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Chemical Data Processing Library C++ API - Version 1.1.1
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Chemical Data Processing Library C++ API - Version 1.1.1
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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... | |
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 |
| CDPL::Chem::INCHIMoleculeReader::INCHIMoleculeReader | ( | std::istream & | is | ) |
Constructs a INCHIMoleculeReader instance that will read the molecule data from the input stream is.
| is | The input stream to read from. |
| int CDPL::Chem::INCHIMoleculeReader::getReturnCode | ( | ) | const |
Returns the error code of the last read operation.
Possible return values are defined in namespace Chem::INCHIReturnCode.
| const std::string& CDPL::Chem::INCHIMoleculeReader::getMessage | ( | ) | const |
Returns the error message associated with the last read operation.
| const std::string& CDPL::Chem::INCHIMoleculeReader::getLogOutput | ( | ) | const |
Returns the log output that was generated for the last read operation.
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1.8.20