Chemical Data Processing Library C++ API - Version 1.1.1
Public Member Functions | List of all members
CDPL::Chem::INCHIMolecularGraphWriter Class Reference

A writer for molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...

#include <INCHIMolecularGraphWriter.hpp>

+ Inheritance diagram for CDPL::Chem::INCHIMolecularGraphWriter:

Public Member Functions

 INCHIMolecularGraphWriter (std::ostream &os)
 Constructs a INCHIMolecularGraphWriter instance that will write data of molecular graphs to the output stream os. More...
 
 ~INCHIMolecularGraphWriter ()
 Destructor. More...
 
Base::DataWriter< MolecularGraph > & write (const MolecularGraph &molgraph)
 Writes data of the molecular graph molgraph to the output stream specified in the constructor. More...
 
int getReturnCode () const
 Returns the error code of the last write operation. More...
 
const std::string & getMessage () const
 Returns the error message associated with the last write operation. More...
 
const std::string & getLogOutput () const
 Returns the log output that was generated for the last write operation. More...
 
 operator const void * () const
 
bool operator! () const
 
- Public Member Functions inherited from CDPL::Base::DataWriter< MolecularGraph >
virtual DataWriterwrite (const DataType &obj)=0
 Writes the data object obj. More...
 
virtual void close ()
 Writes format dependent data (if required) to mark the end of output. More...
 
virtual operator const void * () const=0
 Returns a pointer whose value indicates the error state of the writer. More...
 
virtual bool operator! () const=0
 Tells whether the writer is in a bad state. 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 AnygetParameter (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 ControlParameterContainergetParent () 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 ControlParameterContainergetParameters () const
 Returns a const reference to itself. More...
 

Additional Inherited Members

- Public Types inherited from CDPL::Base::DataWriter< MolecularGraph >
typedef std::shared_ptr< DataWriterSharedPointer
 A reference-counted smart pointer [SHPTR] for dynamically allocated DataWriter instances. More...
 
typedef MolecularGraph DataType
 The type of the written data objects. 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::DataWriter< MolecularGraph >
DataWriteroperator= (const DataWriter &writer)
 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...
 
DataIOBaseoperator= (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...
 
ControlParameterContaineroperator= (const ControlParameterContainer &cntnr)
 Assignment operator. More...
 

Detailed Description

A writer for molecular graph data in the IUPAC International Chemical Identifier (InChI) [INCHI] format.

INCHIMolecularGraphWriter implements the generation of InChI strings from Chem::MolecularGraph objects. The output data are written by means of a std::ostream object that was provided to the INCHIMolecularGraphWriter constructor.

For the generation of the InChI output, INCHIMolecularGraphWriter uses the function GetINCHI() of the InChI C-API. The return value of the 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.

The generation of InChI strings requires values of the following Chem::Atom and Chem::Bond properties:

Chem::Atom Property Description Notes
Chem::AtomProperty::COORDINATES_2D Specifies the 2D position of the atom Only required if 2D atom coordinates are written
Chem::AtomProperty::COORDINATES_3D Specifies the 3D-coordinates of the atom Only required if 3D atom coordinates are written
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 -
Chem::AtomProperty::RADICAL_TYPE Specifies the radical type (see Chem::RadicalType) -
Chem::AtomProperty::STEREO_DESCRIPTOR Specifies the atom stereo descriptor (see Chem::AtomConfiguration, Chem::StereoDescriptor) Only required if no atom coordinates are written
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 required if 2D or 3D atom coordinates are written
Chem::BondProperty::STEREO_DESCRIPTOR Specifies the stereo descriptor of the bond (see Chem::BondConfiguration, Chem::StereoDescriptor) Only required if no atom coordinates are written

INCHIMolecularGraphWriter can be configured with the following control-parameters:

Control-Parameter Default Value (see Chem::ControlParameterDefault) Description
Chem::ControlParameter::COORDINATES_DIMENSION 1 Specifies the dimension of the atom coordinates (a value of 2 specifies 2D, a value of 3 specifies 3D, a value of zero specifies that no atom coordinates shall be written; any other value specifies that 3D-coordinates shall be written if they are available, and no coordinates otherwise)
Chem::ControlParameter::STRICT_ERROR_CHECKING false Specifies whether non-fatal recoverable errors should be ignored or cause a write operation to fail
Chem::ControlParameter::RECORD_SEPARATOR "\n" Specifies the data record separator
Chem::ControlParameter::INCHI_OUTPUT_OPTIONS "/WarnOnEmptyStructure /AuxNone /NEWPSOFF" Specifies options for InChI generation

Constructor & Destructor Documentation

◆ INCHIMolecularGraphWriter()

CDPL::Chem::INCHIMolecularGraphWriter::INCHIMolecularGraphWriter ( std::ostream &  os)

Constructs a INCHIMolecularGraphWriter instance that will write data of molecular graphs to the output stream os.

Parameters
osThe output stream to write to.

◆ ~INCHIMolecularGraphWriter()

CDPL::Chem::INCHIMolecularGraphWriter::~INCHIMolecularGraphWriter ( )

Destructor.

Member Function Documentation

◆ write()

Base::DataWriter<MolecularGraph>& CDPL::Chem::INCHIMolecularGraphWriter::write ( const MolecularGraph molgraph)

Writes data of the molecular graph molgraph to the output stream specified in the constructor.

Parameters
molgraphThe molecular graph to write.
Returns
A reference to itself.

◆ getReturnCode()

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

Returns the error code of the last write operation.

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

Returns
The error code of the last write operation.

◆ getMessage()

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

Returns the error message associated with the last write operation.

Returns
The error message associated with the last write operation.

◆ getLogOutput()

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

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

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

◆ operator const void *()

CDPL::Chem::INCHIMolecularGraphWriter::operator const void * ( ) const

◆ operator!()

bool CDPL::Chem::INCHIMolecularGraphWriter::operator! ( ) const

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