Class List

• 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()
• IO Classes
  • Class Avogadro::Io::CjsonFormat
    • CjsonFormat
      • CjsonFormat::CjsonFormat()
      • CjsonFormat::~CjsonFormat()
      • CjsonFormat::supportedOperations()
      • CjsonFormat::newInstance()
      • CjsonFormat::identifier()
      • CjsonFormat::name()
      • CjsonFormat::description()
      • CjsonFormat::specificationUrl()
      • CjsonFormat::fileExtensions()
      • CjsonFormat::mimeTypes()
      • CjsonFormat::read()
      • CjsonFormat::write()
      • CjsonFormat::deserialize()
      • CjsonFormat::serialize()
  • Class Avogadro::Io::CmlFormat
    • CmlFormat
      • CmlFormat::CmlFormat()
      • CmlFormat::~CmlFormat()
      • CmlFormat::supportedOperations()
      • CmlFormat::newInstance()
      • CmlFormat::identifier()
      • CmlFormat::name()
      • CmlFormat::description()
      • CmlFormat::specificationUrl()
      • CmlFormat::fileExtensions()
      • CmlFormat::mimeTypes()
      • CmlFormat::read()
      • CmlFormat::write()
  • Class Avogadro::Io::DcdFormat
    • DcdFormat
      • DcdFormat::DcdFormat()
      • DcdFormat::~DcdFormat()
      • DcdFormat::supportedOperations()
      • DcdFormat::newInstance()
      • DcdFormat::identifier()
      • DcdFormat::name()
      • DcdFormat::description()
      • DcdFormat::specificationUrl()
      • DcdFormat::fileExtensions()
      • DcdFormat::mimeTypes()
      • DcdFormat::read()
      • DcdFormat::write()
  • Class Avogadro::Io::FileFormat
    • FileFormat
      • FileFormat::Operation
        • FileFormat::Operation::None
        • FileFormat::Operation::Read
        • FileFormat::Operation::Write
        • FileFormat::Operation::ReadWrite
        • FileFormat::Operation::MultiMolecule
        • FileFormat::Operation::Stream
        • FileFormat::Operation::String
        • FileFormat::Operation::File
        • FileFormat::Operation::All
      • FileFormat::Operations
      • FileFormat::FileFormat()
      • FileFormat::~FileFormat()
      • FileFormat::supportedOperations()
      • FileFormat::open()
      • FileFormat::mode()
      • FileFormat::isMode()
      • FileFormat::close()
      • FileFormat::readMolecule()
      • FileFormat::writeMolecule()
      • FileFormat::read()
      • FileFormat::write()
      • FileFormat::readFile()
      • FileFormat::writeFile()
      • FileFormat::readString()
      • FileFormat::writeString()
      • FileFormat::error()
      • FileFormat::fileName()
      • FileFormat::setOptions()
      • FileFormat::options()
      • FileFormat::clear()
      • FileFormat::newInstance()
      • FileFormat::identifier()
      • FileFormat::name()
      • FileFormat::description()
      • FileFormat::specificationUrl()
      • FileFormat::fileExtensions()
      • FileFormat::mimeTypes()
      • FileFormat::validateFileName()
      • FileFormat::appendError()
  • Class Avogadro::Io::FileFormatManager
    • FileFormatManager
      • FileFormatManager::readFile()
      • FileFormatManager::writeFile()
      • FileFormatManager::readString()
      • FileFormatManager::writeString()
      • FileFormatManager::addFormat()
      • FileFormatManager::removeFormat()
      • FileFormatManager::newFormatFromIdentifier()
      • FileFormatManager::newFormatFromMimeType()
      • FileFormatManager::newFormatFromFileExtension()
      • FileFormatManager::identifiers()
      • FileFormatManager::mimeTypes()
      • FileFormatManager::fileExtensions()
      • FileFormatManager::fileFormats()
      • FileFormatManager::fileFormatsFromMimeType()
      • FileFormatManager::fileFormatsFromFileExtension()
      • FileFormatManager::error()
      • FileFormatManager::instance()
      • FileFormatManager::registerFormat()
      • FileFormatManager::unregisterFormat()
  • Class Avogadro::Io::GromacsFormat
    • GromacsFormat
      • GromacsFormat::GromacsFormat()
      • GromacsFormat::~GromacsFormat()
      • GromacsFormat::supportedOperations()
      • GromacsFormat::newInstance()
      • GromacsFormat::identifier()
      • GromacsFormat::name()
      • GromacsFormat::description()
      • GromacsFormat::specificationUrl()
      • GromacsFormat::fileExtensions()
      • GromacsFormat::mimeTypes()
      • GromacsFormat::read()
      • GromacsFormat::write()
  • Class Avogadro::Io::Hdf5DataFormat
    • Hdf5DataFormat
      • Hdf5DataFormat::OpenMode
        • Hdf5DataFormat::OpenMode::ReadOnly
        • Hdf5DataFormat::OpenMode::ReadWriteTruncate
        • Hdf5DataFormat::OpenMode::ReadWriteAppend
      • Hdf5DataFormat::Hdf5DataFormat()
      • Hdf5DataFormat::~Hdf5DataFormat()
      • Hdf5DataFormat::isOpen()
      • Hdf5DataFormat::openFile()
      • Hdf5DataFormat::filename()
      • Hdf5DataFormat::closeFile()
      • Hdf5DataFormat::setThreshold()
      • Hdf5DataFormat::threshold()
      • Hdf5DataFormat::exceedsThreshold()
      • Hdf5DataFormat::exceedsThreshold()
      • Hdf5DataFormat::exceedsThreshold()
      • Hdf5DataFormat::exceedsThreshold()
      • Hdf5DataFormat::datasetExists()
      • Hdf5DataFormat::removeDataset()
      • Hdf5DataFormat::datasetDimensions()
      • Hdf5DataFormat::writeDataset()
      • Hdf5DataFormat::writeDataset()
      • Hdf5DataFormat::writeDataset()
      • Hdf5DataFormat::readDataset()
      • Hdf5DataFormat::readDataset()
      • Hdf5DataFormat::readDataset()
      • Hdf5DataFormat::datasets()
  • Class Avogadro::Io::LammpsDataFormat
    • LammpsDataFormat
      • LammpsDataFormat::LammpsDataFormat()
      • LammpsDataFormat::~LammpsDataFormat()
      • LammpsDataFormat::supportedOperations()
      • LammpsDataFormat::newInstance()
      • LammpsDataFormat::identifier()
      • LammpsDataFormat::name()
      • LammpsDataFormat::description()
      • LammpsDataFormat::specificationUrl()
      • LammpsDataFormat::fileExtensions()
      • LammpsDataFormat::mimeTypes()
      • LammpsDataFormat::read()
      • LammpsDataFormat::write()
  • Class Avogadro::Io::LammpsTrajectoryFormat
    • LammpsTrajectoryFormat
      • LammpsTrajectoryFormat::LammpsTrajectoryFormat()
      • LammpsTrajectoryFormat::~LammpsTrajectoryFormat()
      • LammpsTrajectoryFormat::supportedOperations()
      • LammpsTrajectoryFormat::newInstance()
      • LammpsTrajectoryFormat::identifier()
      • LammpsTrajectoryFormat::name()
      • LammpsTrajectoryFormat::description()
      • LammpsTrajectoryFormat::specificationUrl()
      • LammpsTrajectoryFormat::fileExtensions()
      • LammpsTrajectoryFormat::mimeTypes()
      • LammpsTrajectoryFormat::read()
      • LammpsTrajectoryFormat::write()
  • Class Avogadro::Io::MMTFFormat
    • MMTFFormat
      • MMTFFormat::MMTFFormat()
      • MMTFFormat::~MMTFFormat()
      • MMTFFormat::supportedOperations()
      • MMTFFormat::newInstance()
      • MMTFFormat::identifier()
      • MMTFFormat::name()
      • MMTFFormat::description()
      • MMTFFormat::specificationUrl()
      • MMTFFormat::fileExtensions()
      • MMTFFormat::mimeTypes()
      • MMTFFormat::read()
      • MMTFFormat::write()
  • Class Avogadro::Io::MdlFormat
    • MdlFormat
      • MdlFormat::MdlFormat()
      • MdlFormat::~MdlFormat()
      • MdlFormat::supportedOperations()
      • MdlFormat::newInstance()
      • MdlFormat::identifier()
      • MdlFormat::name()
      • MdlFormat::description()
      • MdlFormat::specificationUrl()
      • MdlFormat::fileExtensions()
      • MdlFormat::mimeTypes()
      • MdlFormat::read()
      • MdlFormat::write()
  • Class Avogadro::Io::OutcarFormat
    • OutcarFormat
      • OutcarFormat::OutcarFormat()
      • OutcarFormat::~OutcarFormat()
      • OutcarFormat::supportedOperations()
      • OutcarFormat::newInstance()
      • OutcarFormat::identifier()
      • OutcarFormat::name()
      • OutcarFormat::description()
      • OutcarFormat::specificationUrl()
      • OutcarFormat::fileExtensions()
      • OutcarFormat::mimeTypes()
      • OutcarFormat::read()
      • OutcarFormat::write()
  • Class Avogadro::Io::PdbFormat
    • PdbFormat
      • PdbFormat::PdbFormat()
      • PdbFormat::~PdbFormat()
      • PdbFormat::supportedOperations()
      • PdbFormat::newInstance()
      • PdbFormat::identifier()
      • PdbFormat::name()
      • PdbFormat::description()
      • PdbFormat::specificationUrl()
      • PdbFormat::fileExtensions()
      • PdbFormat::mimeTypes()
      • PdbFormat::read()
      • PdbFormat::write()
      • PdbFormat::perceiveSubstitutedCations()
  • Class Avogadro::Io::PoscarFormat
    • PoscarFormat
      • PoscarFormat::PoscarFormat()
      • PoscarFormat::~PoscarFormat()
      • PoscarFormat::supportedOperations()
      • PoscarFormat::newInstance()
      • PoscarFormat::identifier()
      • PoscarFormat::name()
      • PoscarFormat::description()
      • PoscarFormat::specificationUrl()
      • PoscarFormat::fileExtensions()
      • PoscarFormat::mimeTypes()
      • PoscarFormat::read()
      • PoscarFormat::write()
  • Class Avogadro::Io::TrrFormat
    • TrrFormat
      • TrrFormat::TrrFormat()
      • TrrFormat::~TrrFormat()
      • TrrFormat::supportedOperations()
      • TrrFormat::newInstance()
      • TrrFormat::identifier()
      • TrrFormat::name()
      • TrrFormat::description()
      • TrrFormat::specificationUrl()
      • TrrFormat::fileExtensions()
      • TrrFormat::mimeTypes()
      • TrrFormat::read()
      • TrrFormat::write()
  • Class Avogadro::Io::XyzFormat
    • XyzFormat
      • XyzFormat::XyzFormat()
      • XyzFormat::~XyzFormat()
      • XyzFormat::supportedOperations()
      • XyzFormat::newInstance()
      • XyzFormat::identifier()
      • XyzFormat::name()
      • XyzFormat::description()
      • XyzFormat::specificationUrl()
      • XyzFormat::fileExtensions()
      • XyzFormat::mimeTypes()
      • XyzFormat::read()
      • XyzFormat::write()
  • Class Avogadro::QuantumIO::GAMESSUSOutput
    • GAMESSUSOutput
      • GAMESSUSOutput::GAMESSUSOutput()
      • GAMESSUSOutput::~GAMESSUSOutput()
      • GAMESSUSOutput::supportedOperations()
      • GAMESSUSOutput::newInstance()
      • GAMESSUSOutput::identifier()
      • GAMESSUSOutput::name()
      • GAMESSUSOutput::description()
      • GAMESSUSOutput::specificationUrl()
      • GAMESSUSOutput::fileExtensions()
      • GAMESSUSOutput::mimeTypes()
      • GAMESSUSOutput::read()
      • GAMESSUSOutput::write()
  • Class Avogadro::QuantumIO::GUKBasisSet
    • GUKBasisSet
      • GUKBasisSet::GUKBasisSet()
      • GUKBasisSet::~GUKBasisSet()
      • GUKBasisSet::outputCoord()
      • GUKBasisSet::outputBasis()
      • GUKBasisSet::labelIndex()
      • GUKBasisSet::shellTypeFromString()
      • GUKBasisSet::atomLabels
      • GUKBasisSet::coordinates
      • GUKBasisSet::shellLabels
      • GUKBasisSet::shells
      • GUKBasisSet::gtoIndicies
      • GUKBasisSet::gtoExponents
      • GUKBasisSet::gtoCoefficients
      • GUKBasisSet::moEnergies
      • GUKBasisSet::moVectors
      • GUKBasisSet::nShell
      • GUKBasisSet::nBasisFunctions
      • GUKBasisSet::nElectrons
  • Class Avogadro::QuantumIO::GamessukOut
    • GamessukOut
      • GamessukOut::GamessukOut()
      • GamessukOut::~GamessukOut()
      • GamessukOut::GamessukOutNoQt()
      • GamessukOut::outputParsedData()
  • Class Avogadro::QuantumIO::GaussianCube
    • GaussianCube
      • GaussianCube::GaussianCube()
      • GaussianCube::~GaussianCube()
      • GaussianCube::supportedOperations()
      • GaussianCube::newInstance()
      • GaussianCube::identifier()
      • GaussianCube::name()
      • GaussianCube::description()
      • GaussianCube::specificationUrl()
      • GaussianCube::fileExtensions()
      • GaussianCube::mimeTypes()
      • GaussianCube::read()
      • GaussianCube::write()
  • Class Avogadro::QuantumIO::GaussianFchk
    • GaussianFchk
      • GaussianFchk::GaussianFchk()
      • GaussianFchk::~GaussianFchk()
      • GaussianFchk::supportedOperations()
      • GaussianFchk::newInstance()
      • GaussianFchk::identifier()
      • GaussianFchk::name()
      • GaussianFchk::description()
      • GaussianFchk::specificationUrl()
      • GaussianFchk::fileExtensions()
      • GaussianFchk::mimeTypes()
      • GaussianFchk::read()
      • GaussianFchk::write()
      • GaussianFchk::outputAll()
  • Class Avogadro::QuantumIO::MoldenFile
    • MoldenFile
      • MoldenFile::MoldenFile()
      • MoldenFile::~MoldenFile()
      • MoldenFile::supportedOperations()
      • MoldenFile::newInstance()
      • MoldenFile::identifier()
      • MoldenFile::name()
      • MoldenFile::description()
      • MoldenFile::specificationUrl()
      • MoldenFile::fileExtensions()
      • MoldenFile::mimeTypes()
      • MoldenFile::read()
      • MoldenFile::write()
  • Class Avogadro::QuantumIO::MopacAux
    • MopacAux
      • MopacAux::MopacAux()
      • MopacAux::~MopacAux()
      • MopacAux::outputAll()
      • MopacAux::supportedOperations()
      • MopacAux::newInstance()
      • MopacAux::identifier()
      • MopacAux::name()
      • MopacAux::description()
      • MopacAux::specificationUrl()
      • MopacAux::fileExtensions()
      • MopacAux::mimeTypes()
      • MopacAux::read()
      • MopacAux::write()
  • Class Avogadro::QuantumIO::NWChemJson
    • NWChemJson
      • NWChemJson::NWChemJson()
      • NWChemJson::~NWChemJson()
      • NWChemJson::supportedOperations()
      • NWChemJson::newInstance()
      • NWChemJson::identifier()
      • NWChemJson::name()
      • NWChemJson::description()
      • NWChemJson::specificationUrl()
      • NWChemJson::fileExtensions()
      • NWChemJson::mimeTypes()
      • NWChemJson::read()
      • NWChemJson::write()
  • Class Avogadro::QuantumIO::NWChemLog
    • NWChemLog
      • NWChemLog::NWChemLog()
      • NWChemLog::~NWChemLog()
      • NWChemLog::outputAll()
      • NWChemLog::supportedOperations()
      • NWChemLog::newInstance()
      • NWChemLog::identifier()
      • NWChemLog::name()
      • NWChemLog::description()
      • NWChemLog::specificationUrl()
      • NWChemLog::fileExtensions()
      • NWChemLog::mimeTypes()
      • NWChemLog::read()
      • NWChemLog::write()
• MoleQueue Classes
  • Class Avogadro::MoleQueue::BatchJob
    • BatchJob
      • BatchJob::setInputGeneratorOptions()
      • BatchJob::inputGeneratorOptions()
      • BatchJob::setMoleQueueOptions()
      • BatchJob::moleQueueOptions()
      • BatchJob::moleQueueJobTemplate()
      • BatchJob::inputGenerator()
      • BatchJob::inputGenerator()
      • BatchJob::JobState
        • BatchJob::JobState::Rejected
        • BatchJob::JobState::Unknown
        • BatchJob::JobState::None
        • BatchJob::JobState::Accepted
        • BatchJob::JobState::QueuedLocal
        • BatchJob::JobState::Submitted
        • BatchJob::JobState::QueuedRemote
        • BatchJob::JobState::RunningLocal
        • BatchJob::JobState::RunningRemote
        • BatchJob::JobState::Finished
        • BatchJob::JobState::Canceled
        • BatchJob::JobState::Error
      • BatchJob::BatchId
      • BatchJob::RequestId
      • BatchJob::ServerId
      • BatchJob::BatchJob()
      • BatchJob::BatchJob()
      • BatchJob::~BatchJob()
      • BatchJob::description()
      • BatchJob::jobState()
      • BatchJob::serverId()
      • BatchJob::jobObject()
      • BatchJob::hasUnfinishedJobs()
      • BatchJob::unfinishedJobCount()
      • BatchJob::finishedJobCount()
      • BatchJob::jobCount()
      • BatchJob::submitNextJob()
      • BatchJob::lookupJob()
      • BatchJob::jobUpdated()
      • BatchJob::jobCompleted()
      • BatchJob::isTerminal()
      • BatchJob::InvalidBatchId
      • BatchJob::InvalidRequestId
      • BatchJob::InvalidServerId
  • Class Avogadro::MoleQueue::InputGenerator
    • InputGenerator
      • InputGenerator::InputGenerator()
      • InputGenerator::InputGenerator()
      • InputGenerator::~InputGenerator()
      • InputGenerator::debug()
      • InputGenerator::isValid()
      • InputGenerator::options()
      • InputGenerator::displayName()
      • InputGenerator::scriptFilePath()
      • InputGenerator::setScriptFilePath()
      • InputGenerator::reset()
      • InputGenerator::generateInput()
      • InputGenerator::numberOfInputFiles()
      • InputGenerator::fileNames()
      • InputGenerator::mainFileName()
      • InputGenerator::fileContents()
      • InputGenerator::createFileHighlighter()
      • InputGenerator::hasErrors()
      • InputGenerator::clearErrors()
      • InputGenerator::errorList()
      • InputGenerator::warningList()
      • InputGenerator::setDebug()
  • Class Avogadro::MoleQueue::InputGeneratorDialog
    • InputGeneratorDialog
      • InputGeneratorDialog::widget()
      • InputGeneratorDialog::widget()
      • InputGeneratorDialog::InputGeneratorDialog()
      • InputGeneratorDialog::InputGeneratorDialog()
      • InputGeneratorDialog::~InputGeneratorDialog()
      • InputGeneratorDialog::setInputGeneratorScript()
      • InputGeneratorDialog::configureBatchJob()
      • InputGeneratorDialog::setMolecule()
  • Class Avogadro::MoleQueue::InputGeneratorWidget
    • InputGeneratorWidget
      • InputGeneratorWidget::inputGenerator()
      • InputGeneratorWidget::batchMode()
      • InputGeneratorWidget::configureBatchJob()
      • InputGeneratorWidget::setMolecule()
      • InputGeneratorWidget::setBatchMode()
      • InputGeneratorWidget::closeClicked()
      • InputGeneratorWidget::openJobOutput()
      • InputGeneratorWidget::showEvent()
      • InputGeneratorWidget::updateOptions()
      • InputGeneratorWidget::InputGeneratorWidget()
      • InputGeneratorWidget::~InputGeneratorWidget()
      • InputGeneratorWidget::setInputGeneratorScript()
  • Class Avogadro::MoleQueue::MoleQueueDialog
    • MoleQueueDialog
      • MoleQueueDialog::widget()
      • MoleQueueDialog::widget()
      • MoleQueueDialog::SubmitOption
        • MoleQueueDialog::SubmitOption::WaitForSubmissionResponse
        • MoleQueueDialog::SubmitOption::SelectProgramFromTemplate
      • MoleQueueDialog::SubmitStatus
        • MoleQueueDialog::SubmitStatus::SubmissionSuccessful
        • MoleQueueDialog::SubmitStatus::SubmissionFailed
        • MoleQueueDialog::SubmitStatus::SubmissionAttempted
        • MoleQueueDialog::SubmitStatus::SubmissionAborted
        • MoleQueueDialog::SubmitStatus::JobFailed
        • MoleQueueDialog::SubmitStatus::JobFinished
      • MoleQueueDialog::MoleQueueDialog()
      • MoleQueueDialog::~MoleQueueDialog()
      • MoleQueueDialog::done()
      • MoleQueueDialog::submitJob()
      • MoleQueueDialog::promptForJobOptions()
  • Class Avogadro::MoleQueue::MoleQueueManager
    • MoleQueueManager
      • MoleQueueManager::client()
      • MoleQueueManager::client()
      • MoleQueueManager::MoleQueueManager()
      • MoleQueueManager::~MoleQueueManager()
      • MoleQueueManager::connectIfNeeded()
      • MoleQueueManager::queueListModel()
      • MoleQueueManager::requestQueueList()
      • MoleQueueManager::queueListUpdated()
      • MoleQueueManager::instance()
  • Class Avogadro::MoleQueue::MoleQueueQueueListModel
    • MoleQueueQueueListModel
      • MoleQueueQueueListModel::~MoleQueueQueueListModel()
      • MoleQueueQueueListModel::queues()
      • MoleQueueQueueListModel::programs()
      • MoleQueueQueueListModel::findQueueIndices()
      • MoleQueueQueueListModel::findProgramIndices()
      • MoleQueueQueueListModel::lookupProgram()
      • MoleQueueQueueListModel::data()
      • MoleQueueQueueListModel::flags()
      • MoleQueueQueueListModel::headerData()
      • MoleQueueQueueListModel::index()
      • MoleQueueQueueListModel::parent()
      • MoleQueueQueueListModel::rowCount()
      • MoleQueueQueueListModel::columnCount()
      • MoleQueueQueueListModel::@10
        • MoleQueueQueueListModel::@10::QueueProgramRole
      • MoleQueueQueueListModel::MoleQueueQueueListModel()
      • MoleQueueQueueListModel::setQueueList()
  • Class Avogadro::MoleQueue::MoleQueueWidget
    • MoleQueueWidget
      • MoleQueueWidget::jobTemplate()
      • MoleQueueWidget::jobTemplate()
      • MoleQueueWidget::setJobTemplate()
      • MoleQueueWidget::MoleQueueWidget()
      • MoleQueueWidget::~MoleQueueWidget()
      • MoleQueueWidget::showAndSelectProgram()
      • MoleQueueWidget::submissionSuccess()
      • MoleQueueWidget::jobState()
      • MoleQueueWidget::jobCompleted()
      • MoleQueueWidget::jobSuccess()
      • MoleQueueWidget::requestId()
      • MoleQueueWidget::moleQueueId()
      • MoleQueueWidget::submissionError()
      • MoleQueueWidget::openOutput()
      • MoleQueueWidget::requestJobLookup()
      • MoleQueueWidget::setBatchMode()
      • MoleQueueWidget::batchMode()
      • MoleQueueWidget::programSelected()
      • MoleQueueWidget::configuredJob()
      • MoleQueueWidget::refreshPrograms()
      • MoleQueueWidget::submitJobRequest()
      • MoleQueueWidget::jobSubmitted()
      • MoleQueueWidget::jobFinished()
      • MoleQueueWidget::jobUpdated()
      • MoleQueueWidget::InvalidMoleQueueId
• QtGui Classes
  • Class Avogadro::QtGui::BackgroundFileFormat
    • BackgroundFileFormat
      • BackgroundFileFormat::setMolecule()
      • BackgroundFileFormat::molecule()
      • BackgroundFileFormat::setFileName()
      • BackgroundFileFormat::fileName()
      • BackgroundFileFormat::BackgroundFileFormat()
      • BackgroundFileFormat::~BackgroundFileFormat()
      • BackgroundFileFormat::fileFormat()
      • BackgroundFileFormat::success()
      • BackgroundFileFormat::error()
      • BackgroundFileFormat::read()
      • BackgroundFileFormat::write()
      • BackgroundFileFormat::finished()
  • Class Avogadro::QtGui::ContainerWidget
    • ContainerWidget
      • ContainerWidget::ContainerWidget()
      • ContainerWidget::~ContainerWidget()
      • ContainerWidget::setViewWidget()
      • ContainerWidget::viewWidget()
      • ContainerWidget::setActive()
      • ContainerWidget::isActive()
      • ContainerWidget::splitVertical()
      • ContainerWidget::splitHorizontal()
      • ContainerWidget::closeView()
  • Class Avogadro::QtGui::CustomElementDialog
    • CustomElementDialog
      • CustomElementDialog::CustomElementDialog()
      • CustomElementDialog::~CustomElementDialog()
      • CustomElementDialog::apply()
      • CustomElementDialog::resolve()
  • Class Avogadro::QtGui::ElementDetail
    • ElementDetail
      • ElementDetail::ElementDetail()
      • ElementDetail::boundingRect()
      • ElementDetail::shape()
      • ElementDetail::paint()
      • ElementDetail::setElement()
  • Class Avogadro::QtGui::ElementItem
    • ElementItem
      • ElementItem::ElementItem()
      • ElementItem::~ElementItem()
      • ElementItem::boundingRect()
      • ElementItem::shape()
      • ElementItem::paint()
  • Class Avogadro::QtGui::ElementTranslator
    • ElementTranslator
      • ElementTranslator::ElementTranslator()
      • ElementTranslator::name()
      • ElementTranslator::numberOfElements()
  • Class Avogadro::QtGui::ExtensionPlugin
    • ExtensionPlugin
      • ExtensionPlugin::ExtensionPlugin()
      • ExtensionPlugin::~ExtensionPlugin()
      • ExtensionPlugin::name()
      • ExtensionPlugin::description()
      • ExtensionPlugin::actions()
      • ExtensionPlugin::menuPath()
      • ExtensionPlugin::fileFormats()
      • ExtensionPlugin::registerCommands()
      • ExtensionPlugin::setMolecule()
      • ExtensionPlugin::readMolecule()
      • ExtensionPlugin::setScene()
      • ExtensionPlugin::setCamera()
      • ExtensionPlugin::setActiveWidget()
      • ExtensionPlugin::handleCommand()
      • ExtensionPlugin::moleculeReady()
      • ExtensionPlugin::fileFormatsReady()
      • ExtensionPlugin::requestActiveTool()
      • ExtensionPlugin::requestActiveDisplayTypes()
      • ExtensionPlugin::registerCommand()
  • Class Avogadro::QtGui::ExtensionPluginFactory
    • ExtensionPluginFactory
      • ExtensionPluginFactory::~ExtensionPluginFactory()
  • Class Avogadro::QtGui::FileBrowseWidget
    • FileBrowseWidget
      • FileBrowseWidget::Mode
        • FileBrowseWidget::Mode::ExistingFile
        • FileBrowseWidget::Mode::ExecutableFile
      • FileBrowseWidget::FileBrowseWidget()
      • FileBrowseWidget::~FileBrowseWidget()
      • FileBrowseWidget::fileName()
      • FileBrowseWidget::validFileName()
      • FileBrowseWidget::browseButton()
      • FileBrowseWidget::lineEdit()
      • FileBrowseWidget::setMode()
      • FileBrowseWidget::mode()
      • FileBrowseWidget::setFileName()
      • FileBrowseWidget::fileNameChanged()
      • FileBrowseWidget::searchSystemPathForFile()
      • FileBrowseWidget::searchSystemPathForFiles()
  • Class Avogadro::QtGui::FileFormatDialog
    • FileFormatDialog
      • FileFormatDialog::FilterStringOption
        • FileFormatDialog::FilterStringOption::NoFilterStringOption
        • FileFormatDialog::FilterStringOption::AllFormats
        • FileFormatDialog::FilterStringOption::AllFiles
        • FileFormatDialog::FilterStringOption::WriteFormats
      • FileFormatDialog::FormatFilePair
      • FileFormatDialog::fileToRead()
      • FileFormatDialog::fileToWrite()
      • FileFormatDialog::findFileFormat()
  • Class Avogadro::QtGui::GenericHighlighter
    • GenericHighlighter
      • GenericHighlighter::GenericHighlighter()
      • GenericHighlighter::~GenericHighlighter()
      • GenericHighlighter::GenericHighlighter()
      • GenericHighlighter::operator=()
      • GenericHighlighter::operator+=()
      • GenericHighlighter::addRule()
      • GenericHighlighter::ruleCount()
      • GenericHighlighter::rule()
      • GenericHighlighter::rule()
      • GenericHighlighter::rules()
      • GenericHighlighter::highlightBlock()
      • GenericHighlighter::swap()
      • GenericHighlighter::Rule
        • GenericHighlighter::Rule::Rule()
        • GenericHighlighter::Rule::~Rule()
        • GenericHighlighter::Rule::addPattern()
        • GenericHighlighter::Rule::setFormat()
        • GenericHighlighter::Rule::apply()
  • Class Avogadro::QtGui::GenericHighlighter::Rule
    • Rule
      • Rule::Rule()
      • Rule::~Rule()
      • Rule::addPattern()
      • Rule::setFormat()
      • Rule::apply()
  • Class Avogadro::QtGui::HydrogenTools
    • HydrogenTools
      • HydrogenTools::Adjustment
        • HydrogenTools::Adjustment::Add
        • HydrogenTools::Adjustment::Remove
        • HydrogenTools::Adjustment::AddAndRemove
      • HydrogenTools::removeAllHydrogens()
      • HydrogenTools::adjustHydrogens()
      • HydrogenTools::adjustHydrogens()
      • HydrogenTools::valencyAdjustment()
      • HydrogenTools::extraHydrogenIndices()
      • HydrogenTools::generateNewHydrogenPositions()
  • Class Avogadro::QtGui::InterfaceScript
    • InterfaceScript
      • InterfaceScript::InterfaceScript()
      • InterfaceScript::InterfaceScript()
      • InterfaceScript::~InterfaceScript()
      • InterfaceScript::debug()
      • InterfaceScript::isValid()
      • InterfaceScript::options()
      • InterfaceScript::displayName()
      • InterfaceScript::menuPath()
      • InterfaceScript::scriptFilePath()
      • InterfaceScript::setScriptFilePath()
      • InterfaceScript::reset()
      • InterfaceScript::runCommand()
      • InterfaceScript::processCommand()
      • InterfaceScript::generateInput()
      • InterfaceScript::numberOfInputFiles()
      • InterfaceScript::fileNames()
      • InterfaceScript::mainFileName()
      • InterfaceScript::fileContents()
      • InterfaceScript::createFileHighlighter()
      • InterfaceScript::hasErrors()
      • InterfaceScript::clearErrors()
      • InterfaceScript::errorList()
      • InterfaceScript::warningList()
      • InterfaceScript::setDebug()
      • InterfaceScript::commandFinished()
      • InterfaceScript::finished()
  • Class Avogadro::QtGui::InterfaceWidget
    • InterfaceWidget
      • InterfaceWidget::InterfaceWidget()
      • InterfaceWidget::~InterfaceWidget()
      • InterfaceWidget::setInterfaceScript()
      • InterfaceWidget::interfaceScript()
  • Class Avogadro::QtGui::MeshGenerator
    • MeshGenerator
      • MeshGenerator::MeshGenerator()
      • MeshGenerator::MeshGenerator()
      • MeshGenerator::~MeshGenerator()
      • MeshGenerator::initialize()
      • MeshGenerator::run()
      • MeshGenerator::cube()
      • MeshGenerator::mesh()
      • MeshGenerator::clear()
      • MeshGenerator::progressMinimum()
      • MeshGenerator::progressMaximum()
      • MeshGenerator::progressValueChanged()
      • MeshGenerator::normal()
      • MeshGenerator::offset()
      • MeshGenerator::duplicate()
      • MeshGenerator::marchingCube()
      • MeshGenerator::m_iso
      • MeshGenerator::m_passes
      • MeshGenerator::m_reverseWinding
      • MeshGenerator::m_cube
      • MeshGenerator::m_mesh
      • MeshGenerator::m_stepSize
      • MeshGenerator::m_min
      • MeshGenerator::m_dim
      • MeshGenerator::m_vertices
      • MeshGenerator::m_normals
      • MeshGenerator::m_indices
      • MeshGenerator::m_progmin
      • MeshGenerator::m_progmax
      • MeshGenerator::a2fVertexOffset
      • MeshGenerator::a2iVertexOffset
      • MeshGenerator::a2iEdgeConnection
      • MeshGenerator::a2fEdgeDirection
      • MeshGenerator::a2iTetrahedronEdgeConnection
      • MeshGenerator::a2iTetrahedronsInACube
      • MeshGenerator::aiTetrahedronEdgeFlags
      • MeshGenerator::a2iTetrahedronTriangles
      • MeshGenerator::aiCubeEdgeFlags
      • MeshGenerator::a2iTriangleConnectionTable
  • Class Avogadro::QtGui::Molecule
    • Molecule
      • Molecule::atomUniqueId()
      • Molecule::atomUniqueId()
      • Molecule::removeBond()
      • Molecule::removeBond()
      • Molecule::bondUniqueId()
      • Molecule::bondUniqueId()
      • Molecule::MoleculeChange
        • Molecule::MoleculeChange::NoChange
        • Molecule::MoleculeChange::Atoms
        • Molecule::MoleculeChange::Bonds
        • Molecule::MoleculeChange::UnitCell
        • Molecule::MoleculeChange::Selection
        • Molecule::MoleculeChange::Layers
        • Molecule::MoleculeChange::Properties
        • Molecule::MoleculeChange::Added
        • Molecule::MoleculeChange::Removed
        • Molecule::MoleculeChange::Modified
      • Molecule::AtomType
      • Molecule::PersistentAtomType
      • Molecule::BondType
      • Molecule::PersistentBondType
      • Molecule::Molecule()
      • Molecule::~Molecule()
      • Molecule::Molecule()
      • Molecule::Molecule()
      • Molecule::operator=()
      • Molecule::operator=()
      • Molecule::addAtom()
      • Molecule::addAtom()
      • Molecule::addAtom()
      • Molecule::removeAtom()
      • Molecule::removeAtom()
      • Molecule::atomByUniqueId()
      • Molecule::atomUniqueIds()
      • Molecule::addBond()
      • Molecule::addBond()
      • Molecule::addBonds()
      • Molecule::addBond()
      • Molecule::addBond()
      • Molecule::removeBond()
      • Molecule::removeBond()
      • Molecule::bondByUniqueId()
      • Molecule::bondUniqueIds()
      • Molecule::findAtomUniqueId()
      • Molecule::findBondUniqueId()
      • Molecule::undoMolecule()
      • Molecule::swapBond()
      • Molecule::swapAtom()
      • Molecule::emitChanged()
      • Molecule::changed()
  • Class Avogadro::QtGui::MoleculeModel
    • MoleculeModel
      • MoleculeModel::MoleculeModel()
      • MoleculeModel::parent()
      • MoleculeModel::rowCount()
      • MoleculeModel::columnCount()
      • MoleculeModel::flags()
      • MoleculeModel::setData()
      • MoleculeModel::data()
      • MoleculeModel::index()
      • MoleculeModel::clear()
      • MoleculeModel::molecules()
      • MoleculeModel::activeMolecules()
      • MoleculeModel::activeMolecule()
      • MoleculeModel::setActiveMolecule()
      • MoleculeModel::addItem()
      • MoleculeModel::removeItem()
      • MoleculeModel::itemChanged()
      • MoleculeModel::moleculeStateChanged()
  • Class Avogadro::QtGui::MultiViewWidget
    • MultiViewWidget
      • MultiViewWidget::MultiViewWidget()
      • MultiViewWidget::~MultiViewWidget()
      • MultiViewWidget::addWidget()
      • MultiViewWidget::activeWidget()
      • MultiViewWidget::setActiveWidget()
      • MultiViewWidget::setFactory()
      • MultiViewWidget::setDefaultView()
      • MultiViewWidget::splitHorizontal()
      • MultiViewWidget::splitVertical()
      • MultiViewWidget::createView()
      • MultiViewWidget::removeView()
      • MultiViewWidget::activeWidgetChanged()
  • Class Avogadro::QtGui::PeriodicTableScene
    • PeriodicTableScene
      • PeriodicTableScene::PeriodicTableScene()
      • PeriodicTableScene::changeElement()
      • PeriodicTableScene::elementChanged()
      • PeriodicTableScene::mousePressEvent()
  • Class Avogadro::QtGui::PeriodicTableView
    • PeriodicTableView
      • PeriodicTableView::PeriodicTableView()
      • PeriodicTableView::~PeriodicTableView()
      • PeriodicTableView::element()
      • PeriodicTableView::setElement()
      • PeriodicTableView::clearKeyPressBuffer()
      • PeriodicTableView::elementChanged()
      • PeriodicTableView::mouseDoubleClickEvent()
      • PeriodicTableView::keyPressEvent()
      • PeriodicTableView::resizeEvent()
  • Class Avogadro::QtGui::PersistentAtom
    • PersistentAtom
      • PersistentAtom::MoleculeType
      • PersistentAtom::AtomType
      • PersistentAtom::PersistentAtom()
      • PersistentAtom::PersistentAtom()
      • PersistentAtom::set()
      • PersistentAtom::set()
      • PersistentAtom::reset()
      • PersistentAtom::isValid()
      • PersistentAtom::molecule()
      • PersistentAtom::uniqueIdentifier()
      • PersistentAtom::atom()
  • Class Avogadro::QtGui::PersistentBond
    • PersistentBond
      • PersistentBond::MoleculeType
      • PersistentBond::BondType
      • PersistentBond::PersistentBond()
      • PersistentBond::PersistentBond()
      • PersistentBond::set()
      • PersistentBond::set()
      • PersistentBond::reset()
      • PersistentBond::isValid()
      • PersistentBond::molecule()
      • PersistentBond::uniqueIdentifier()
      • PersistentBond::bond()
  • Class Avogadro::QtGui::PythonScript
    • PythonScript
      • PythonScript::PythonScript()
      • PythonScript::PythonScript()
      • PythonScript::~PythonScript()
      • PythonScript::debug()
      • PythonScript::scriptFilePath()
      • PythonScript::setScriptFilePath()
      • PythonScript::hasErrors()
      • PythonScript::clearErrors()
      • PythonScript::errorList()
      • PythonScript::setDefaultPythonInterpreter()
      • PythonScript::execute()
      • PythonScript::asyncExecute()
      • PythonScript::asyncWriteAndResponse()
      • PythonScript::asyncTerminate()
      • PythonScript::asyncResponse()
      • PythonScript::setDebug()
      • PythonScript::processFinished()
      • PythonScript::finished()
      • PythonScript::m_debug
      • PythonScript::m_pythonInterpreter
      • PythonScript::m_scriptFilePath
      • PythonScript::m_errors
      • PythonScript::m_process
  • Class Avogadro::QtGui::RWAtom
    • RWAtom
      • RWAtom::RWAtom()
      • RWAtom::RWAtom()
  • Class Avogadro::QtGui::RWBond
    • RWBond
      • RWBond::RWBond()
      • RWBond::RWBond()
  • Class Avogadro::QtGui::RWMolecule
    • RWMolecule
      • RWMolecule::atomUniqueId()
      • RWMolecule::atomUniqueId()
      • RWMolecule::removeAtom()
      • RWMolecule::removeAtom()
      • RWMolecule::addBond()
      • RWMolecule::addBond()
      • RWMolecule::removeBond()
      • RWMolecule::removeBond()
      • RWMolecule::removeBond()
      • RWMolecule::removeBond()
      • RWMolecule::undoStack()
      • RWMolecule::undoStack()
      • RWMolecule::AtomType
      • RWMolecule::PersistentAtomType
      • RWMolecule::BondType
      • RWMolecule::PersistentBondType
      • RWMolecule::RWMolecule()
      • RWMolecule::~RWMolecule()
      • RWMolecule::molecule()
      • RWMolecule::molecule()
      • RWMolecule::addAtom()
      • RWMolecule::addAtom()
      • RWMolecule::atom()
      • RWMolecule::atomByUniqueId()
      • RWMolecule::atomCount()
      • RWMolecule::atomCount()
      • RWMolecule::clearAtoms()
      • RWMolecule::adjustHydrogens()
      • RWMolecule::adjustHydrogens()
      • RWMolecule::atomicNumbers()
      • RWMolecule::atomicNumber()
      • RWMolecule::setAtomicNumbers()
      • RWMolecule::setAtomicNumber()
      • RWMolecule::atomPositions3d()
      • RWMolecule::atomPosition3d()
      • RWMolecule::setAtomPositions3d()
      • RWMolecule::setAtomPosition3d()
      • RWMolecule::atomLabel()
      • RWMolecule::setAtomLabel()
      • RWMolecule::setAtomSelected()
      • RWMolecule::atomSelected()
      • RWMolecule::setAtomPosition2d()
      • RWMolecule::atomPosition2d()
      • RWMolecule::atomPositions2d()
      • RWMolecule::hybridization()
      • RWMolecule::setHybridization()
      • RWMolecule::formalCharge()
      • RWMolecule::setFormalCharge()
      • RWMolecule::color()
      • RWMolecule::setColor()
      • RWMolecule::setLayer()
      • RWMolecule::layer()
      • RWMolecule::bond()
      • RWMolecule::bond()
      • RWMolecule::bond()
      • RWMolecule::bondByUniqueId()
      • RWMolecule::bondUniqueId()
      • RWMolecule::bondUniqueId()
      • RWMolecule::bondCount()
      • RWMolecule::clearBonds()
      • RWMolecule::bonds()
      • RWMolecule::bonds()
      • RWMolecule::bondOrders()
      • RWMolecule::bondOrder()
      • RWMolecule::setBondOrders()
      • RWMolecule::setBondOrder()
      • RWMolecule::bondPairs()
      • RWMolecule::bondPair()
      • RWMolecule::setBondPairs()
      • RWMolecule::setBondPair()
      • RWMolecule::addUnitCell()
      • RWMolecule::removeUnitCell()
      • RWMolecule::modifyMolecule()
      • RWMolecule::appendMolecule()
      • RWMolecule::editUnitCell()
      • RWMolecule::wrapAtomsToCell()
      • RWMolecule::rotateCellToStandardOrientation()
      • RWMolecule::setCellVolume()
      • RWMolecule::buildSupercell()
      • RWMolecule::niggliReduceCell()
      • RWMolecule::reduceCellToPrimitive()
      • RWMolecule::conventionalizeCell()
      • RWMolecule::symmetrizeCell()
      • RWMolecule::fillUnitCell()
      • RWMolecule::reduceCellToAsymmetricUnit()
      • RWMolecule::beginMergeMode()
      • RWMolecule::endMergeMode()
      • RWMolecule::setInteractive()
      • RWMolecule::isInteractive()
      • RWMolecule::forceVectors()
      • RWMolecule::setForceVector()
      • RWMolecule::emitChanged()
      • RWMolecule::changed()
      • RWMolecule::findAtomUniqueId()
      • RWMolecule::findBondUniqueId()
      • RWMolecule::m_molecule
      • RWMolecule::m_interactive
      • RWMolecule::m_undoStack
      • RWMolecule::UndoCommand
        • RWMolecule::UndoCommand::UndoCommand()
        • RWMolecule::UndoCommand::positions3d()
        • RWMolecule::UndoCommand::atomUniqueIds()
        • RWMolecule::UndoCommand::bondUniqueIds()
        • RWMolecule::UndoCommand::m_mol
        • RWMolecule::UndoCommand::m_molecule
  • Class Avogadro::QtGui::ScenePlugin
    • ScenePlugin
      • ScenePlugin::DefaultBehavior
        • ScenePlugin::DefaultBehavior::Ignore
        • ScenePlugin::DefaultBehavior::False
        • ScenePlugin::DefaultBehavior::True
      • ScenePlugin::ScenePlugin()
      • ScenePlugin::~ScenePlugin()
      • ScenePlugin::process()
      • ScenePlugin::processEditable()
      • ScenePlugin::name()
      • ScenePlugin::description()
      • ScenePlugin::isEnabled()
      • ScenePlugin::isActiveLayerEnabled()
      • ScenePlugin::setEnabled()
      • ScenePlugin::setupWidget()
      • ScenePlugin::hasSetupWidget()
      • ScenePlugin::defaultBehavior()
      • ScenePlugin::drawablesChanged()
      • ScenePlugin::m_layerManager
  • Class Avogadro::QtGui::ScenePluginFactory
    • ScenePluginFactory
      • ScenePluginFactory::~ScenePluginFactory()
  • Class Avogadro::QtGui::ScenePluginModel
    • ScenePluginModel
      • ScenePluginModel::ScenePluginModel()
      • ScenePluginModel::parent()
      • ScenePluginModel::rowCount()
      • ScenePluginModel::columnCount()
      • ScenePluginModel::flags()
      • ScenePluginModel::setData()
      • ScenePluginModel::data()
      • ScenePluginModel::index()
      • ScenePluginModel::clear()
      • ScenePluginModel::scenePlugins()
      • ScenePluginModel::activeScenePlugins()
      • ScenePluginModel::addItem()
      • ScenePluginModel::removeItem()
      • ScenePluginModel::itemChanged()
      • ScenePluginModel::pluginStateChanged()
      • ScenePluginModel::pluginConfigChanged()
  • Class Avogadro::QtGui::ScriptLoader
    • ScriptLoader
      • ScriptLoader::ScriptLoader()
      • ScriptLoader::~ScriptLoader()
      • ScriptLoader::scriptList()
      • ScriptLoader::queryProgramName()
  • Class Avogadro::QtGui::ToolPlugin
    • ToolPlugin
      • ToolPlugin::mousePressEvent()
      • ToolPlugin::mouseReleaseEvent()
      • ToolPlugin::mouseMoveEvent()
      • ToolPlugin::mouseDoubleClickEvent()
      • ToolPlugin::wheelEvent()
      • ToolPlugin::keyPressEvent()
      • ToolPlugin::keyReleaseEvent()
      • ToolPlugin::ToolPlugin()
      • ToolPlugin::~ToolPlugin()
      • ToolPlugin::name()
      • ToolPlugin::description()
      • ToolPlugin::priority()
      • ToolPlugin::activateAction()
      • ToolPlugin::setIcon()
      • ToolPlugin::toolWidget()
      • ToolPlugin::draw()
      • ToolPlugin::handleCommand()
      • ToolPlugin::registerCommands()
      • ToolPlugin::setMolecule()
      • ToolPlugin::setEditMolecule()
      • ToolPlugin::setGLWidget()
      • ToolPlugin::setActiveWidget()
      • ToolPlugin::setGLRenderer()
      • ToolPlugin::drawablesChanged()
      • ToolPlugin::updateRequested()
      • ToolPlugin::registerCommand()
      • ToolPlugin::requestActiveDisplayTypes()
  • Class Avogadro::QtGui::ToolPluginFactory
    • ToolPluginFactory
      • ToolPluginFactory::~ToolPluginFactory()
      • ToolPluginFactory::createInstance()
      • ToolPluginFactory::identifier()
  • Class Avogadro::QtGui::ViewFactory
    • ViewFactory
      • ViewFactory::ViewFactory()
      • ViewFactory::~ViewFactory()
      • ViewFactory::views()
      • ViewFactory::createView()
  • Class Avogadro::QtOpenGL::ActiveObjects
    • ActiveObjects
      • ActiveObjects::activeGLWidget()
      • ActiveObjects::activeWidget()
      • ActiveObjects::activeMolecule()
      • ActiveObjects::setActiveGLWidget()
      • ActiveObjects::setActiveWidget()
      • ActiveObjects::setActiveMolecule()
      • ActiveObjects::activeGLWidgetChanged()
      • ActiveObjects::activeWidgetChanged()
      • ActiveObjects::activeMoleculeChanged()
      • ActiveObjects::instance()
  • Class Avogadro::QtOpenGL::GLWidget
    • GLWidget
      • GLWidget::molecule()
      • GLWidget::molecule()
      • GLWidget::sceneModel()
      • GLWidget::sceneModel()
      • GLWidget::setActiveTool()
      • GLWidget::setActiveTool()
      • GLWidget::setDefaultTool()
      • GLWidget::setDefaultTool()
      • GLWidget::mouseDoubleClickEvent()
      • GLWidget::mousePressEvent()
      • GLWidget::mouseMoveEvent()
      • GLWidget::mouseReleaseEvent()
      • GLWidget::wheelEvent()
      • GLWidget::keyPressEvent()
      • GLWidget::keyReleaseEvent()
      • GLWidget::GLWidget()
      • GLWidget::~GLWidget()
      • GLWidget::setMolecule()
      • GLWidget::renderer()
      • GLWidget::tools()
      • GLWidget::activeTool()
      • GLWidget::defaultTool()
      • GLWidget::isValid()
      • GLWidget::error()
      • GLWidget::updateScene()
      • GLWidget::clearScene()
      • GLWidget::resetCamera()
      • GLWidget::resetGeometry()
      • GLWidget::setTools()
      • GLWidget::addTool()
      • GLWidget::requestUpdate()
      • GLWidget::rendererInvalid()
      • GLWidget::initializeGL()
      • GLWidget::resizeGL()
      • GLWidget::paintGL()
      • GLWidget::updateTimeout()
  • Class Avogadro::QtOpenGL::QtTextRenderStrategy
    • QtTextRenderStrategy
      • QtTextRenderStrategy::preserveArgb()
      • QtTextRenderStrategy::setPreserveArgb()
      • QtTextRenderStrategy::QtTextRenderStrategy()
      • QtTextRenderStrategy::~QtTextRenderStrategy()
      • QtTextRenderStrategy::newInstance()
      • QtTextRenderStrategy::boundingBox()
      • QtTextRenderStrategy::render()
• Rendering Classes
  • Class Avogadro::Rendering::AmbientOcclusionSphereGeometry
    • AmbientOcclusionSphereGeometry
      • AmbientOcclusionSphereGeometry::AmbientOcclusionSphereGeometry()
      • AmbientOcclusionSphereGeometry::AmbientOcclusionSphereGeometry()
      • AmbientOcclusionSphereGeometry::~AmbientOcclusionSphereGeometry()
      • AmbientOcclusionSphereGeometry::operator=()
      • AmbientOcclusionSphereGeometry::accept()
      • AmbientOcclusionSphereGeometry::update()
      • AmbientOcclusionSphereGeometry::render()
      • AmbientOcclusionSphereGeometry::hits()
      • AmbientOcclusionSphereGeometry::addSphere()
      • AmbientOcclusionSphereGeometry::spheres()
      • AmbientOcclusionSphereGeometry::spheres()
      • AmbientOcclusionSphereGeometry::clear()
      • AmbientOcclusionSphereGeometry::size()
      • AmbientOcclusionSphereGeometry::swap()
  • Class Avogadro::Rendering::ArrowGeometry
    • ArrowGeometry
      • ArrowGeometry::addSingleArrow()
      • ArrowGeometry::ArrowGeometry()
      • ArrowGeometry::ArrowGeometry()
      • ArrowGeometry::~ArrowGeometry()
      • ArrowGeometry::operator=()
      • ArrowGeometry::accept()
      • ArrowGeometry::render()
      • ArrowGeometry::clear()
      • ArrowGeometry::drawLine()
      • ArrowGeometry::drawCone()
      • ArrowGeometry::vertices()
      • ArrowGeometry::InvalidIndex
      • ArrowGeometry::swap()
  • Class Avogadro::Rendering::BufferObject
    • BufferObject
      • BufferObject::ObjectType
        • BufferObject::ObjectType::ArrayBuffer
        • BufferObject::ObjectType::ElementArrayBuffer
      • BufferObject::BufferObject()
      • BufferObject::~BufferObject()
      • BufferObject::type()
      • BufferObject::handle()
      • BufferObject::ready()
      • BufferObject::upload()
      • BufferObject::bind()
      • BufferObject::release()
      • BufferObject::error()
  • Class Avogadro::Rendering::Camera
    • Camera
      • Camera::Camera()
      • Camera::Camera()
      • Camera::operator=()
      • Camera::~Camera()
      • Camera::translate()
      • Camera::preTranslate()
      • Camera::rotate()
      • Camera::preRotate()
      • Camera::scale()
      • Camera::lookAt()
      • Camera::distance()
      • Camera::project()
      • Camera::unProject()
      • Camera::unProject()
      • Camera::calculatePerspective()
      • Camera::calculatePerspective()
      • Camera::calculatePerspective()
      • Camera::calculateOrthographic()
      • Camera::setViewport()
      • Camera::width()
      • Camera::height()
      • Camera::setIdentity()
      • Camera::setProjection()
      • Camera::projection()
      • Camera::setModelView()
      • Camera::modelView()
      • Camera::setProjectionType()
      • Camera::projectionType()
      • Camera::setOrthographicScale()
      • Camera::orthographicScale()
      • Camera::setFocus()
      • Camera::focus()
  • Class Avogadro::Rendering::Cylinder
    • Cylinder
      • Cylinder::Cylinder()
      • Cylinder::position()
      • Cylinder::setPosition()
      • Cylinder::direction()
      • Cylinder::setDirection()
      • Cylinder::length()
      • Cylinder::setLength()
      • Cylinder::radius()
      • Cylinder::setRadius()
  • Class Avogadro::Rendering::CylinderGeometry
    • CylinderGeometry
      • CylinderGeometry::CylinderGeometry()
      • CylinderGeometry::CylinderGeometry()
      • CylinderGeometry::~CylinderGeometry()
      • CylinderGeometry::operator=()
      • CylinderGeometry::accept()
      • CylinderGeometry::update()
      • CylinderGeometry::render()
      • CylinderGeometry::hits()
      • CylinderGeometry::addCylinder()
      • CylinderGeometry::addCylinder()
      • CylinderGeometry::addCylinder()
      • CylinderGeometry::addCylinder()
      • CylinderGeometry::cylinders()
      • CylinderGeometry::cylinders()
      • CylinderGeometry::clear()
      • CylinderGeometry::size()
      • CylinderGeometry::swap()
  • Class Avogadro::Rendering::Drawable
    • Drawable
      • Drawable::setRenderPass()
      • Drawable::renderPass()
      • Drawable::Drawable()
      • Drawable::Drawable()
      • Drawable::~Drawable()
      • Drawable::operator=()
      • Drawable::accept()
      • Drawable::parent()
      • Drawable::parent()
      • Drawable::setVisible()
      • Drawable::isVisible()
      • Drawable::render()
      • Drawable::identifier()
      • Drawable::identifier()
      • Drawable::hits()
      • Drawable::areaHits()
      • Drawable::clear()
      • Drawable::setParent()
      • Drawable::m_parent
      • Drawable::m_visible
      • Drawable::m_renderPass
      • Drawable::m_identifier
      • Drawable::swap()
  • Class Avogadro::Rendering::GLRenderVisitor
    • GLRenderVisitor
      • GLRenderVisitor::setRenderPass()
      • GLRenderVisitor::renderPass()
      • GLRenderVisitor::setTextRenderStrategy()
      • GLRenderVisitor::textRenderStrategy()
      • GLRenderVisitor::GLRenderVisitor()
      • GLRenderVisitor::~GLRenderVisitor()
      • GLRenderVisitor::visit()
      • GLRenderVisitor::visit()
      • GLRenderVisitor::visit()
      • GLRenderVisitor::visit()
      • GLRenderVisitor::visit()
      • GLRenderVisitor::visit()
      • GLRenderVisitor::visit()
      • GLRenderVisitor::visit()
      • GLRenderVisitor::visit()
      • GLRenderVisitor::visit()
      • GLRenderVisitor::visit()
      • GLRenderVisitor::visit()
      • GLRenderVisitor::setCamera()
      • GLRenderVisitor::camera()
  • Class Avogadro::Rendering::GLRenderer
    • GLRenderer
      • GLRenderer::textRenderStrategy()
      • GLRenderer::textRenderStrategy()
      • GLRenderer::setTextRenderStrategy()
      • GLRenderer::GLRenderer()
      • GLRenderer::~GLRenderer()
      • GLRenderer::initialize()
      • GLRenderer::resize()
      • GLRenderer::setPixelRatio()
      • GLRenderer::render()
      • GLRenderer::resetCamera()
      • GLRenderer::resetGeometry()
      • GLRenderer::hits()
      • GLRenderer::hit()
      • GLRenderer::hit()
      • GLRenderer::hits()
      • GLRenderer::isValid()
      • GLRenderer::error()
      • GLRenderer::camera()
      • GLRenderer::camera()
      • GLRenderer::overlayCamera()
      • GLRenderer::overlayCamera()
      • GLRenderer::scene()
      • GLRenderer::scene()
      • GLRenderer::solidPipeline()
      • GLRenderer::solidPipeline()
      • GLRenderer::m_perspectiveFrustum
      • GLRenderer::m_orthographicFrustum
  • Class Avogadro::Rendering::GeometryNode
    • GeometryNode
      • GeometryNode::GeometryNode()
      • GeometryNode::~GeometryNode()
      • GeometryNode::accept()
      • GeometryNode::addDrawable()
      • GeometryNode::removeDrawable()
      • GeometryNode::drawable()
      • GeometryNode::drawables()
      • GeometryNode::drawables()
      • GeometryNode::clearDrawables()
      • GeometryNode::render()
      • GeometryNode::hits()
      • GeometryNode::areaHits()
      • GeometryNode::m_drawables
  • Class Avogadro::Rendering::GeometryVisitor
    • GeometryVisitor
      • GeometryVisitor::GeometryVisitor()
      • GeometryVisitor::~GeometryVisitor()
      • GeometryVisitor::visit()
      • GeometryVisitor::visit()
      • GeometryVisitor::visit()
      • GeometryVisitor::visit()
      • GeometryVisitor::visit()
      • GeometryVisitor::visit()
      • GeometryVisitor::visit()
      • GeometryVisitor::visit()
      • GeometryVisitor::visit()
      • GeometryVisitor::visit()
      • GeometryVisitor::visit()
      • GeometryVisitor::visit()
      • GeometryVisitor::clear()
      • GeometryVisitor::center()
      • GeometryVisitor::radius()
  • Class Avogadro::Rendering::GroupNode
    • GroupNode
      • GroupNode::NodeType
        • GroupNode::NodeType::ALL
        • GroupNode::NodeType::NONE
        • GroupNode::NodeType::UI
        • GroupNode::NodeType::GEOMETRY
      • GroupNode::GroupNode()
      • GroupNode::~GroupNode()
      • GroupNode::accept()
      • GroupNode::addChild()
      • GroupNode::addUIChild()
      • GroupNode::removeChild()
      • GroupNode::child()
      • GroupNode::hasChild()
      • GroupNode::childCount()
      • GroupNode::children()
      • GroupNode::children()
      • GroupNode::clear()
      • GroupNode::clearUI()
      • GroupNode::clear()
      • GroupNode::m_children
      • GroupNode::NodeInfo
        • GroupNode::NodeInfo::NodeInfo()
        • GroupNode::NodeInfo::NodeInfo()
        • GroupNode::NodeInfo::ui
        • GroupNode::NodeInfo::node
  • Class Avogadro::Rendering::LineStripGeometry
    • LineStripGeometry
      • LineStripGeometry::addLineStrip()
      • LineStripGeometry::addLineStrip()
      • LineStripGeometry::addLineStrip()
      • LineStripGeometry::addLineStrip()
      • LineStripGeometry::setColor()
      • LineStripGeometry::color()
      • LineStripGeometry::setOpacity()
      • LineStripGeometry::opacity()
      • LineStripGeometry::LineStripGeometry()
      • LineStripGeometry::LineStripGeometry()
      • LineStripGeometry::~LineStripGeometry()
      • LineStripGeometry::operator=()
      • LineStripGeometry::accept()
      • LineStripGeometry::render()
      • LineStripGeometry::clear()
      • LineStripGeometry::vertices()
      • LineStripGeometry::InvalidIndex
      • LineStripGeometry::swap()
      • LineStripGeometry::PackedVertex
        • LineStripGeometry::PackedVertex::PackedVertex()
        • LineStripGeometry::PackedVertex::vertex
        • LineStripGeometry::PackedVertex::color
        • LineStripGeometry::PackedVertex::vertexOffset()
        • LineStripGeometry::PackedVertex::colorOffset()
  • Class Avogadro::Rendering::MeshGeometry
    • MeshGeometry
      • MeshGeometry::addVertices()
      • MeshGeometry::addVertices()
      • MeshGeometry::addVertices()
      • MeshGeometry::addTriangle()
      • MeshGeometry::addTriangles()
      • MeshGeometry::setColor()
      • MeshGeometry::color()
      • MeshGeometry::setOpacity()
      • MeshGeometry::opacity()
      • MeshGeometry::MeshGeometry()
      • MeshGeometry::MeshGeometry()
      • MeshGeometry::~MeshGeometry()
      • MeshGeometry::operator=()
      • MeshGeometry::accept()
      • MeshGeometry::render()
      • MeshGeometry::clear()
      • MeshGeometry::vertexCount()
      • MeshGeometry::indexCount()
      • MeshGeometry::triangleCount()
      • MeshGeometry::vertices()
      • MeshGeometry::triangles()
      • MeshGeometry::InvalidIndex
      • MeshGeometry::swap()
      • MeshGeometry::PackedVertex
        • MeshGeometry::PackedVertex::PackedVertex()
        • MeshGeometry::PackedVertex::color
        • MeshGeometry::PackedVertex::normal
        • MeshGeometry::PackedVertex::vertex
        • MeshGeometry::PackedVertex::padding
        • MeshGeometry::PackedVertex::colorOffset()
        • MeshGeometry::PackedVertex::normalOffset()
        • MeshGeometry::PackedVertex::vertexOffset()
  • Class Avogadro::Rendering::Node
    • Node
      • Node::Node()
      • Node::~Node()
      • Node::accept()
      • Node::parent()
      • Node::parent()
      • Node::setVisible()
      • Node::isVisible()
      • Node::cast()
      • Node::cast()
      • Node::setParent()
      • Node::m_parent
      • Node::m_visible
  • Class Avogadro::Rendering::POVRayVisitor
    • POVRayVisitor
      • POVRayVisitor::POVRayVisitor()
      • POVRayVisitor::~POVRayVisitor()
      • POVRayVisitor::begin()
      • POVRayVisitor::end()
      • POVRayVisitor::visit()
      • POVRayVisitor::visit()
      • POVRayVisitor::visit()
      • POVRayVisitor::visit()
      • POVRayVisitor::visit()
      • POVRayVisitor::visit()
      • POVRayVisitor::visit()
      • POVRayVisitor::visit()
      • POVRayVisitor::visit()
      • POVRayVisitor::visit()
      • POVRayVisitor::visit()
      • POVRayVisitor::visit()
      • POVRayVisitor::setCamera()
      • POVRayVisitor::camera()
      • POVRayVisitor::setBackgroundColor()
      • POVRayVisitor::setAmbientColor()
      • POVRayVisitor::setAspectRatio()
  • Class Avogadro::Rendering::Primitive
    • Primitive
      • Primitive::Type
        • Primitive::Type::Invalid
        • Primitive::Type::Atom
        • Primitive::Type::Bond
      • Primitive::Primitive()
      • Primitive::identifier()
      • Primitive::setIdentifier()
      • Primitive::color()
      • Primitive::setColor()
      • Primitive::Identifier
        • Primitive::Identifier::Identifier()
        • Primitive::Identifier::operator==()
        • Primitive::Identifier::operator!=()
        • Primitive::Identifier::isValid()
        • Primitive::Identifier::molecule
        • Primitive::Identifier::type
        • Primitive::Identifier::index
  • Class Avogadro::Rendering::Scene
    • Scene
      • Scene::Scene()
      • Scene::~Scene()
      • Scene::center()
      • Scene::radius()
      • Scene::rootNode()
      • Scene::rootNode()
      • Scene::setBackgroundColor()
      • Scene::backgroundColor()
      • Scene::setDirty()
      • Scene::isDirty()
      • Scene::clear()
  • Class Avogadro::Rendering::Shader
    • Shader
      • Shader::Type
        • Shader::Type::Vertex
        • Shader::Type::Fragment
        • Shader::Type::Unknown
      • Shader::Shader()
      • Shader::~Shader()
      • Shader::setType()
      • Shader::type()
      • Shader::setSource()
      • Shader::source()
      • Shader::error()
      • Shader::handle()
      • Shader::compile()
      • Shader::cleanup()
      • Shader::m_type
      • Shader::m_handle
      • Shader::m_dirty
      • Shader::m_source
      • Shader::m_error
  • Class Avogadro::Rendering::ShaderProgram
    • ShaderProgram
      • ShaderProgram::setUniformValue()
      • ShaderProgram::setUniformValue()
      • ShaderProgram::setUniformValue()
      • ShaderProgram::NormalizeOption
        • ShaderProgram::NormalizeOption::Normalize
        • ShaderProgram::NormalizeOption::NoNormalize
      • ShaderProgram::ShaderProgram()
      • ShaderProgram::~ShaderProgram()
      • ShaderProgram::attachShader()
      • ShaderProgram::detachShader()
      • ShaderProgram::link()
      • ShaderProgram::bind()
      • ShaderProgram::release()
      • ShaderProgram::error()
      • ShaderProgram::enableAttributeArray()
      • ShaderProgram::disableAttributeArray()
      • ShaderProgram::useAttributeArray()
      • ShaderProgram::setAttributeArray()
      • ShaderProgram::setTextureSampler()
      • ShaderProgram::setUniformValue()
      • ShaderProgram::setUniformValue()
      • ShaderProgram::setUniformValue()
      • ShaderProgram::setUniformValue()
      • ShaderProgram::setAttributeArrayInternal()
      • ShaderProgram::m_handle
      • ShaderProgram::m_vertexShader
      • ShaderProgram::m_fragmentShader
      • ShaderProgram::m_linked
      • ShaderProgram::m_error
      • ShaderProgram::m_attributes
      • ShaderProgram::m_textureUnitBindings
      • ShaderProgram::m_boundTextureUnits
  • Class Avogadro::Rendering::Sphere
    • Sphere
      • Sphere::Sphere()
      • Sphere::position()
      • Sphere::setPosition()
      • Sphere::radius()
      • Sphere::setRadius()
  • Class Avogadro::Rendering::SphereGeometry
    • SphereGeometry
      • SphereGeometry::SphereGeometry()
      • SphereGeometry::SphereGeometry()
      • SphereGeometry::~SphereGeometry()
      • SphereGeometry::operator=()
      • SphereGeometry::accept()
      • SphereGeometry::update()
      • SphereGeometry::render()
      • SphereGeometry::hits()
      • SphereGeometry::areaHits()
      • SphereGeometry::setOpacity()
      • SphereGeometry::addSphere()
      • SphereGeometry::spheres()
      • SphereGeometry::spheres()
      • SphereGeometry::clear()
      • SphereGeometry::size()
      • SphereGeometry::swap()
  • Class Avogadro::Rendering::TextLabel2D
    • TextLabel2D
      • TextLabel2D::setAnchor()
      • TextLabel2D::anchor()
      • TextLabel2D::TextLabel2D()
      • TextLabel2D::~TextLabel2D()
      • TextLabel2D::accept()
  • Class Avogadro::Rendering::TextLabel3D
    • TextLabel3D
      • TextLabel3D::setAnchor()
      • TextLabel3D::anchor()
      • TextLabel3D::setRadius()
      • TextLabel3D::radius()
      • TextLabel3D::TextLabel3D()
      • TextLabel3D::~TextLabel3D()
      • TextLabel3D::accept()
  • Class Avogadro::Rendering::TextLabelBase
    • TextLabelBase
      • TextLabelBase::setText()
      • TextLabelBase::text()
      • TextLabelBase::setTextProperties()
      • TextLabelBase::textProperties()
      • TextLabelBase::TextLabelBase()
      • TextLabelBase::TextLabelBase()
      • TextLabelBase::~TextLabelBase()
      • TextLabelBase::operator=()
      • TextLabelBase::render()
      • TextLabelBase::buildTexture()
      • TextLabelBase::resetTexture()
      • TextLabelBase::setAnchorInternal()
      • TextLabelBase::getAnchorInternal()
      • TextLabelBase::setRadiusInternal()
      • TextLabelBase::getRadiusInternal()
      • TextLabelBase::markDirty()
      • TextLabelBase::m_text
      • TextLabelBase::m_textProperties
      • TextLabelBase::m_imageDimensions
      • TextLabelBase::m_imageRgba
      • TextLabelBase::swap()
  • Class Avogadro::Rendering::TextProperties
    • TextProperties
      • TextProperties::setColorRgba()
      • TextProperties::setColorRgba()
      • TextProperties::setColorRgba()
      • TextProperties::colorRgba()
      • TextProperties::colorRgba()
      • TextProperties::setColorRgb()
      • TextProperties::setColorRgb()
      • TextProperties::setColorRgb()
      • TextProperties::colorRgb()
      • TextProperties::colorRgb()
      • TextProperties::setRed()
      • TextProperties::red()
      • TextProperties::setGreen()
      • TextProperties::green()
      • TextProperties::setBlue()
      • TextProperties::blue()
      • TextProperties::setAlpha()
      • TextProperties::alpha()
      • TextProperties::FontFamily
        • TextProperties::FontFamily::SansSerif
        • TextProperties::FontFamily::Serif
        • TextProperties::FontFamily::Mono
      • TextProperties::HAlign
        • TextProperties::HAlign::HLeft
        • TextProperties::HAlign::HCenter
        • TextProperties::HAlign::HRight
      • TextProperties::VAlign
        • TextProperties::VAlign::VTop
        • TextProperties::VAlign::VCenter
        • TextProperties::VAlign::VBottom
      • TextProperties::FontStyle
        • TextProperties::FontStyle::NoFontStyle
        • TextProperties::FontStyle::Bold
        • TextProperties::FontStyle::Italic
        • TextProperties::FontStyle::Underline
      • TextProperties::FontStyles
      • TextProperties::TextProperties()
      • TextProperties::TextProperties()
      • TextProperties::~TextProperties()
      • TextProperties::operator=()
      • TextProperties::swap()
      • TextProperties::operator==()
      • TextProperties::operator!=()
      • TextProperties::setPixelHeight()
      • TextProperties::pixelHeight()
      • TextProperties::setHAlign()
      • TextProperties::hAlign()
      • TextProperties::setVAlign()
      • TextProperties::vAlign()
      • TextProperties::setAlign()
      • TextProperties::setRotationDegreesCW()
      • TextProperties::rotationDegreesCW()
      • TextProperties::setFontFamily()
      • TextProperties::fontFamily()
      • TextProperties::setFontStyles()
      • TextProperties::fontStyles()
      • TextProperties::setBold()
      • TextProperties::bold()
      • TextProperties::setItalic()
      • TextProperties::italic()
      • TextProperties::setUnderline()
      • TextProperties::underline()
  • Class Avogadro::Rendering::TextRenderStrategy
    • TextRenderStrategy
      • TextRenderStrategy::TextRenderStrategy()
      • TextRenderStrategy::~TextRenderStrategy()
      • TextRenderStrategy::newInstance()
      • TextRenderStrategy::boundingBox()
      • TextRenderStrategy::render()
  • Class Avogadro::Rendering::Texture2D
    • Texture2D
      • Texture2D::setWrappingS()
      • Texture2D::wrappingS()
      • Texture2D::setWrappingT()
      • Texture2D::wrappingT()
      • Texture2D::FilterOption
        • Texture2D::FilterOption::InvalidFilter
        • Texture2D::FilterOption::Nearest
        • Texture2D::FilterOption::Linear
      • Texture2D::WrappingOption
        • Texture2D::WrappingOption::InvalidWrapping
        • Texture2D::WrappingOption::ClampToEdge
        • Texture2D::WrappingOption::MirroredRepeat
        • Texture2D::WrappingOption::Repeat
      • Texture2D::InternalFormat
        • Texture2D::InternalFormat::InvalidInternalFormat
        • Texture2D::InternalFormat::InternalDepth
        • Texture2D::InternalFormat::InternalDepthStencil
        • Texture2D::InternalFormat::InternalR
        • Texture2D::InternalFormat::InternalRG
        • Texture2D::InternalFormat::InternalRGB
        • Texture2D::InternalFormat::InternalRGBA
      • Texture2D::IncomingFormat
        • Texture2D::IncomingFormat::InvalidIncomingFormat
        • Texture2D::IncomingFormat::IncomingR
        • Texture2D::IncomingFormat::IncomingRG
        • Texture2D::IncomingFormat::IncomingRGB
        • Texture2D::IncomingFormat::IncomingBGR
        • Texture2D::IncomingFormat::IncomingRGBA
        • Texture2D::IncomingFormat::IncomingBGRA
        • Texture2D::IncomingFormat::IncomingDepth
        • Texture2D::IncomingFormat::IncomingDepthStencil
      • Texture2D::Texture2D()
      • Texture2D::~Texture2D()
      • Texture2D::handle()
      • Texture2D::ready()
      • Texture2D::setMinFilter()
      • Texture2D::minFilter()
      • Texture2D::setMagFilter()
      • Texture2D::magFilter()
      • Texture2D::upload()
      • Texture2D::bind()
      • Texture2D::release()
      • Texture2D::error()
  • Class Avogadro::Rendering::TransformNode
    • TransformNode
      • TransformNode::TransformNode()
      • TransformNode::~TransformNode()
  • Class Avogadro::Rendering::VRMLVisitor
    • VRMLVisitor
      • VRMLVisitor::VRMLVisitor()
      • VRMLVisitor::~VRMLVisitor()
      • VRMLVisitor::begin()
      • VRMLVisitor::end()
      • VRMLVisitor::visit()
      • VRMLVisitor::visit()
      • VRMLVisitor::visit()
      • VRMLVisitor::visit()
      • VRMLVisitor::visit()
      • VRMLVisitor::visit()
      • VRMLVisitor::visit()
      • VRMLVisitor::visit()
      • VRMLVisitor::visit()
      • VRMLVisitor::visit()
      • VRMLVisitor::visit()
      • VRMLVisitor::visit()
      • VRMLVisitor::setCamera()
      • VRMLVisitor::camera()
      • VRMLVisitor::setBackgroundColor()
      • VRMLVisitor::setAmbientColor()
      • VRMLVisitor::setAspectRatio()
  • Class Avogadro::Rendering::Visitor
    • Visitor
      • Visitor::Visitor()
      • Visitor::~Visitor()
      • Visitor::visit()
      • Visitor::visit()
      • Visitor::visit()
      • Visitor::visit()
      • Visitor::visit()
      • Visitor::visit()
      • Visitor::visit()
      • Visitor::visit()
      • Visitor::visit()
      • Visitor::visit()
      • Visitor::visit()
      • Visitor::visit()
  • Class Avogadro::Rendering::VolumeGeometry
    • VolumeGeometry
      • VolumeGeometry::VolumeGeometry()
      • VolumeGeometry::~VolumeGeometry()
• VTK Classes
  • Class Avogadro::VTK::VtkPlot
  • Class Avogadro::VTK::vtkGLWidget
    • vtkGLWidget
      • vtkGLWidget::molecule()
      • vtkGLWidget::molecule()
      • vtkGLWidget::sceneModel()
      • vtkGLWidget::sceneModel()
      • vtkGLWidget::vtkGLWidget()
      • vtkGLWidget::~vtkGLWidget()
      • vtkGLWidget::setMolecule()
      • vtkGLWidget::renderer()
      • vtkGLWidget::lut()
      • vtkGLWidget::opacityFunction()
      • vtkGLWidget::imageData()
      • vtkGLWidget::setCube()
      • vtkGLWidget::cube()
      • vtkGLWidget::renderVolume()
      • vtkGLWidget::renderIsosurface()
      • vtkGLWidget::setIsoValue()
      • vtkGLWidget::setOpacity()
      • vtkGLWidget::updateScene()
      • vtkGLWidget::clearScene()
      • vtkGLWidget::resetCamera()
      • vtkGLWidget::resetGeometry()
      • vtkGLWidget::cubeVolume()
      • vtkGLWidget::imageDataUpdated()
  • Class vtkAvogadroActor
    • vtkAvogadroActor
      • vtkAvogadroActor::RenderOpaqueGeometry()
      • vtkAvogadroActor::RenderTranslucentPolygonalGeometry()
      • vtkAvogadroActor::HasTranslucentPolygonalGeometry()
      • vtkAvogadroActor::GetBounds()
      • vtkAvogadroActor::setScene()
      • vtkAvogadroActor::GetScene()
      • vtkAvogadroActor::New()
      • vtkAvogadroActor::vtkAvogadroActor()
      • vtkAvogadroActor::~vtkAvogadroActor()
      • vtkAvogadroActor::m_scene
      • vtkAvogadroActor::m_bounds
      • vtkAvogadroActor::m_initialized