A writer for molecular graph data in the MDL Mol-File [CTFILE] format. More...

#include <SDFMolecularGraphWriter.hpp>

Inheritance diagram for CDPL::Chem::SDFMolecularGraphWriter:

Public Member Functions
	SDFMolecularGraphWriter (std::ostream &os)
	Constructs a `SDFMolecularGraphWriter` instance that will write data of molecular graphs to the output stream os. More...

	SDFMolecularGraphWriter (const SDFMolecularGraphWriter &)=delete

	~SDFMolecularGraphWriter ()
	Destructor. More...

SDFMolecularGraphWriter &	operator= (const SDFMolecularGraphWriter &)=delete

Base::DataWriter< MolecularGraph > &	write (const MolecularGraph &molgraph)
	Writes data of the molecular graph molgraph to the output stream specified in the constructor. More...

	operator const void * () const
	Returns a pointer whose value indicates the error state of the writer. More...

bool	operator! () const
	Tells whether the writer is in a bad state. More...

Public Member Functions inherited from CDPL::Base::DataWriter< MolecularGraph >
virtual DataWriter &	write (const DataType &obj)=0
	Writes the data object obj. More...

virtual void	close ()
	Writes format dependent data (if required) to mark the end of output. More...

Public Member Functions inherited from CDPL::Base::DataIOBase
std::size_t	registerIOCallback (const IOCallbackFunction &func)
	Registers an I/O callback target function. More...

void	unregisterIOCallback (std::size_t id)
	Unregisters the I/O callback function specified by id. More...

void	invokeIOCallbacks (double progress) const
	Invokes all registered I/O callback functions with the argument `*this`. More...

void	clearIOCallbacks ()
	Clears all registered I/O callback functions. More...

Public Member Functions inherited from CDPL::Base::ControlParameterContainer
std::size_t	getNumParameters () const
	Returns the number of container entries. More...

template<typename T >
void	setParameter (const LookupKey &key, T &&val)
	Sets the value of the control-parameter specified by key to val. More...

const Any &	getParameter (const LookupKey &key, bool throw_=false, bool local=false) const
	Returns the value of the control-parameter specified by key. More...

template<typename T >
const T &	getParameter (const LookupKey &key, bool local=false) const
	Returns the value of the control-parameter specified by key as a `const` reference to an object of type T. More...

template<typename T >
const T &	getParameterOrDefault (const LookupKey &key, const T &def_val, bool local=false) const
	Returns the value of the control-parameter specified by key as a `const` reference to an object of type T, or the default value def_val if a stored value does not exist. More...

bool	removeParameter (const LookupKey &key)
	Removes the entry for the control-parameter specified by key. More...

void	clearParameters ()
	Erases all container entries. More...

bool	isParameterSet (const LookupKey &key, bool local=false) const
	Tells whether or not a value has been assigned to the control-parameter specified by key. More...

void	addParameters (const ControlParameterContainer &cntnr)
	Adds the control-parameter value entries in the `ControlParameterContainer` instance cntnr. More...

void	copyParameters (const ControlParameterContainer &cntnr)
	Replaces the current set of properties by a copy of the entries in cntnr. More...

ConstParameterIterator	getParametersBegin () const
	Returns a constant iterator pointing to the beginning of the entries. More...

ConstParameterIterator	getParametersEnd () const
	Returns a constant iterator pointing to the end of the entries. More...

ConstParameterIterator	begin () const
	Returns a constant iterator pointing to the beginning of the entries. More...

ConstParameterIterator	end () const
	Returns a constant iterator pointing to the end of the entries. More...

void	setParent (const ControlParameterContainer *cntnr)
	Sets or removes the parent control-parameter container used to resolve requests for missing entries. More...

const ControlParameterContainer *	getParent () const
	Returns a pointer to the parent control-parameter container. More...

std::size_t	registerParameterChangedCallback (const ParameterChangedCallbackFunction &func)
	Registers a callback target function that gets invoked when the value of a control-parameter has changed. More...

void	unregisterParameterChangedCallback (std::size_t id)
	Unregisters the callback specified by id. More...

std::size_t	registerParameterRemovedCallback (const ParameterRemovedCallbackFunction &func)
	Registers a callback target function that gets invoked when a control-parameter entry has been removed. More...

void	unregisterParameterRemovedCallback (std::size_t id)
	Unregisters the callback specified by id. More...

std::size_t	registerParentChangedCallback (const ParentChangedCallbackFunction &func)
	Registers a callback target function that gets invoked when the parent container has been changed or was detached. More...

void	unregisterParentChangedCallback (std::size_t id)
	Unregisters the callback specified by id. More...

const ControlParameterContainer &	getParameters () const
	Returns a `const` reference to itself. More...

Additional Inherited Members
Public Types inherited from CDPL::Base::DataWriter< MolecularGraph >
typedef std::shared_ptr< DataWriter >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `DataWriter` instances. More...

typedef MolecularGraph	DataType
	The type of the written data objects. More...

Public Types inherited from CDPL::Base::DataIOBase
typedef std::function< void(const DataIOBase &, double)>	IOCallbackFunction
	A functor class used to wrap I/O callback target functions. More...

Public Types inherited from CDPL::Base::ControlParameterContainer
typedef ParameterMap::value_type	ParameterEntry
	A Base::LookupKey / Base::Any pair used to store the control-parameter values and associated keys. More...

typedef ParameterMap::const_iterator	ConstParameterIterator
	A constant iterator used to iterate over the control-parameter entries. More...

typedef std::function< void(const LookupKey &, const Any &)>	ParameterChangedCallbackFunction
	A functor class that wraps callback target functions which get invoked when the value of a control-parameter has changed. More...

typedef std::function< void(const LookupKey &)>	ParameterRemovedCallbackFunction
	A functor class that wraps callback target functions which get invoked when a control-parameter entry has been removed. More...

typedef std::function< void()>	ParentChangedCallbackFunction
	A functor class that wraps callback target functions which get invoked when the parent container has been changed or was detached. More...

Protected Member Functions inherited from CDPL::Base::DataWriter< MolecularGraph >
DataWriter &	operator= (const DataWriter &writer)
	Assignment operator. More...

Protected Member Functions inherited from CDPL::Base::DataIOBase
	DataIOBase ()
	Default constructor. More...

	DataIOBase (const DataIOBase &io_base)
	Copy constructor. More...

	~DataIOBase ()
	Destructor. More...

DataIOBase &	operator= (const DataIOBase &io_base)
	Assignment operator. More...

Protected Member Functions inherited from CDPL::Base::ControlParameterContainer
	ControlParameterContainer ()
	Constructs an empty `ControlParameterContainer` instance. More...

	ControlParameterContainer (const ControlParameterContainer &cntnr)
	Constructs a copy of the `ControlParameterContainer` instance cntnr. More...

virtual	~ControlParameterContainer ()
	Destructor. More...

ControlParameterContainer &	operator= (const ControlParameterContainer &cntnr)
	Assignment operator. More...

Detailed Description

A writer for molecular graph data in the MDL Mol-File [CTFILE] format.

SDFMolecularGraphWriter supports the following control-parameters:

Control-Parameter	Default Value (see Chem::ControlParameterDefault)	Description
Chem::ControlParameter::COORDINATES_DIMENSION	`0`	Specifies the dimension of atom coordinates
Chem::ControlParameter::STRICT_ERROR_CHECKING	`false`	Specifies whether non-fatal recoverable errors should be ignored or cause a write operation to fail
Chem::ControlParameter::BOND_MEMBER_SWAP_STEREO_FIX	`true`	Specifies whether reverse stereo bonds shall be converted to regular stereo bonds by swapping bond start and end atoms
Chem::ControlParameter::MULTI_CONF_EXPORT	`true`	Specifies whether to write all molecule conformations on output
Chem::ControlParameter::MDL_CTAB_VERSION	`0`	Specifies the desired connection table format
Chem::ControlParameter::MDL_IGNORE_PARITY	`true`	Specifies whether the stereo parity of atoms shall be ignored
Chem::ControlParameter::MDL_UPDATE_TIMESTAMP	`false`	Specifies whether the timestamp of Mol- and Rxn-File header blocks has to be updated
Chem::ControlParameter::MDL_TRIM_STRINGS	`true`	Specifies whether to remove leading and trailing whitespace from string values
Chem::ControlParameter::MDL_TRIM_LINES	`false`	Specifies whether to remove leading and trailing whitespace from data lines
Chem::ControlParameter::MDL_TRUNCATE_STRINGS	`false`	Specifies whether string values that exceed the size of an output data field may be truncated
Chem::ControlParameter::MDL_TRUNCATE_LINES	`false`	Specifies whether data lines that exceed the maximum allowed line length may be truncated
Chem::ControlParameter::MDL_IGNORE_LINE_LENGTH_LIMIT	`true`	Specifies whether to check if data lines exceed the maximum allowed line length

Constructor & Destructor Documentation

◆ SDFMolecularGraphWriter() [1/2]

CDPL::Chem::SDFMolecularGraphWriter::SDFMolecularGraphWriter ( std::ostream & os )

Constructs a SDFMolecularGraphWriter instance that will write data of molecular graphs to the output stream os.

Parameters

os	The output stream to write to.

◆ SDFMolecularGraphWriter() [2/2]

CDPL::Chem::SDFMolecularGraphWriter::SDFMolecularGraphWriter ( const SDFMolecularGraphWriter & )

delete

◆ ~SDFMolecularGraphWriter()

CDPL::Chem::SDFMolecularGraphWriter::~SDFMolecularGraphWriter ( )

Destructor.

Member Function Documentation

◆ operator=()

SDFMolecularGraphWriter& CDPL::Chem::SDFMolecularGraphWriter::operator= ( const SDFMolecularGraphWriter & )

delete

◆ write()

Base::DataWriter<MolecularGraph>& CDPL::Chem::SDFMolecularGraphWriter::write ( const MolecularGraph & molgraph )

Writes data of the molecular graph molgraph to the output stream specified in the constructor.

Parameters

molgraph The molecular graph to write.

Returns: A reference to itself.

◆ operator const void *()

CDPL::Chem::SDFMolecularGraphWriter::operator const void * ( ) const

virtual

Returns a pointer whose value indicates the error state of the writer.

The operator allows to write expressions like:

if (writer) { ...

if (writer.write(...)) { ...

Returns: A non-null pointer if the writer is in a good state, a null pointer otherwise.

Note: The returned pointer is not meant to be dereferenced, it is just a state indicator.

See also: operator!()

Implements CDPL::Base::DataWriter< MolecularGraph >.

◆ operator!()

bool CDPL::Chem::SDFMolecularGraphWriter::operator! ( ) const

virtual

Tells whether the writer is in a bad state.