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| INCHIMoleculeReader (std::istream &is) |
| Constructs a INCHIMoleculeReader instance that will read the molecule data from the input stream is. More...
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int | getReturnCode () const |
| Returns the error code of the last read operation. More...
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const std::string & | getMessage () const |
| Returns the error message associated with the last read operation. More...
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const std::string & | getLogOutput () const |
| Returns the log output that was generated for the last read operation. More...
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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...
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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...
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Base::DataReader< DataType > & | skip () |
| Skips the data record at the current record index. More...
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bool | hasMoreData () |
| Tells if there are any data records left to read. More...
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std::size_t | getRecordIndex () const |
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void | setRecordIndex (std::size_t idx) |
| Sets the index of the current data record to idx. More...
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std::size_t | getNumRecords () |
| Returns the total number of available data records. More...
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| operator const void * () const |
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bool | operator! () const |
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virtual std::size_t | getRecordIndex () const=0 |
| Returns the index of the current data record. More...
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virtual | operator const void * () const=0 |
| Returns a pointer whose value indicates the error state of the reader. More...
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virtual bool | operator! () const=0 |
| Tells whether the reader is in a bad state. More...
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virtual void | close () |
| Performs a reader specific shutdown operation (if required). More...
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std::size_t | registerIOCallback (const IOCallbackFunction &func) |
| Registers an I/O callback target function. More...
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void | unregisterIOCallback (std::size_t id) |
| Unregisters the I/O callback function specified by id. More...
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void | invokeIOCallbacks (double progress) const |
| Invokes all registered I/O callback functions with the argument *this . More...
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void | clearIOCallbacks () |
| Clears all registered I/O callback functions. More...
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std::size_t | getNumParameters () const |
| Returns the number of container entries. More...
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template<typename T > |
void | setParameter (const LookupKey &key, T &&val) |
| Sets the value of the control-parameter specified by key to val. More...
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const Any & | getParameter (const LookupKey &key, bool throw_=false, bool local=false) const |
| Returns the value of the control-parameter specified by key. More...
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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...
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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...
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bool | removeParameter (const LookupKey &key) |
| Removes the entry for the control-parameter specified by key. More...
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void | clearParameters () |
| Erases all container entries. More...
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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...
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void | addParameters (const ControlParameterContainer &cntnr) |
| Adds the control-parameter value entries in the ControlParameterContainer instance cntnr. More...
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void | copyParameters (const ControlParameterContainer &cntnr) |
| Replaces the current set of properties by a copy of the entries in cntnr. More...
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ConstParameterIterator | getParametersBegin () const |
| Returns a constant iterator pointing to the beginning of the entries. More...
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ConstParameterIterator | getParametersEnd () const |
| Returns a constant iterator pointing to the end of the entries. More...
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ConstParameterIterator | begin () const |
| Returns a constant iterator pointing to the beginning of the entries. More...
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ConstParameterIterator | end () const |
| Returns a constant iterator pointing to the end of the entries. More...
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void | setParent (const ControlParameterContainer *cntnr) |
| Sets or removes the parent control-parameter container used to resolve requests for missing entries. More...
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const ControlParameterContainer * | getParent () const |
| Returns a pointer to the parent control-parameter container. More...
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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...
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void | unregisterParameterChangedCallback (std::size_t id) |
| Unregisters the callback specified by id. More...
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std::size_t | registerParameterRemovedCallback (const ParameterRemovedCallbackFunction &func) |
| Registers a callback target function that gets invoked when a control-parameter entry has been removed. More...
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void | unregisterParameterRemovedCallback (std::size_t id) |
| Unregisters the callback specified by id. More...
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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...
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void | unregisterParentChangedCallback (std::size_t id) |
| Unregisters the callback specified by id. More...
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const ControlParameterContainer & | getParameters () const |
| Returns a const reference to itself. More...
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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:
INCHIMoleculeReader
can be configured with the following control-parameters: