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Chemical Data Processing Library Python API - Version 1.2.0
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Chemical Data Processing Library Python API - Version 1.2.0
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A reader for molecule data in the IUPAC International Chemical Identifier (InChI) [INCHI] format. More...
Inheritance diagram for CDPL.Chem.INCHIMoleculeReader:Public Member Functions | |
| None | __init__ (Base.IStream is) |
Constructs a INCHIMoleculeReader instance that will read the molecule data from the input stream is. More... | |
| int | getReturnCode () |
| Returns the error code of the last read operation. More... | |
| str | getMessage () |
| Returns the error message associated with the last read operation. More... | |
| str | getLogOutput () |
| Returns the log output that was generated for the last read operation. More... | |
| Public Member Functions inherited from CDPL.Chem.MoleculeReaderBase | |
| None | __init__ () |
| Initializes the MoleculeReaderBase instance. | |
| MoleculeReaderBase | read (Molecule mol, bool overwrite=True) |
| Reads the data record at the current record index and stores the read data in mol. More... | |
| MoleculeReaderBase | read (int idx, Molecule mol, bool overwrite=True) |
| Reads the data record at index idx and stores the read data in mol. More... | |
| MoleculeReaderBase | skip () |
| Skips the data record at the current record index. More... | |
| bool | hasMoreData () |
| Tells if there are any data records left to read. More... | |
| int | getRecordIndex () |
| Returns the index of the current data record. More... | |
| None | setRecordIndex (int idx) |
| Sets the index of the current data record to idx. More... | |
| int | getNumRecords () |
| Returns the total number of available data records. More... | |
| None | close () |
| Performs a reader specific shutdown operation (if required). More... | |
| bool | __nonzero__ () |
| bool | __bool__ () |
| Public Member Functions inherited from CDPL.Base.DataIOBase | |
| int | registerIOCallback (VoidDataIOBaseFunctor func) |
| Registers an I/O callback target function. More... | |
| None | unregisterIOCallback (int id) |
| Unregisters the I/O callback function specified by id. More... | |
| None | invokeIOCallbacks (float progress) |
Invokes all registered I/O callback functions with the argument self. More... | |
| None | clearIOCallbacks () |
| Clears all registered I/O callback functions. | |
| Public Member Functions inherited from CDPL.Base.ControlParameterContainer | |
| None | setParameter (LookupKey key, Any value) |
| bool | removeParameter (LookupKey key) |
| Removes the entry for the control-parameter specified by key. More... | |
| Any | getParameter (LookupKey key, bool throw_=False, bool local=False) |
| Returns the value of the control-parameter specified by key. More... | |
| Any | getParameterOrDefault (LookupKey key, Any def_value, bool local=False) |
| bool | isParameterSet (LookupKey key, bool local=False) |
| Tells whether or not a value has been assigned to the control-parameter specified by key. More... | |
| None | clearParameters () |
| Erases all container entries. More... | |
| None | addParameters (ControlParameterContainer cntnr) |
Adds the control-parameter value entries in the ControlParameterContainer instance cntnr. More... | |
| None | copyParameters (ControlParameterContainer cntnr) |
| Replaces the current set of properties by a copy of the entries in cntnr. More... | |
| int | getNumParameters () |
| Returns the number of container entries. More... | |
| int | registerParameterChangedCallback (VoidLookupKeyAnyFunctor func) |
| Registers a callback target function that gets invoked when the value of a control-parameter has changed. More... | |
| None | unregisterParameterChangedCallback (int id) |
| Unregisters the callback specified by id. More... | |
| int | registerParameterRemovedCallback (VoidLookupKeyFunctor func) |
| Registers a callback target function that gets invoked when a control-parameter entry has been removed. More... | |
| None | unregisterParameterRemovedCallback (int id) |
| Unregisters the callback specified by id. More... | |
| int | registerParentChangedCallback (VoidFunctor func) |
| Registers a callback target function that gets invoked when the parent container has been changed or was detached. More... | |
| None | unregisterParentChangedCallback (int id) |
| Unregisters the callback specified by id. More... | |
| ControlParameterContainer | getParent () |
| Returns a reference to the parent control-parameter container. More... | |
| None | setParent (ControlParameterContainer cntnr) |
| Sets or removes the parent control-parameter container used to resolve requests for missing entries. More... | |
| list | getParameterKeys () |
| list | getParameterValues () |
| list | getParameters () |
| Returns a reference to itself. More... | |
| int | getObjectID () |
| Returns the numeric identifier (ID) of the wrapped C++ class instance. More... | |
| Any | __getitem__ (LookupKey key) |
| None | __setitem__ (LookupKey key, Any value) |
| bool | __delitem__ (LookupKey self) |
| bool | __contains__ (LookupKey self, bool key) |
Returns the result of the membership test operation self in arg1. More... | |
| int | __len__ () |
Properties | |
| returnCode = property(getReturnCode) | |
| message = property(getMessage) | |
| logOutput = property(getLogOutput) | |
| Properties inherited from CDPL.Chem.MoleculeReaderBase | |
| numRecords = property(getNumRecords) | |
| Properties inherited from CDPL.Base.ControlParameterContainer | |
| objectID = property(getObjectID) | |
| parent = property(getParent, setParent) | |
| parameterKeys = property(getParameterKeys) | |
| parameterValues = property(getParameterValues) | |
| parameters = property(getParameters) | |
| numParameters = property(getNumParameters) | |
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 |
| None CDPL.Chem.INCHIMoleculeReader.__init__ | ( | Base.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 | ( | ) |
Returns the error code of the last read operation.
Possible return values are defined in namespace Chem.INCHIReturnCode.
| str CDPL.Chem.INCHIMoleculeReader.getMessage | ( | ) |
Returns the error message associated with the last read operation.
| str CDPL.Chem.INCHIMoleculeReader.getLogOutput | ( | ) |
Returns the log output that was generated for the last read operation.
1.9.1