CDPL.Chem.SDFMoleculeReader Class Reference

A Reader for molecule data in the MDL SD-File [CTFILE] format. More...

Inheritance diagram for CDPL.Chem.SDFMoleculeReader:

Public Member Functions
None	__init__ (Base.IStream is)
	Constructs a SDFMoleculeReader instance that will read the molecule data from the input stream is. 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__ ()

Additional Inherited Members
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)

Detailed Description

A Reader for molecule data in the MDL SD-File [CTFILE] format.

SDFMoleculeReader supports 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.MULTI_CONF_IMPORT	True	Specifies whether to check for and import multi-conformer molecules
Chem.ControlParameter.MULTI_CONF_INPUT_PROCESSOR	reference to a Chem.DefaultMultiConfMoleculeInputProcessor instance	Specifies an instance of Chem.MultiConfMoleculeInputProcessor that implements the logic of multi-conformer molecule detection and conformational data processing
Chem.ControlParameter.MDL_IGNORE_PARITY	False	Specifies whether the stereo parity of atoms shall be ignored
Chem.ControlParameter.MDL_TRIM_STRINGS	True	Specifies whether to remove leading and trailing whitespace from string values
Chem.ControlParameter.MDL_TRIM_LINES	False	Specifies whether to remove leading and trailing whitespace from data lines
Chem.ControlParameter.MDL_IGNORE_LINE_LENGTH_LIMIT	True	Specifies whether to check if data lines exceed the maximum allowed line length

Constructor & Destructor Documentation

__init__()

None CDPL.Chem.SDFMoleculeReader.__init__

(

Base.IStream

is

)

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

Parameters

is	The input stream to read from.