CDPL::Chem::JMEMoleculeReader Class Reference

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

#include <JMEMoleculeReader.hpp>

Inheritance diagram for CDPL::Chem::JMEMoleculeReader:

Public Member Functions
	JMEMoleculeReader (std::istream &is)
	Constructs a JMEMoleculeReader instance that will read the molecule data from the input stream is. More...
	~JMEMoleculeReader ()
	Destructor. More...
Public Member Functions inherited from CDPL::Util::StreamDataReader< Molecule, JMEMoleculeReader >
Base::DataReader< Molecule > &	read (Molecule &obj, bool overwrite=true)
	Reads the data record at the current record index and stores the read data in obj. More...
Base::DataReader< Molecule > &	read (std::size_t idx, Molecule &obj, bool overwrite=true)
	Reads the data record at index idx and stores the read data in obj. More...
Base::DataReader< Molecule > &	skip ()
	Skips the data record at the current record index. More...
bool	hasMoreData ()
	Tells if there are any data records left to read. More...
std::size_t	getRecordIndex () const
void	setRecordIndex (std::size_t idx)
	Sets the index of the current data record to idx. More...
std::size_t	getNumRecords ()
	Returns the total number of available data records. More...
	operator const void * () const
bool	operator! () const
Public Member Functions inherited from CDPL::Base::DataReader< Molecule >
virtual DataReader &	read (DataType &obj, bool overwrite=true)=0
	Reads the data record at the current record index and stores the read data in obj. More...
virtual DataReader &	read (std::size_t idx, DataType &obj, bool overwrite=true)=0
	Reads the data record at index idx and stores the read data in obj. More...
virtual void	close ()
	Performs a reader specific shutdown operation (if required). 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...

Friends
class	Util::StreamDataReader< Molecule, JMEMoleculeReader >

Additional Inherited Members
Public Types inherited from CDPL::Base::DataReader< Molecule >
typedef Molecule	DataType
	The type of the read data objects. More...
typedef std::shared_ptr< DataReader >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated DataReader instances. 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::Util::StreamDataReader< Molecule, JMEMoleculeReader >
	StreamDataReader (std::istream &is)
	Constructs a StreamDataReader instance that will read from the input stream is. More...
Protected Member Functions inherited from CDPL::Base::DataReader< Molecule >
DataReader &	operator= (const DataReader &reader)
	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 reader for molecule data in the native I/O format of the JME Molecular Editor [JME] java applet.

JMEMoleculeReader implements the reading of Chem::Molecule objects from a std::istream instance that provides the molecule data in the native I/O format of the JME Molecular Editor applet.

Attributes of the atoms and bonds of a read input molecule are stored as properties of allocated Chem::Atom and Chem::Bond objects. The affected properties are summarized in the tables below:

Chem::Atom Property	Description	Notes
Chem::AtomProperty::MATCH_CONSTRAINTS	Specifies atom matching constraints	Only set if constraints have been specified
Chem::AtomProperty::COORDINATES_2D	Specifies the 2D position of the atom	-
Chem::AtomProperty::TYPE	Specifies the type of the atom (see Chem::AtomType)	Only set if the atom is a query atom and the specified type is not a member of an atom list
Chem::AtomProperty::SYMBOL	Specifies the atom symbol (e.g. element symbol)	Only set if the atom is not a query atom, or the symbol cannot be mapped to a valid atom type and is not a member of an atom list
Chem::AtomProperty::FORMAL_CHARGE	Specifies the formal charge of the atom	Only set if the charge has been specified outside of an atom list
Chem::AtomProperty::REACTION_ATOM_MAPPING_ID	Specifies the reactant to product atom mapping class	Only set if a mapping number has been specified that is greater than zero

Chem::Bond Property	Description
Chem::BondProperty::ORDER	Specifies the order of the bond
Chem::BondProperty::STEREO_2D_FLAG	Specifies the 2D stereo bond type (see Chem::BondStereoFlag)

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 such constraints are encountered during the processing of an atom specification, the constraint primitives are converted to corresponding Chem::MatchConstraint objects and stored as the value of the Chem::Atom property Chem::AtomProperty::MATCH_CONSTRAINTS in a Chem::MatchConstraintList data structure.

The following table lists all of the supported JME atom matching constraints and specifies how they are represented by Chem::MatchConstraint instances (in the table <n> denotes a positive integer value and <S> the symbol of a chemical element):

Expression Primitive	Description	Mapped Chem::MatchConstraint object
		Constraint ID	Operator	Value
c	Aromatic carbon	Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object
		The sub-constraint list has the logical type Chem::MatchConstraintList::AND_LIST and contains the elements:
		Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::C
		Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	true
n	Aromatic nitrogen	Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object
		The sub-constraint list has the logical type Chem::MatchConstraintList::AND_LIST and contains the elements:
		Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::N
		Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	true
o	Aromatic oxygen	Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object
		The sub-constraint list has the logical type Chem::MatchConstraintList::AND_LIST and contains the elements:
		Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::O
		Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	true
s	Aromatic sulfur	Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object
		The sub-constraint list has the logical type Chem::MatchConstraintList::AND_LIST and contains the elements:
		Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::S
		Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	true
p	Aromatic phosphorus	Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object
		The sub-constraint list has the logical type Chem::MatchConstraintList::AND_LIST and contains the elements:
		Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::P
		Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	true
a	Any aromatic atom	Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object
		The sub-constraint list has the logical type Chem::MatchConstraintList::AND_LIST and contains the elements:
		Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::ANY
		Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	true
A	Any non-aromatic atom	Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object
		The sub-constraint list has the logical type Chem::MatchConstraintList::AND_LIST and contains the elements:
		Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::ANY
		Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	false
<S>	A non-aromatic atom of element <S>	Chem::AtomMatchConstraint::CONSTRAINT_LIST	Chem::MatchConstraint::EQUAL	A pointer to a Chem::MatchConstraintList object
		The sub-constraint list has the logical type Chem::MatchConstraintList::AND_LIST and contains the elements:
		Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Atom type associated with the element <S>
		Chem::AtomMatchConstraint::AROMATICITY	Chem::MatchConstraint::EQUAL	false
#<n>	An atom with atomic number <n>	Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	<n>
!#6	Any atom except carbon	Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::QH
*	Any atom	Chem::AtomMatchConstraint::TYPE	Chem::MatchConstraint::EQUAL	Chem::AtomType::ANY
R	Any ring atom	Chem::AtomMatchConstraint::RING_TOPOLOGY	Chem::MatchConstraint::EQUAL	true
!R	Any non-ring atom	Chem::AtomMatchConstraint::RING_TOPOLOGY	Chem::MatchConstraint::EQUAL	false
+<n>	Positive charge	Chem::AtomMatchConstraint::CHARGE	Chem::MatchConstraint::EQUAL	+<n>
-<n>	Negative charge	Chem::AtomMatchConstraint::CHARGE	Chem::MatchConstraint::EQUAL	-<n>
H<n>	Hydrogen count	Chem::AtomMatchConstraint::H_COUNT	Chem::MatchConstraint::EQUAL	<n>
D<n>	Heavy bond count	Chem::AtomMatchConstraint::HEAVY_BOND_COUNT	Chem::MatchConstraint::EQUAL	<n>

The error handling behaviour of a JMEMoleculeReader instance can be configured with the following control-parameter:

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 read operation to fail
Chem::ControlParameter::COORDINATES_DIMENSION	2	Specifies the dimension of atom coordinates

Constructor & Destructor Documentation

JMEMoleculeReader()

CDPL::Chem::JMEMoleculeReader::JMEMoleculeReader

(

std::istream &

is

)

Constructs a JMEMoleculeReader instance that will read the molecule data from the input stream is.

Parameters

is	The input stream to read from.

~JMEMoleculeReader()

CDPL::Chem::JMEMoleculeReader::~JMEMoleculeReader

(

)

Destructor.

Friends And Related Function Documentation

Util::StreamDataReader< Molecule, JMEMoleculeReader >

friend class Util::StreamDataReader< Molecule, JMEMoleculeReader >

friend

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

• JMEMoleculeReader.hpp