A reader for molecule data in the MDL Mol-File [CTFILE] format. More...

#include <MOLMoleculeReader.hpp>

Inheritance diagram for CDPL::Chem::MOLMoleculeReader:

Public Member Functions
	MOLMoleculeReader (std::istream &is)
	Constructs a `MOLMoleculeReader` instance that will read the molecule data from the input stream is. More...

	~MOLMoleculeReader ()
	Destructor. More...

Public Member Functions inherited from CDPL::Util::StreamDataReader< Molecule, MOLMoleculeReader >
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, MOLMoleculeReader >

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, MOLMoleculeReader >
	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 MDL Mol-File [CTFILE] format.

MOLMoleculeReader 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 read operation to fail
Chem::ControlParameter::MULTI_CONF_IMPORT	`true`	Specifies whether to check for and import multi-conformer molecules
Chem::ControlParameter::MULTI_CONF_INPUT_PROCESSOR	pointer to a Chem::DefaultMultiConfMoleculeInputProcessor instance	Specifies an instance of Chem::MultiConfMoleculeInputProcessor that implements the logic of multi-conformer molecule detection and conformational data processing
Chem::ControlParameter::MDL_IGNORE_PARITY	`false`	Specifies whether the stereo parity of atoms shall be ignored
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_IGNORE_LINE_LENGTH_LIMIT	`true`	Specifies whether to check if data lines exceed the maximum allowed line length

Constructor & Destructor Documentation

◆ MOLMoleculeReader()

CDPL::Chem::MOLMoleculeReader::MOLMoleculeReader ( std::istream & is )

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

Parameters

is	The input stream to read from.

◆ ~MOLMoleculeReader()

CDPL::Chem::MOLMoleculeReader::~MOLMoleculeReader ( )

Destructor.

Friends And Related Function Documentation

◆ Util::StreamDataReader< Molecule, MOLMoleculeReader >

friend class Util::StreamDataReader< Molecule, MOLMoleculeReader >

friend

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

MOLMoleculeReader.hpp

Public Member Functions