A writer for reaction data in the native I/O format of the JME Molecular Editor [JME] java applet. More...

#include <JMEReactionWriter.hpp>

Inheritance diagram for CDPL::Chem::JMEReactionWriter:

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

	JMEReactionWriter (const JMEReactionWriter &)=delete

	~JMEReactionWriter ()
	Destructor. More...

JMEReactionWriter &	operator= (const JMEReactionWriter &)=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 native I/O format of the JME Molecular Editor [JME] java applet.

JMEReactionWriter implements the output of Chem::Reaction objects in the native I/O format used by the JME Molecular Editor applet. The output data are written by means of a std::ostream object that was provided to the JMEReactionWriter constructor.

Atom and bond attributes that get written for a component of the output reaction are defined by the following Chem::Atom, Chem::Bond and Chem::BondContainer properties:

Chem::Atom Property	Description	Notes
Chem::AtomProperty::MATCH_CONSTRAINTS	Specifies atom matching constraints	Only written if the constraints have been explicitly assigned and can be expressed by corresponding JME constraints
Chem::AtomProperty::COORDINATES_2D	Specifies the 2D position of the atom	-
Chem::AtomProperty::TYPE	Specifies the type of the atom (see Chem::AtomType)	Only written if the atom is a query atom and the type is supported by the JME format.
Chem::AtomProperty::SYMBOL	Specifies the atom symbol (e.g. element symbol)	Only written if the atom is not a query atom
Chem::AtomProperty::FORMAL_CHARGE	Specifies the fromal charge of the atom	Only written if the atom is not a query atom and the specified charge is different from zero
Chem::AtomProperty::H_COUNT	Specifies the hydrogen count of the atom	Only written if the atom is a query atom and a corresponding matching constraint has been specified
Chem::AtomProperty::RING_FLAG	Tells whether the atom is a member of a ring	Only written if the atom is a query atom and a corresponding matching constraint has been specified
Chem::AtomProperty::AROMATICITY_FLAG	Tells whether the atom is a member of an aromatic ring	Only written if the atom is a query atom and a corresponding matching constraint has been specified
Chem::AtomProperty::REACTION_ATOM_MAPPING_ID	Specifies the reactant to product atom mapping class	Only written if the specified mapping number is greater than zero

Chem::Bond Property	Description	Notes
Chem::BondProperty::ORDER	Specifies the order of the bond	-
Chem::BondProperty::STEREO_FLAG	Specifies the 2D stereo bond type (see Chem::BondStereoFlag)	Either stereo bonds are not supported by the JME format and are written as plain single bonds

Chem::BondContainer Property	Description	Notes
Chem::BondContainerProperty::HEAVY_BOND_COUNT	Specifies the heavy bond count of the atoms	Only written if the atom is a query atom and a corresponding matching constraint has been specified

Beside the editing of conventional chemical structures, the JME applet allows to some extent the specification of atom matching constraints for the definition of substructure search queries. If an atom of a component of the output reaction specifies any constraints by a Chem::MatchConstraintList data structure that has been assigned to the property Chem::AtomProperty::MATCH_CONSTRAINTS, an attempt is made to convert the contained Chem::MatchConstraint objects to equivalent JME query expression primitives.

Different types of constraints specified by Chem::MatchConstraint instances and the corresponding JME expression primitives are listed in the table below (<n> denotes a positive integer value and <S> the symbol of a chemical element; * the value is either provided by the Chem::MatchConstraint instance (see Chem::MatchConstraint::getValue()) or, if no value has been set, by the property specified in parentheses):

Chem::MatchConstraint object			Written Expression Primitive	Description
Constraint ID	Operator	Value*	Written Expression Primitive	Description
Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object	c	Aromatic carbon
The sub-constraint list must have the logical type Chem::MatchConstraintList::AND_LIST and has to contain the elements:
Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::C (Chem::AtomProperty::TYPE)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	`true` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::NOT_EQUAL	`false` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object	n	Aromatic nitrogen
The sub-constraint list must have the logical type Chem::MatchConstraintList::AND_LIST and has to contain the elements:
Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::N (Chem::AtomProperty::TYPE)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	`true` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::NOT_EQUAL	`false` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object	o	Aromatic oxygen
The sub-constraint list must have the logical type Chem::MatchConstraintList::AND_LIST and has to contain the elements:
Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::O (Chem::AtomProperty::TYPE)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	`true` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::NOT_EQUAL	`false` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object	s	Aromatic sulfur
The sub-constraint list must have the logical type Chem::MatchConstraintList::AND_LIST and has to contain the elements:
Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::S (Chem::AtomProperty::TYPE)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	`true` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::NOT_EQUAL	`false` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object	p	Aromatic phosphorus
The sub-constraint list must have the logical type Chem::MatchConstraintList::AND_LIST and has to contain the elements:
Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::P (Chem::AtomProperty::TYPE)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	`true` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::NOT_EQUAL	`false` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object	a	Any aromatic atom
The sub-constraint list must have the logical type Chem::MatchConstraintList::AND_LIST and has to contain the elements:
Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::ANY (Chem::AtomProperty::TYPE)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	`true` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::NOT_EQUAL	`false` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object	A	Any non-aromatic atom
The sub-constraint list must have the logical type Chem::MatchConstraintList::AND_LIST and has to contain the elements:
Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::ANY (Chem::AtomProperty::TYPE)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	`false` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::NOT_EQUAL	`true` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object	<S>	A non-aromatic atom of element <S>
The sub-constraint list must have the logical type Chem::MatchConstraintList::AND_LIST and has to contain the elements:
Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Atom type associated with the element <S> (Chem::AtomProperty::TYPE)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	`false` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::NOT_EQUAL	`true` (Chem::AtomProperty::AROMATICITY_FLAG)
Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	<n> (Chem::AtomProperty::TYPE)	#<n>	An atom with atomic number <n>
Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::QH (Chem::AtomProperty::TYPE)	!#6	Any atom except carbon
Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::ANY (Chem::AtomProperty::TYPE)	*	Any atom
Chem::AtomMatchConstraint::RING_TOPOLOGY	Chem::MatchConstraint::EQUAL	`true` (Chem::AtomProperty::RING_FLAG)	R	Any ring atom
Chem::AtomMatchConstraint::RING_TOPOLOGY	Chem::MatchConstraint::NOT_EQUAL	`false` (Chem::AtomProperty::RING_FLAG)	R	Any ring atom
Chem::AtomMatchConstraint::RING_TOPOLOGY	Chem::MatchConstraint::EQUAL	`false` (Chem::AtomProperty::RING_FLAG)	!R	Any non-ring atom
Chem::AtomMatchConstraint::RING_TOPOLOGY	Chem::MatchConstraint::NOT_EQUAL	`true` (Chem::AtomProperty::RING_FLAG)	!R	Any non-ring atom
Chem::AtomMatchConstraint::H_COUNT	Chem::MatchConstraint::EQUAL	<n> (Chem::getAtomCount(const Chem::Atom&, const Chem::MolecularGraph&, unsigned int))	H<n>	Hydrogen count
Chem::AtomMatchConstraint::HEAVY_BOND_COUNT	Chem::MatchConstraint::EQUAL	<n> (Chem::getHeavyBondCount(const Chem::Atom&, const Chem::MolecularGraph&))	D<n>	Heavy bond count

JMEReactionWriter can be configured with 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::COORDINATES_DIMENSION	`2`	Specifies the dimension of atom coordinates
Chem::ControlParameter::RECORD_SEPARATOR	`"\n"`	Specifies the data record separator
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::JME_SEPARATE_COMPONENTS	`true`	Specifies whether the components of a molecule shall be written separately or combined as a single JME component

Constructor & Destructor Documentation

◆ JMEReactionWriter() [1/2]

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

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

Parameters

os	The output stream to write to.

◆ JMEReactionWriter() [2/2]

CDPL::Chem::JMEReactionWriter::JMEReactionWriter ( const JMEReactionWriter & )

delete

◆ ~JMEReactionWriter()

CDPL::Chem::JMEReactionWriter::~JMEReactionWriter ( )

Destructor.

Member Function Documentation

◆ operator=()

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

delete

◆ write()

Base::DataWriter<Reaction>& CDPL::Chem::JMEReactionWriter::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::JMEReactionWriter::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::JMEReactionWriter::operator! ( ) const

virtual

Tells whether the writer is in a bad state.