A writer for reaction data in the Daylight SMILES [SMILES] format. More...

#include <SMILESReactionWriter.hpp>

Inheritance diagram for CDPL::Chem::SMILESReactionWriter:

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

	SMILESReactionWriter (const SMILESReactionWriter &)=delete

	~SMILESReactionWriter ()
	Destructor. More...

SMILESReactionWriter &	operator= (const SMILESReactionWriter &)=delete

Base::DataWriter< Reaction > &	write (const Reaction &rxn)
	Writes the reaction rxn 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< Reaction >
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< Reaction >
typedef std::shared_ptr< DataWriter >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `DataWriter` instances. More...

typedef Reaction	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< Reaction >
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 reaction data in the Daylight SMILES [SMILES] format.

SMILESReactionWriter supports the following control-parameters:

Control-Parameter	Default Value (see Chem::ControlParameterDefault)	Description
Chem::ControlParameter::STRICT_ERROR_CHECKING	`false`	Specifies whether non-fatal recoverable errors should be ignored or cause a write operation to fail
Chem::ControlParameter::ORDINARY_HYDROGEN_DEPLETE	`true`	Specifies whether or not to write explicit ordinary hydrogen atoms
Chem::ControlParameter::SMILES_RECORD_FORMAT	`"S"`	Specifies the data record format
Chem::ControlParameter::SMILES_WRITE_CANONICAL_FORM	`false`	Specifies whether to generate canonical SMILES strings
Chem::ControlParameter::SMILES_WRITE_KEKULE_FORM	`false`	Specifies whether to output aromatic rings as Kekulé structures
Chem::ControlParameter::SMILES_WRITE_ATOM_STEREO	`true`	Specifies whether to output the chirality of tetrahedral stereogenic atoms
Chem::ControlParameter::SMILES_WRITE_BOND_STEREO	`true`	Specifies whether to output directional bonds for the specification of chain double bond geometries
Chem::ControlParameter::SMILES_WRITE_RING_BOND_STEREO	`true`	Specifies whether to output directional bonds for the specification of ring double bond geometries
Chem::ControlParameter::SMILES_MIN_STEREO_BOND_RING_SIZE	`8`	Specifies the minimum ring size that is required for the specification of ring double bond geometries
Chem::ControlParameter::SMILES_WRITE_ISOTOPE	`true`	Specifies whether to output the mass of isotopes
Chem::ControlParameter::SMILES_RXN_WRITE_ATOM_MAPPING_ID	`true`	Specifies whether to output reaction atom-atom mapping numbers
Chem::ControlParameter::SMILES_WRITE_SINGLE_BONDS	`false`	Specifies whether to output single bonds
Chem::ControlParameter::SMILES_WRITE_AROMATIC_BONDS	`false`	Specifies whether to output aromatic bonds
Chem::ControlParameter::SMILES_NO_ORGANIC_SUBSET	`false`	Specifies whether ordinary C, N, O, S, P, F, Cl, Br and I atoms shall be enclosed in brackets

Constructor & Destructor Documentation

◆ SMILESReactionWriter() [1/2]

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

Constructs a SMILESReactionWriter instance that will write the reaction data to the output stream os.

Parameters

os	The output stream to write to.

◆ SMILESReactionWriter() [2/2]

CDPL::Chem::SMILESReactionWriter::SMILESReactionWriter ( const SMILESReactionWriter & )

delete

◆ ~SMILESReactionWriter()

CDPL::Chem::SMILESReactionWriter::~SMILESReactionWriter ( )

Destructor.

Member Function Documentation

◆ operator=()

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

delete

◆ write()

Base::DataWriter<Reaction>& CDPL::Chem::SMILESReactionWriter::write ( const Reaction & rxn )

Writes the reaction rxn to the output stream specified in the constructor.

Parameters

rxn	The reaction to write.

Returns: A reference to itself.

◆ operator const void *()

CDPL::Chem::SMILESReactionWriter::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< Reaction >.

◆ operator!()

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

virtual

Tells whether the writer is in a bad state.