule::dataMap()
    • Molecule::dataMap()
    • Molecule::spectra()
    • Molecule::setSpectra()
    • Molecule::spectraTypes()
    • Molecule::setPartialCharges()
    • Molecule::partialCharges()
    • Molecule::partialChargeTypes()
    • Molecule::hybridizations()
    • Molecule::hybridizations()
    • Molecule::hybridization()
    • Molecule::setHybridizations()
    • Molecule::setHybridization()
    • Molecule::formalCharges()
    • Molecule::formalCharges()
    • Molecule::totalCharge()
    • Molecule::totalSpinMultiplicity()
    • Molecule::formalCharge()
    • Molecule::setFormalCharges()
    • Molecule::setFormalCharge()
    • Molecule::colors()
    • Molecule::colors()
    • Molecule::color()
    • Molecule::setColors()
    • Molecule::setColor()
    • Molecule::setLayer()
    • Molecule::layer()
    • Molecule::atomPositions2d()
    • Molecule::atomPositions2d()
    • Molecule::atomPosition2d()
    • Molecule::setAtomPositions2d()
    • Molecule::setAtomPosition2d()
    • Molecule::atomPositions3d()
    • Molecule::atomPositions3d()
    • Molecule::atomPosition3d()
    • Molecule::setAtomPositions3d()
    • Molecule::setAtomPosition3d()
    • Molecule::atomLabel()
    • Molecule::setAtomLabel()
    • Molecule::atomLabels()
    • Molecule::setAtomLabels()
    • Molecule::setAtomSelected()
    • Molecule::atomSelected()
    • Molecule::isSelectionEmpty()
    • Molecule::elements()
    • Molecule::addAtom()
    • Molecule::addAtom()
    • Molecule::removeAtom()
    • Molecule::removeAtom()
    • Molecule::clearAtoms()
    • Molecule::atom()
    • Molecule::removeBond()
    • Molecule::removeBond()
    • Molecule::clearBonds()
    • Molecule::bond()
    • Molecule::bond()
    • Molecule::bond()
    • Molecule::bondLabel()
    • Molecule::setBondLabel()
    • Molecule::bondLabels()
    • Molecule::setBondLabels()
    • Molecule::addMesh()
    • Molecule::mesh()
    • Molecule::mesh()
    • Molecule::meshCount()
    • Molecule::clearMeshes()
    • Molecule::addCube()
    • Molecule::cube()
    • Molecule::cube()
    • Molecule::cubeCount()
    • Molecule::clearCubes()
    • Molecule::cubes()
    • Molecule::cubes()
    • Molecule::formula()
    • Molecule::mass()
    • Molecule::centerOfGeometry()
    • Molecule::centerOfMass()
    • Molecule::radius()
    • Molecule::bestFitPlane()
    • Molecule::setBasisSet()
    • Molecule::basisSet()
    • Molecule::basisSet()
    • Molecule::vibrationFrequencies()
    • Molecule::setVibrationFrequencies()
    • Molecule::vibrationIRIntensities()
    • Molecule::setVibrationIRIntensities()
    • Molecule::vibrationRamanIntensities()
    • Molecule::setVibrationRamanIntensities()
    • Molecule::vibrationLx()
    • Molecule::setVibrationLx()
    • Molecule::perceiveBondsSimple()
    • Molecule::perceiveBondsFromResidueData()
    • Molecule::perceiveBondOrders()
    • Molecule::perceiveSubstitutedCations()
    • Molecule::coordinate3dCount()
    • Molecule::setCoordinate3d()
    • Molecule::coordinate3d()
    • Molecule::setCoordinate3d()
    • Molecule::clearCoordinate3d()
    • Molecule::setTimeStep()
    • Molecule::timeStep()
    • Molecule::forceVectors()
    • Molecule::forceVectors()
    • Molecule::forceVector()
    • Molecule::setForceVectors()
    • Molecule::setForceVector()
    • Molecule::addResidue()
    • Molecule::addResidue()
    • Molecule::residue()
    • Molecule::residues()
    • Molecule::residues()
    • Molecule::residueCount()
    • Molecule::atomCount()
    • Molecule::atomCount()
    • Molecule::bondCount()
    • Molecule::bondPair()
    • Molecule::setBondPairs()
    • Molecule::bondPairs()
    • Molecule::bondOrders()
    • Molecule::graph()
    • Molecule::atomicNumbers()
    • Molecule::atomicNumber()
    • Molecule::setBondOrders()
    • Molecule::setBondOrder()
    • Molecule::hasCustomElements()
    • Molecule::setBondPair()
    • Molecule::bondOrder()
    • Molecule::setAtomicNumbers()
    • Molecule::setAtomicNumber()
    • Molecule::setFrozenAtom()
    • Molecule::frozenAtom()
    • Molecule::setFrozenAtomAxis()
    • Molecule::frozenAtomMask()
    • Molecule::composition()
    • Molecule::getAtomBonds()
    • Molecule::getAtomOrders()
    • Molecule::removeBonds()
    • Molecule::addBonds()
    • Molecule::swapBond()
    • Molecule::swapAtom()
    • Molecule::getAtomsAtLayer()
    • Molecule::layer()
    • Molecule::layer()
    • Molecule::boundingBox()
    • Molecule::bestFitPlane()
    • Molecule::makeBondPair()
    • Molecule::m_data
    • Molecule::m_partialCharges
    • Molecule::m_spectra
    • Molecule::m_customElementMap
    • Molecule::m_elements
    • Molecule::m_positions2d
    • Molecule::m_positions3d
    • Molecule::m_atomLabels
    • Molecule::m_bondLabels
    • Molecule::m_coordinates3d
    • Molecule::m_timesteps
    • Molecule::m_hybridizations
    • Molecule::m_formalCharges
    • Molecule::m_forceVectors
    • Molecule::m_colors
    • Molecule::m_vibrationFrequencies
    • Molecule::m_vibrationIRIntensities
    • Molecule::m_vibrationRamanIntensities
    • Molecule::m_vibrationLx
    • Molecule::m_selectedAtoms
    • Molecule::m_meshes
    • Molecule::m_cubes
    • Molecule::m_basisSet
    • Molecule::m_unitCell
    • Molecule::m_residues
    • Molecule::m_hallNumber
    • Molecule::m_frozenAtomMask
• Class Avogadro::Core::MoleculeDeserializer
• Class Avogadro::Core::MoleculeSerializer
• Class Avogadro::Core::Mutex
  • Mutex
    • Mutex::Mutex()
    • Mutex::~Mutex()
    • Mutex::lock()
    • Mutex::tryLock()
    • Mutex::unlock()
• Class Avogadro::Core::NameAtomTyper
  • NameAtomTyper
    • NameAtomTyper::NameAtomTyper()
    • NameAtomTyper::~NameAtomTyper()
    • NameAtomTyper::type()
• Class Avogadro::Core::Residue
  • Residue
    • Residue::SecondaryStructure
      • Residue::SecondaryStructure::piHelix
      • Residue::SecondaryStructure::bend
      • Residue::SecondaryStructure::alphaHelix
      • Residue::SecondaryStructure::betaSheet
      • Residue::SecondaryStructure::helix310
      • Residue::SecondaryStructure::betaBridge
      • Residue::SecondaryStructure::turn
      • Residue::SecondaryStructure::coil
      • Residue::SecondaryStructure::maybeBeta
      • Residue::SecondaryStructure::undefined
    • Residue::AtomNameMap
    • Residue::Residue()
    • Residue::Residue()
    • Residue::Residue()
    • Residue::Residue()
    • Residue::Residue()
    • Residue::operator=()
    • Residue::~Residue()
    • Residue::residueName()
    • Residue::setResidueName()
    • Residue::residueId()
    • Residue::setResidueId()
    • Residue::chainId()
    • Residue::setChainId()
    • Residue::secondaryStructure()
    • Residue::setSecondaryStructure()
    • Residue::addResidueAtom()
    • Residue::residueAtoms()
    • Residue::atomNameMap()
    • Residue::resolveResidueBonds()
    • Residue::getAtomByName()
    • Residue::getAtomicNumber()
    • Residue::getAtomName()
    • Residue::getAtomName()
    • Residue::hasAtomByIndex()
    • Residue::setHeterogen()
    • Residue::isHeterogen()
    • Residue::setColor()
    • Residue::color()
    • Residue::m_residueName
    • Residue::m_residueId
    • Residue::m_chainId
    • Residue::m_atomNameMap
    • Residue::m_heterogen
    • Residue::m_color
    • Residue::m_customColorSet
    • Residue::m_secondaryStructure
• Class Avogadro::Core::ResidueData
  • ResidueData
    • ResidueData::ResidueData()
    • ResidueData::ResidueData()
    • ResidueData::ResidueData()
    • ResidueData::operator=()
    • ResidueData::residueAtoms()
    • ResidueData::residueSingleBonds()
    • ResidueData::residueDoubleBonds()
• Class Avogadro::Core::RingPerceiver
  • RingPerceiver
    • RingPerceiver::RingPerceiver()
    • RingPerceiver::~RingPerceiver()
    • RingPerceiver::setMolecule()
    • RingPerceiver::molecule()
    • RingPerceiver::rings()
• Class Avogadro::Core::SharedMutex
  • SharedMutex
    • SharedMutex::SharedMutex()
    • SharedMutex::~SharedMutex()
    • SharedMutex::lockForRead()
    • SharedMutex::tryLockForRead()
    • SharedMutex::unlockForRead()
    • SharedMutex::lockForWrite()
    • SharedMutex::tryLockForWrite()
    • SharedMutex::unlockForWrite()
• Class Avogadro::Core::SlaterSet
  • SlaterSet
    • SlaterSet::slater
      • SlaterSet::slater::S
      • SlaterSet::slater::PX
      • SlaterSet::slater::PY
      • SlaterSet::slater::PZ
      • SlaterSet::slater::X2
      • SlaterSet::slater::XZ
      • SlaterSet::slater::Z2
      • SlaterSet::slater::YZ
      • SlaterSet::slater::XY
      • SlaterSet::slater::UU
    • SlaterSet::SlaterSet()
    • SlaterSet::~SlaterSet()
    • SlaterSet::clone()
    • SlaterSet::addSlaterIndices()
    • SlaterSet::addSlaterTypes()
    • SlaterSet::addZetas()
    • SlaterSet::addPQNs()
    • SlaterSet::addOverlapMatrix()
    • SlaterSet::addEigenVectors()
    • SlaterSet::addDensityMatrix()
    • SlaterSet::molecularOrbitalCount()
    • SlaterSet::isValid()
    • SlaterSet::initCalculation()
    • SlaterSet::slaterIndices()
    • SlaterSet::slaterTypes()
    • SlaterSet::zetas()
    • SlaterSet::factors()
    • SlaterSet::PQNs()
    • SlaterSet::normalizedMatrix()
    • SlaterSet::densityMatrix()
    • SlaterSet::outputAll()
• Class Avogadro::Core::SlaterSetTools
  • SlaterSetTools
    • SlaterSetTools::SlaterSetTools()
    • SlaterSetTools::~SlaterSetTools()
    • SlaterSetTools::calculateMolecularOrbital()
    • SlaterSetTools::calculateElectronDensity()
    • SlaterSetTools::calculateSpinDensity()
    • SlaterSetTools::isValid()
• Class Avogadro::Core::SpaceGroups
  • SpaceGroups
    • SpaceGroups::SpaceGroups()
    • SpaceGroups::~SpaceGroups()
    • SpaceGroups::hallNumber()
    • SpaceGroups::crystalSystem()
    • SpaceGroups::internationalNumber()
    • SpaceGroups::schoenflies()
    • SpaceGroups::hallSymbol()
    • SpaceGroups::international()
    • SpaceGroups::internationalFull()
    • SpaceGroups::internationalShort()
    • SpaceGroups::setting()
    • SpaceGroups::transformsCount()
    • SpaceGroups::getTransforms()
    • SpaceGroups::fillUnitCell()
    • SpaceGroups::reduceToAsymmetricUnit()
• Class Avogadro::Core::SymbolAtomTyper
  • SymbolAtomTyper
    • SymbolAtomTyper::SymbolAtomTyper()
    • SymbolAtomTyper::~SymbolAtomTyper()
    • SymbolAtomTyper::type()
• Class Avogadro::Core::UnitCell
  • UnitCell
    • UnitCell::aVector()
    • UnitCell::bVector()
    • UnitCell::cVector()
    • UnitCell::setAVector()
    • UnitCell::setBVector()
    • UnitCell::setCVector()
    • UnitCell::a()
    • UnitCell::b()
    • UnitCell::c()
    • UnitCell::cellMatrix()
    • UnitCell::setCellMatrix()
    • UnitCell::toFractional()
    • UnitCell::toFractional()
    • UnitCell::toCartesian()
    • UnitCell::toCartesian()
    • UnitCell::wrapFractional()
    • UnitCell::wrapFractional()
    • UnitCell::wrapCartesian()
    • UnitCell::wrapCartesian()
    • UnitCell::UnitCell()
    • UnitCell::UnitCell()
    • UnitCell::UnitCell()
    • UnitCell::UnitCell()
    • UnitCell::UnitCell()
    • UnitCell::~UnitCell()
    • UnitCell::operator=()
    • UnitCell::alpha()
    • UnitCell::beta()
    • UnitCell::gamma()
    • UnitCell::setCellParameters()
    • UnitCell::volume()
    • UnitCell::imageOffset()
    • UnitCell::fractionalMatrix()
    • UnitCell::setFractionalMatrix()
    • UnitCell::minimumImage()
    • UnitCell::distance()
    • UnitCell::minimumImageFractional()
    • UnitCell::swap()
• Class Avogadro::Core::Variant
  • Variant
    • Variant::Type
      • Variant::Type::Null
      • Variant::Type::Bool
      • Variant::Type::Int
      • Variant::Type::Long
      • Variant::Type::Float
      • Variant::Type::Double
      • Variant::Type::Pointer
      • Variant::Type::String
      • Variant::Type::Matrix
    • Variant::Variant()
    • Variant::Variant()
    • Variant::Variant()
    • Variant::~Variant()
    • Variant::type()
    • Variant::isNull()
    • Variant::setValue()
    • Variant::value()
    • Variant::clear()
    • Variant::toBool()
    • Variant::toChar()
    • Variant::toUChar()
    • Variant::toShort()
    • Variant::toUShort()
    • Variant::toInt()
    • Variant::toUInt()
    • Variant::toLong()
    • Variant::toULong()
    • Variant::toFloat()
    • Variant::toDouble()
    • Variant::toReal()
    • Variant::toPointer()
    • Variant::toString()
    • Variant::toMatrix()
    • Variant::toMatrixRef()
    • Variant::operator=()
    • Variant::Variant()
    • Variant::Variant()
    • Variant::setValue()
    • Variant::setValue()
    • Variant::setValue()
    • Variant::setValue()
    • Variant::setValue()
    • Variant::setValue()
    • Variant::setValue()
    • Variant::setValue()
    • Variant::setValue()
    • Variant::setValue()
    • Variant::setValue()
    • Variant::value()
    • Variant::_bool
    • Variant::_char
    • Variant::_int
    • Variant::_long
    • Variant::_float
    • Variant::_double
    • Variant::pointer
    • Variant::string
    • Variant::matrix
• Class Avogadro::Core::VariantMap
  • VariantMap
    • VariantMap::iterator
    • VariantMap::const_iterator
    • VariantMap::VariantMap()
    • VariantMap::~VariantMap()
    • VariantMap::size()
    • VariantMap::isEmpty()
    • VariantMap::names()
    • VariantMap::setValue()
    • VariantMap::value()
    • VariantMap::hasValue()
    • VariantMap::clear()
    • VariantMap::begin()
    • VariantMap::begin()
    • VariantMap::constBegin()
    • VariantMap::end()
    • VariantMap::end()
    • VariantMap::constEnd()
• Class Avogadro::Core::internal::ArrayRefContainer
  • ArrayRefContainer
    • ArrayRefContainer::ValueType
    • ArrayRefContainer::Parent
    • ArrayRefContainer::value_type
    • ArrayRefContainer::allocator_type
    • ArrayRefContainer::reference
    • ArrayRefContainer::const_reference
    • ArrayRefContainer::pointer
    • ArrayRefContainer::const_pointer
    • ArrayRefContainer::iterator
    • ArrayRefContainer::const_iterator
    • ArrayRefContainer::reverse_iterator
    • ArrayRefContainer::const_reverse_iterator
    • ArrayRefContainer::difference_type
    • ArrayRefContainer::size_type
    • ArrayRefContainer::ArrayRefContainer()
    • ArrayRefContainer::ArrayRefContainer()
    • ArrayRefContainer::ArrayRefContainer()
    • ArrayRefContainer::ArrayRefContainer()
    • ArrayRefContainer::reref()
    • ArrayRefContainer::deref()
    • ArrayRefContainer::ref()
    • ArrayRefContainer::m_ref
    • ArrayRefContainer::data
• Class Avogadro::TypeTraits
  • TypeTraits
    • TypeTraits::@0
      • TypeTraits::@0::EnumValue
    • TypeTraits::name()
• Class Avogadro::TypeTraits< char >
  • TypeTraits
    • TypeTraits::@1
      • TypeTraits::@1::EnumValue
    • TypeTraits::name()
• Class Avogadro::TypeTraits< double >
  • TypeTraits
    • TypeTraits::@8
      • TypeTraits::@8::EnumValue
    • TypeTraits::name()
• Class Avogadro::TypeTraits< float >
  • TypeTraits
    • TypeTraits::@7
      • TypeTraits::@7::EnumValue
    • TypeTraits::name()
• Class Avogadro::TypeTraits< int >
  • TypeTraits
    • TypeTraits::@5
      • TypeTraits::@5::EnumValue
    • TypeTraits::name()
• Class Avogadro::TypeTraits< short >
  • TypeTraits
    • TypeTraits::@3
      • TypeTraits::@3::EnumValue
    • TypeTraits::name()
• Class Avogadro::TypeTraits< unsigned char >
  • TypeTraits
    • TypeTraits::@2
      • TypeTraits::@2::EnumValue
    • TypeTraits::name()
• Class Avogadro::TypeTraits< unsigned int >
  • TypeTraits
    • TypeTraits::@6
      • TypeTraits::@6::EnumValue
    • TypeTraits::name()
• Class Avogadro::TypeTraits< unsigned short >
  • TypeTraits
    • TypeTraits::@4
      • TypeTraits::@4::EnumValue
    • TypeTraits::name()