A reader for molecule data in the PSD-format of the CDPL. 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 ()

PSDMoleculeReader &	read (Chem::Molecule &mol, bool overwrite=true)
	Reads the data record at the current record index and stores the read data in obj. More...

PSDMoleculeReader &	read (std::size_t idx, Chem::Molecule &mol, bool overwrite=true)
	Reads the data record at index idx and stores the read data in obj. More...

PSDMoleculeReader &	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< Chem::Molecule >
virtual std::size_t	getRecordIndex () const=0
	Returns the index of the current data record. More...

virtual	operator const void * () const=0
	Returns a pointer whose value indicates the error state of the reader. More...

virtual bool	operator! () const=0
	Tells whether the reader is in a bad state. 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...

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 ()
	Destructor. More...

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

Detailed Description

A reader for molecule data in the PSD-format of the CDPL.

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 ( )

Member Function Documentation

◆ read() [1/2]

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

virtual

Reads the data record at the current record index and stores the read data in obj.

If the read operation was successful, the record index is incremented by 1.

Parameters

obj	The object storing the read data.
overwrite	Specifies whether any existing data in obj shall be replaced by the newly read data or if the read data should be appended (if supported by the reader and data type).

Returns: A reference to itself.

Exceptions

Base::IOError if an I/O error occurred.

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

◆ read() [2/2]

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

virtual

Reads the data record at index idx and stores the read data in obj.

If the read operation was successful, the record index is set to idx + 1.

Parameters

idx	The zero-based index of the data record to read.
obj	The object storing the read data.
overwrite	Specifies whether any existing data in obj shall be replaced by the newly read data or if the read data should be appended (if supported by the reader and data type).

Returns: A reference to itself.

Exceptions

Base::IndexError if idx is greater or equal to the number of records. Base::IOError if an I/O error occurred.

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

◆ skip()

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

virtual

Skips the data record at the current record index.

If the operation was successful, the record index is incremented by 1.

Returns: A reference to itself.

Exceptions

Base::IOError if an I/O error occurred.

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

◆ hasMoreData()

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

virtual

Tells if there are any data records left to read.

Returns: true if there are data records left to read, and false otherwise.

Exceptions

Base::IOError if an I/O error occurred.

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

◆ getRecordIndex()

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

◆ setRecordIndex()

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

virtual

Sets the index of the current data record to idx.

Parameters

idx	The zero-based index of the data record.

Exceptions

Base::IndexError if idx is greater or equal to the number of available data records. Base::IOError if an I/O error occurred.

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

◆ getNumRecords()

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

virtual

Returns the total number of available data records.

Returns: The total number of available data records.

Exceptions

Base::IOError if an I/O error occurred.

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

◆ operator const void *()

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

◆ operator!()

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

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!()