Inheritance diagram for Avogadro::MoleculeFile:

Signals
void	ready ()
void	firstMolReady ()
Public Member Functions
bool	isReady () const
bool	isConformerFile () const
unsigned int	numMolecules () const
QStringList	titles () const
Input (reading molecules)
Molecule *	molecule (unsigned int i=0)
OpenBabel::OBMol *	OBMol (unsigned int i=0)
const std::vector< std::vector < Eigen::Vector3d > * > &	conformers () const
Output (writing molecules)
bool	replaceMolecule (unsigned int i, Molecule *molecule, QString fileName)
bool	insertMolecule (unsigned int i, Molecule *molecule, QString fileName)
bool	appendMolecule (Molecule *molecule, QString fileName)
Error handling
const QString &	errors () const
void	clearErrors ()
Convenience functions
const QString &	fileName () const
const QString &	fileType () const
const QString &	fileOptions () const
Static Public Member Functions
Static methods
static bool	canOpen (const QString &fileName, QIODevice::OpenMode mode)
static Molecule *	readMolecule (const QString &fileName, const QString &fileType=QString(), const QString &fileOptions=QString(), QString *error=0)
static bool	writeMolecule (const Molecule molecule, const QString &fileName, const QString &fileType=QString(), QString error=0)
static bool	writeMolecule (const Molecule molecule, const QString &fileName, const QString &fileType, const QString &fileOptions, QString error=0)
static bool	writeConformers (const Molecule molecule, const QString &fileName, const QString &fileType=QString(), QString error=0)
static MoleculeFile *	readFile (const QString &fileName, const QString &fileType=QString(), const QString &fileOptions=QString(), bool wait=true)
Protected Slots
void	threadFinished ()
Protected Member Functions
	MoleculeFile (const QString &fileName, const QString &fileType, const QString &fileOptions)
QStringList &	titlesRef ()
std::vector< std::streampos > &	streamposRef ()
std::vector< std::vector < Eigen::Vector3d > * > &	conformersRef ()
void	setConformerFile (bool value)
void	setReady (bool value)
void	setFirstReady (bool value)
Protected Attributes
MoleculeFilePrivate *const	d
QString	m_fileName
QString	m_fileType
QString	m_fileOptions
QString	m_error
std::vector< std::vector < Eigen::Vector3d > * >	m_conformers

Member Function Documentation

bool Avogadro::MoleculeFile::appendMolecule	(	Molecule *	molecule,
		QString	fileName
	)

Append molecule to the end of the file.

Parameters:

molecule	The molecule to append.
fileName	The name of the file for saving.

Todo:: implement this method

bool Avogadro::MoleculeFile::canOpen	(	const QString &	fileName,
		QIODevice::OpenMode	mode
	)		`[static]`

Static function to check if a file can be opened in the specified mode.

Parameters:

fileName	The full path to the file to be opened.
mode	QIODevice::OpenMode to check.

Returns:: True if the file can be opened in the specified mode.

References QFile::close(), and QFile::open().

Referenced by readFile(), readMolecule(), and writeConformers().

void Avogadro::MoleculeFile::clearErrors ( )

Clear the errors. Errors are always appended to error(), so unless you clear them explicitly, consecutive calls to errors() returns all errors from before plus the new ones (if any).

References QString::clear().

const std::vector< std::vector< Eigen::Vector3d > * > & Avogadro::MoleculeFile::conformers ( ) const

Get all the conformers from the file. This methods returns an empty vector if the opened file isn't a conformer file (see isConformerFile()).

Referenced by writeConformers().

const QString & Avogadro::MoleculeFile::errors ( ) const

Returns:: Errors from reading/writing to the file.

const QString& Avogadro::MoleculeFile::fileName ( ) const [inline]

Returns:: the filename for this file

Referenced by writeMolecule().

const QString& Avogadro::MoleculeFile::fileOptions ( ) const [inline]

Returns:: any options set for this file

const QString& Avogadro::MoleculeFile::fileType ( ) const [inline]

Returns:: the file type of this file (e.g., extension or Open Babel code)

void Avogadro::MoleculeFile::firstMolReady ( ) [signal]

This signal is emitted when the first molecule is read

bool Avogadro::MoleculeFile::insertMolecule	(	unsigned int	i,
		Molecule *	molecule,
		QString	fileName
	)

Insert a molecule at index i.

Parameters:

i	The index for inserting the molecule
molecule	The molecule to insert
fileName	The name of the file for saving.

Todo:: implement this method

bool Avogadro::MoleculeFile::isConformerFile ( ) const

Returns:: True if the file contains multiple frames/conformers of the same molecule.

bool Avogadro::MoleculeFile::isReady ( ) const

Returns:: True if the MoleculeFile is ready (i.e. completed reading the file)

Molecule * Avogadro::MoleculeFile::molecule ( unsigned int i = 0 )

Get the {i}th molecule. This function returns a new pointer, you are responsible for deleting it.

Parameters:

i	The index for the molecule to get from the file (indexed from 0).

Returns:: The ith molecule or 0 when i > numMolecule(). In FileIO::Output mode, this method always returns 0.

References OBMol(), and Avogadro::Molecule::setOBMol().

unsigned int Avogadro::MoleculeFile::numMolecules ( ) const

Get the number of molecules in the file.

OpenBabel::OBMol * Avogadro::MoleculeFile::OBMol ( unsigned int i = 0 )

Get the original OBMol object for the {i}th molecule. This function returns a new pointer, you are responsible for deleting it.

Parameters:

i	The index for the molecule to get from the file (indexed from 0 to numMolecule()-1).

Returns:: The original OBMol object read by OpenBabel.

References OpenBabel::OBConversion::AddOption(), QString::append(), QByteArray::data(), QString::endsWith(), OpenBabel::OBConversion::FormatFromExt(), OpenBabel::OBConversion::INOPTIONS, QString::isEmpty(), OpenBabel::OBMol::NumAtoms(), OpenBabel::OBConversion::Read(), OpenBabel::OBConversion::SetInFormat(), QString::split(), QString::toAscii(), QString::toLocal8Bit(), and QObject::tr().

Referenced by molecule(), and readFile().

MoleculeFile * Avogadro::MoleculeFile::readFile	(	const QString &	fileName,
		const QString &	fileType = `QString()`,
		const QString &	fileOptions = `QString()`,
		bool	wait = `true`
	)		`[static]`

Read an entire file, possibly containing multiple molecules in a separate thread and return a MoleculeFile object with the result.

By default, the wait parameter is set to true and the function waits for the thread to finish before returning. If set to false, listening to the MoleculeFile::ready() signal will be emitted when the results are ready.

Parameters:

fileName	The full path to the file to be saved.
fileType	Optional file type parameter - override default file extension parsing.
fileOptions	Options for reading the molecule file, such as bonding.
wait	Wait for the thread to finish before returning.

Returns:: MoleculeFile with (future) results.

References QFileInfo::baseName(), canOpen(), QObject::connect(), QByteArray::data(), OBMol(), OpenBabel::OBConversion::ReadFile(), OpenBabel::OBConversion::SetInFormat(), QThread::start(), QObject::thread(), QString::toAscii(), QString::toLocal8Bit(), QObject::tr(), and QThread::wait().

Molecule * Avogadro::MoleculeFile::readMolecule	(	const QString &	fileName,
		const QString &	fileType = `QString()`,
		const QString &	fileOptions = `QString()`,
		QString *	error = `0`
	)		`[static]`

Static function to load a file and return a Molecule pointer. You are responsible for deleting the molecule object.

Parameters:

fileName	The full path to the file to be opened.
fileType	Optional file type parameter - override default file extension parsing.
fileOptions	Newline separated list of options for reading the molecule file, such as bonding.

Returns:: The Molecule object loaded, 0 if the file could not be loaded.

References OpenBabel::OBConversion::AddOption(), QString::append(), canOpen(), QByteArray::data(), OpenBabel::OBConversion::FormatFromExt(), OpenBabel::OBConversion::INOPTIONS, QString::isEmpty(), OpenBabel::OBConversion::Read(), Avogadro::Molecule::setFileName(), OpenBabel::OBConversion::SetInFormat(), Avogadro::Molecule::setOBMol(), QString::split(), QString::toAscii(), QString::toLocal8Bit(), and QObject::tr().

void Avogadro::MoleculeFile::ready ( ) [signal]

This signal is emitted when the results are read (i.e. the file is read).

bool Avogadro::MoleculeFile::replaceMolecule	(	unsigned int	i,
		Molecule *	molecule,
		QString	fileName
	)

Replace the {i}th molecule with molecule. When a molecule returned by molecule() has changed, this function can be used to write it back to the file at the same position.

Parameters:

i	The index for the molecule to replace.
molecule	The changed (or a totally different) molecule
fileName	The name of the file for saving.

References QString::append(), OpenBabel::OBConversion::FormatFromExt(), QString::isEmpty(), Avogadro::Molecule::OBMol(), QFile::remove(), QFile::rename(), OpenBabel::OBConversion::SetOutFormat(), QString::toAscii(), QString::toLocal8Bit(), QObject::tr(), and OpenBabel::OBConversion::Write().

QStringList Avogadro::MoleculeFile::titles ( ) const

Get the titles for the molecules.

bool Avogadro::MoleculeFile::writeConformers	(	const Molecule *	molecule,
		const QString &	fileName,
		const QString &	fileType = `QString()`,
		QString *	error = `0`
	)		`[static]`

Static function to save a all conformers in a molecule to a file. If writing was unsuccessful, a previously existing file will not be overwritten. All formats with support for multiple molecules can be used.

Parameters:

molecule	The Molecule object to be saved.
fileName	The full path to the file to be saved.
fileType	Optional file type parameter - override default file extension parsing.

Returns:: True on success, false on failure.

References QString::append(), OpenBabel::OBMol::BeginAtom(), canOpen(), conformers(), Avogadro::Molecule::conformers(), QString::endsWith(), OpenBabel::OBConversion::FormatFromExt(), QString::isEmpty(), OpenBabel::OBMol::NextAtom(), Avogadro::Molecule::OBMol(), QFile::remove(), QFile::rename(), OpenBabel::OBConversion::SetOutFormat(), QString::toAscii(), QString::toLocal8Bit(), QObject::tr(), and OpenBabel::OBConversion::Write().

static bool Avogadro::MoleculeFile::writeMolecule	(	const Molecule *	molecule,
		const QString &	fileName,
		const QString &	fileType = `QString()`,
		QString *	error = `0`
	)		`[inline, static]`

Static function to save a single molecule to a file. If writing was unsuccessful, a previously existing file will not be overwritten.

Parameters:

molecule	The Molecule object to be saved.
fileName	The full path to the file to be saved.
fileType	Optional file type parameter - override default file extension parsing.

Deprecated:: Use the overload with the options argument instead.

Returns:: True on success, false on failure.

bool Avogadro::MoleculeFile::writeMolecule	(	const Molecule *	molecule,
		const QString &	fileName,
		const QString &	fileType,
		const QString &	fileOptions,
		QString *	error = `0`
	)		`[static]`

Static function to save a single molecule to a file. If writing was unsuccessful, a previously existing file will not be overwritten.

Parameters:

molecule	The Molecule object to be saved.
fileName	The full path to the file to be saved.
fileType	Optional file type parameter - override default file extension parsing.
fileOptions	Newline separated list of options for writing the molecule file.

Returns:: True on success, false on failure.

References OpenBabel::OBConversion::AddOption(), QString::append(), QFile::close(), QByteArray::data(), QFile::exists(), fileName(), OpenBabel::OBConversion::FormatFromExt(), QString::isEmpty(), OB_CHAINS_MOL, Avogadro::Molecule::OBMol(), QFile::open(), OpenBabel::OBConversion::OUTOPTIONS, OpenBabel::OBChainsParser::PerceiveChains(), QFile::remove(), QFile::rename(), QFile::setFileName(), OpenBabel::OBConversion::SetOutFormat(), QString::split(), QString::toAscii(), QString::toLocal8Bit(), QObject::tr(), OpenBabel::OBMol::UnsetFlag(), and OpenBabel::OBConversion::Write().

The documentation for this class was generated from the following files:

/home/kitware/dashboards/avogadro/libavogadro/src/moleculefile.h
/home/kitware/dashboards/avogadro/libavogadro/src/moleculefile.cpp

Signals

Public Member Functions

Static Public Member Functions

Protected Slots

Protected Member Functions

Protected Attributes

Member Function Documentation