A writer for molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...

#include <INCHIMolecularGraphWriter.hpp>

Inheritance diagram for CDPL::Chem::INCHIMolecularGraphWriter:

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

	INCHIMolecularGraphWriter (const INCHIMolecularGraphWriter &)=delete

	~INCHIMolecularGraphWriter ()
	Destructor. More...

INCHIMolecularGraphWriter &	operator= (const INCHIMolecularGraphWriter &)=delete

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

int	getReturnCode () const
	Returns the error code of the last write operation. More...

const std::string &	getMessage () const
	Returns the error message associated with the last write operation. More...

const std::string &	getLogOutput () const
	Returns the log output that was generated for the last write operation. 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 IUPAC International Chemical Identifier (InChI) [INCHI] format.

INCHIMolecularGraphWriter implements the generation of InChI strings from Chem::MolecularGraph objects. The output data are written by means of a std::ostream object that was provided to the INCHIMolecularGraphWriter constructor.

For the generation of the InChI output, INCHIMolecularGraphWriter uses the function GetINCHI() of the InChI C-API. The return value of the function provides information about the status of the performed operation (see Chem::INCHIReturnCode) and can be accessed by the method getReturnCode(). Produced error and log messages are accessible via the methods getMessage() and getLogOutput(), respectively.

The generation of InChI strings requires values of the following Chem::Atom and Chem::Bond properties:

Chem::Atom Property	Description	Notes
Chem::AtomProperty::COORDINATES_2D	Specifies the 2D position of the atom	Only required if 2D atom coordinates are written
Chem::AtomProperty::COORDINATES_3D	Specifies the 3D-coordinates of the atom	Only required if 3D atom coordinates are written
Chem::AtomProperty::SYMBOL	Specifies the symbol of the atom's element	-
Chem::AtomProperty::ISOTOPE	Specifies the isotopic mass of the atom	-
Chem::AtomProperty::FORMAL_CHARGE	Specifies the formal charge of the atom	-
Chem::AtomProperty::RADICAL_TYPE	Specifies the radical type (see Chem::RadicalType)	-
Chem::AtomProperty::STEREO_DESCRIPTOR	Specifies the atom stereo descriptor (see Chem::AtomConfiguration, Chem::StereoDescriptor)	Only required if no atom coordinates are written

Chem::Bond Property	Description	Notes
Chem::BondProperty::ORDER	Specifies the order of the bond	-
Chem::BondProperty::STEREO_2D_FLAG	Specifies the 2D stereo bond type (see Chem::BondStereoFlag)	Only required if 2D or 3D atom coordinates are written
Chem::BondProperty::STEREO_DESCRIPTOR	Specifies the stereo descriptor of the bond (see Chem::BondConfiguration, Chem::StereoDescriptor)	Only required if no atom coordinates are written

INCHIMolecularGraphWriter can be configured with the following control-parameters:

Control-Parameter	Default Value (see Chem::ControlParameterDefault)	Description
Chem::ControlParameter::COORDINATES_DIMENSION	`1`	Specifies the dimension of the atom coordinates (a value of 2 specifies 2D, a value of 3 specifies 3D, a value of zero specifies that no atom coordinates shall be written; any other value specifies that 3D-coordinates shall be written if they are available, and no coordinates otherwise)
Chem::ControlParameter::STRICT_ERROR_CHECKING	`false`	Specifies whether non-fatal recoverable errors should be ignored or cause a write operation to fail
Chem::ControlParameter::RECORD_SEPARATOR	`"\n"`	Specifies the data record separator
Chem::ControlParameter::INCHI_OUTPUT_OPTIONS	`"/WarnOnEmptyStructure /AuxNone /NEWPSOFF"`	Specifies options for InChI generation

Constructor & Destructor Documentation

◆ INCHIMolecularGraphWriter() [1/2]

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

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

Parameters

os	The output stream to write to.

◆ INCHIMolecularGraphWriter() [2/2]

CDPL::Chem::INCHIMolecularGraphWriter::INCHIMolecularGraphWriter ( const INCHIMolecularGraphWriter & )

delete

◆ ~INCHIMolecularGraphWriter()

CDPL::Chem::INCHIMolecularGraphWriter::~INCHIMolecularGraphWriter ( )

Destructor.

Member Function Documentation

◆ operator=()

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

delete

◆ write()

Base::DataWriter<MolecularGraph>& CDPL::Chem::INCHIMolecularGraphWriter::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.

◆ getReturnCode()

int CDPL::Chem::INCHIMolecularGraphWriter::getReturnCode ( ) const

Returns the error code of the last write operation.

Possible return values are defined in namespace Chem::INCHIReturnCode.

Returns: The error code of the last write operation.

◆ getMessage()

const std::string& CDPL::Chem::INCHIMolecularGraphWriter::getMessage ( ) const

Returns the error message associated with the last write operation.

Returns: The error message associated with the last write operation.

◆ getLogOutput()

const std::string& CDPL::Chem::INCHIMolecularGraphWriter::getLogOutput ( ) const

Returns the log output that was generated for the last write operation.

Returns: The log output that was generated for the last write operation.

◆ operator const void *()

CDPL::Chem::INCHIMolecularGraphWriter::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::INCHIMolecularGraphWriter::operator! ( ) const