A reader for molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...

#include <INCHIMoleculeReader.hpp>

Inheritance diagram for CDPL::Chem::INCHIMoleculeReader:

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

int	getReturnCode () const
	Returns the error code of the last read operation. More...

const std::string &	getMessage () const
	Returns the error message associated with the last read operation. More...

const std::string &	getLogOutput () const
	Returns the log output that was generated for the last read operation. More...

Public Member Functions inherited from CDPL::Util::StreamDataReader< DataType, ReaderImpl >
Base::DataReader< DataType > &	read (DataType &obj, bool overwrite=true)
	Reads the data record at the current record index and stores the read data in obj. More...

Base::DataReader< DataType > &	read (std::size_t idx, DataType &obj, bool overwrite=true)
	Reads the data record at index idx and stores the read data in obj. More...

Base::DataReader< DataType > &	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< DataType >
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...

Friends
class	Util::StreamDataReader< Molecule, INCHIMoleculeReader >

Additional Inherited Members
Public Types inherited from CDPL::Base::DataReader< DataType >
typedef DataType	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< DataType, ReaderImpl >
	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< DataType >
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 IUPAC International Chemical Identifier (InChI) [INCHI] format.

INCHIMoleculeReader implements the conversion of InChI strings (or strings with auxiliary InChI information) to corresponding Chem::Molecule objects. The input data are read by means of a std::istream object that was provided to the INCHIMoleculeReader constructor.

For the actual decoding of the InChI input, INCHIMoleculeReader uses an appropriate function (GetStructFromINCHI() for InChI strings and Get_inchi_Input_FromAuxInfo() for auxiliary InChI information) of the InChI C-API. The return value of the called function provides information about the status of the performed operation (see Chem::INCHIReturnCode) and can be accessed by the method getReturnCode(). Produced error and log messages are accessible via the methods getMessage() and getLogOutput(), respectively.

Atom and bond attributes 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::COORDINATES_2D	Specifies the 2D position of the atom	Only set if auxiliary information with 2D-coordinates is available
Chem::AtomProperty::COORDINATES_3D	Specifies the 3D-coordinates of the atom	Only set if auxiliary information with 3D-coordinates is available
Chem::AtomProperty::SYMBOL	Specifies the symbol of the atom's element	-
Chem::AtomProperty::ISOTOPE	Specifies the isotopic mass of the atom	-
Chem::AtomProperty::FORMAL_CHARGE	Specifies the formal charge of the atom	Only set if the charge is different from zero
Chem::AtomProperty::RADICAL_TYPE	Specifies the radical type (see Chem::RadicalType)	Only set if the atom is a radical
Chem::AtomProperty::STEREO_DESCRIPTOR	Specifies the atom stereo descriptor (see Chem::AtomConfiguration, Chem::StereoDescriptor)	Only set if 0D stereo information is available and the atom is a tetrahedral stereogenic center

Chem::Bond Property	Description	Notes
Chem::BondProperty::ORDER	Specifies the order of the bond	-
Chem::BondProperty::STEREO_2D_FLAG	Specifies the 2D stereo bond type (see Chem::BondStereoFlag)	Only set if auxiliary information with 2D stereo information is available
Chem::BondProperty::STEREO_DESCRIPTOR	Specifies the bond stereo descriptor (see Chem::BondConfiguration, Chem::StereoDescriptor)	Only set if 0D stereo information is available and the bond is stereogenic center

INCHIMoleculeReader 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 read operation to fail
Chem::ControlParameter::INCHI_INPUT_OPTIONS	`""`	Specifies options for InChI input

Constructor & Destructor Documentation

◆ INCHIMoleculeReader()

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

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

Parameters

is	The input stream to read from.

Member Function Documentation

◆ getReturnCode()

int CDPL::Chem::INCHIMoleculeReader::getReturnCode ( ) const

Returns the error code of the last read operation.

Possible return values are defined in namespace Chem::INCHIReturnCode.

Returns: The error code of the last read operation.

◆ getMessage()

const std::string& CDPL::Chem::INCHIMoleculeReader::getMessage ( ) const

Returns the error message associated with the last read operation.

Returns: The error message associated with the last read operation.

◆ getLogOutput()

const std::string& CDPL::Chem::INCHIMoleculeReader::getLogOutput ( ) const

Returns the log output that was generated for the last read operation.

Returns: The log output that was generated for the last read operation.

Friends And Related Function Documentation

◆ Util::StreamDataReader< Molecule, INCHIMoleculeReader >

friend class Util::StreamDataReader< Molecule, INCHIMoleculeReader >

friend

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

INCHIMoleculeReader.hpp

Public Member Functions

Friends

Additional Inherited Members