Reader for molecule data in the CDPL PSD-format. More...

#include <PSDMoleculeReader.hpp>

Inheritance diagram for CDPL::Pharm::PSDMoleculeReader:

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

	PSDMoleculeReader (const std::string &file_name)
	Constructs a `PSDMoleculeReader` instance that will read the molecule data from the input file file_name. More...

	~PSDMoleculeReader ()
	Destructor. More...

PSDMoleculeReader &	read (Chem::Molecule &mol, bool overwrite=true)
	Reads the next molecule into mol. More...

PSDMoleculeReader &	read (std::size_t idx, Chem::Molecule &mol, bool overwrite=true)
	Reads the molecule at record index idx into mol. More...

PSDMoleculeReader &	skip ()
	Skips the next molecule record (advances the current record index). More...

bool	hasMoreData ()
	Tells whether the reader has more records to read. More...

std::size_t	getRecordIndex () const
	Returns the current record index. More...

void	setRecordIndex (std::size_t idx)
	Sets the current record index. More...

std::size_t	getNumRecords ()
	Returns the total number of records. More...

	operator const void * () const
	Tells whether the reader is in a good (readable) state. More...

bool	operator! () const
	Tells whether the reader is in a bad (non-readable) state. More...

Public Member Functions inherited from CDPL::Base::DataReader< Chem::Molecule >
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 an entry 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 of the `ControlParameterContainer` instance cntnr. More...

void	copyParameters (const ControlParameterContainer &cntnr)
	Replaces the current control-parameter entries 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::DataReader< Chem::Molecule >
typedef Chem::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::Base::DataReader< Chem::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 ()
	Virtual destructor. More...

ControlParameterContainer &	operator= (const ControlParameterContainer &cntnr)
	Assignment operator. More...

Detailed Description

Reader for molecule data in the CDPL PSD-format.

Constructor & Destructor Documentation

◆ PSDMoleculeReader() [1/2]

CDPL::Pharm::PSDMoleculeReader::PSDMoleculeReader ( std::istream & is )

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

Parameters

is	The input stream to read from.

◆ PSDMoleculeReader() [2/2]

CDPL::Pharm::PSDMoleculeReader::PSDMoleculeReader ( const std::string & file_name )

Constructs a PSDMoleculeReader instance that will read the molecule data from the input file file_name.

Parameters

file_name The input file to read from.

◆ ~PSDMoleculeReader()

CDPL::Pharm::PSDMoleculeReader::~PSDMoleculeReader ( )

Destructor.

Member Function Documentation

◆ read() [1/2]

PSDMoleculeReader& CDPL::Pharm::PSDMoleculeReader::read	(	Chem::Molecule &	mol,
		bool	overwrite = `true`
	)

virtual

Reads the next molecule into mol.

Parameters

mol	The output molecule.
overwrite	If `true`, the output molecule is cleared before the database molecule is copied into it.

Returns: A reference to itself.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ read() [2/2]

PSDMoleculeReader& CDPL::Pharm::PSDMoleculeReader::read	(	std::size_t	idx,
		Chem::Molecule &	mol,
		bool	overwrite = `true`
	)

virtual

Reads the molecule at record index idx into mol.

Parameters

idx	The zero-based record index.
mol	The output molecule.
overwrite	If `true`, the output molecule is cleared before the database molecule is copied into it.

Returns: A reference to itself.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ skip()

PSDMoleculeReader& CDPL::Pharm::PSDMoleculeReader::skip ( )

virtual

Skips the next molecule record (advances the current record index).

Returns: A reference to itself.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ hasMoreData()

bool CDPL::Pharm::PSDMoleculeReader::hasMoreData ( )

virtual

Tells whether the reader has more records to read.

Returns: true if at least one more record is available, and false otherwise.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ getRecordIndex()

std::size_t CDPL::Pharm::PSDMoleculeReader::getRecordIndex ( ) const

virtual

Returns the current record index.

Returns: The zero-based record index of the next record to read.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ setRecordIndex()

void CDPL::Pharm::PSDMoleculeReader::setRecordIndex ( std::size_t idx )

virtual

Sets the current record index.

Parameters

idx	The new zero-based record index.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ getNumRecords()

std::size_t CDPL::Pharm::PSDMoleculeReader::getNumRecords ( )

virtual

Returns the total number of records.

Returns: The record count.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ operator const void *()

CDPL::Pharm::PSDMoleculeReader::operator const void * ( ) const

virtual

Tells whether the reader is in a good (readable) state.

Returns: A non-nullptr pointer if the reader is in a good state, and nullptr otherwise.

Implements CDPL::Base::DataReader< Chem::Molecule >.

◆ operator!()

bool CDPL::Pharm::PSDMoleculeReader::operator! ( ) const

virtual

Tells whether the reader is in a bad (non-readable) state.

Returns: true if the reader is in a bad state, and false otherwise.

Implements CDPL::Base::DataReader< Chem::Molecule >.

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

PSDMoleculeReader.hpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PSDMoleculeReader() [1/2]

◆ PSDMoleculeReader() [2/2]

◆ ~PSDMoleculeReader()

Member Function Documentation

◆ read() [1/2]

◆ read() [2/2]

◆ skip()

◆ hasMoreData()

◆ getRecordIndex()

◆ setRecordIndex()

◆ getNumRecords()

◆ operator const void *()

◆ operator!()