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
- Class Avogadro::Io::DcdFormat
- Class Avogadro::Io::FileFormat
FileFormat
FileFormat::Operation
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::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
- 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
- Class Avogadro::Io::XyzFormat
- 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
- 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
- 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()