IO Classes

The IO classes handle Avogadro’s native file input/output. Beyond these classes, an Open Babel plugin loads translation via obabel command calls and Script Formats allow user scripts to translate to native formats like CJSON and CML.

• 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()