CDPL.ConfGen.FragmentLibraryGenerator Class Reference

Driver for populating a ConfGen.FragmentLibrary with conformers of canonicalized molecular fragments. More...

Inheritance diagram for CDPL.ConfGen.FragmentLibraryGenerator:

Public Member Functions
None	__init__ ()
	Constructs the FragmentLibraryGenerator instance without an associated fragment library.
None	__init__ (FragmentLibrary lib)
	Constructs the FragmentLibraryGenerator instance and associates it with lib. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
None	setFragmentLibrary (FragmentLibrary lib)
	Sets the fragment library to populate. More...
FragmentLibrary	getFragmentLibrary ()
	Returns the currently associated fragment library. More...
None	setAbortCallback (CallbackFunction func)
	Sets the callback invoked periodically to allow conformer generation to be aborted. More...
CallbackFunction	getAbortCallback ()
	Returns the currently configured abort-check callback. More...
None	setTimeoutCallback (CallbackFunction func)
	Sets the callback invoked periodically to check whether the configured timeout has elapsed. More...
CallbackFunction	getTimeoutCallback ()
	Returns the currently configured timeout-check callback. More...
None	setLogMessageCallback (LogMessageCallbackFunction func)
	Sets the callback that receives log messages produced during fragment processing. More...
LogMessageCallbackFunction	getLogMessageCallback ()
	Returns the currently configured log-message callback. More...
int	process (MolecularGraph self, Chem.MolecularGraph frag)
int	getNumGeneratedConformers ()
	Returns the number of conformers generated during the last process() call. More...
int	getLibraryEntryHashCode ()
	Returns the hash code of the library entry created during the last process() call. More...
FragmentConformerGeneratorSettings	getSettings ()
	Returns a reference to the fragment conformer generation settings. More...

Properties
	objectID = property(getObjectID)
	settings = property(getSettings)
	abortCallback = property(getAbortCallback, setAbortCallback)
	timeoutCallback = property(getTimeoutCallback, setTimeoutCallback)
	fragmentLibrary = property(getFragmentLibrary, setFragmentLibrary)
	numGeneratedConformers = property(getNumGeneratedConformers)
	libraryEntryHashCode = property(getLibraryEntryHashCode)
	logMessageCallback = property(getLogMessageCallback, setLogMessageCallback)

Detailed Description

Driver for populating a ConfGen.FragmentLibrary with conformers of canonicalized molecular fragments.

For each input fragment the generator constructs the corresponding ConfGen.CanonicalFragment, computes its hash code and SMILES string, generates a representative conformer ensemble using ConfGen.FragmentConformerGenerator and stores the result as a new FragmentLibraryEntry in the associated FragmentLibrary. Already-present entries (identified by hash code) are skipped.

Constructor & Destructor Documentation

__init__()

None CDPL.ConfGen.FragmentLibraryGenerator.__init__

(

FragmentLibrary

lib

)

Constructs the FragmentLibraryGenerator instance and associates it with lib.

Parameters

lib	The fragment library to populate.

Member Function Documentation

getObjectID()

int CDPL.ConfGen.FragmentLibraryGenerator.getObjectID

(

)

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python FragmentLibraryGenerator instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two FragmentLibraryGenerator instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns

The numeric ID of the internally referenced C++ class instance.

setFragmentLibrary()

None CDPL.ConfGen.FragmentLibraryGenerator.setFragmentLibrary

(

FragmentLibrary

lib

)

Sets the fragment library to populate.

Parameters

lib	The new fragment library.

getFragmentLibrary()

FragmentLibrary CDPL.ConfGen.FragmentLibraryGenerator.getFragmentLibrary

(

)

Returns the currently associated fragment library.

Returns

A reference to the fragment library smart reference.

setAbortCallback()

None CDPL.ConfGen.FragmentLibraryGenerator.setAbortCallback

(

CallbackFunction

func

)

Sets the callback invoked periodically to allow conformer generation to be aborted.

Parameters

func	The abort-check callback.

getAbortCallback()

CallbackFunction CDPL.ConfGen.FragmentLibraryGenerator.getAbortCallback

(

)

Returns the currently configured abort-check callback.

Returns

A reference to the abort-check callback.

setTimeoutCallback()

None CDPL.ConfGen.FragmentLibraryGenerator.setTimeoutCallback

(

CallbackFunction

func

)

Sets the callback invoked periodically to check whether the configured timeout has elapsed.

Parameters

func	The timeout-check callback.

getTimeoutCallback()

CallbackFunction CDPL.ConfGen.FragmentLibraryGenerator.getTimeoutCallback

(

)

Returns the currently configured timeout-check callback.

Returns

A reference to the timeout-check callback.

setLogMessageCallback()

None CDPL.ConfGen.FragmentLibraryGenerator.setLogMessageCallback

(

LogMessageCallbackFunction

func

)

Sets the callback that receives log messages produced during fragment processing.

Parameters

func	The log-message callback.

getLogMessageCallback()

LogMessageCallbackFunction CDPL.ConfGen.FragmentLibraryGenerator.getLogMessageCallback

(

)

Returns the currently configured log-message callback.

Returns

A reference to the log-message callback.

process()

int CDPL.ConfGen.FragmentLibraryGenerator.process	(	MolecularGraph	self,
		Chem.MolecularGraph	frag
	)

Parameters

arg1
frag

Returns

getNumGeneratedConformers()

int CDPL.ConfGen.FragmentLibraryGenerator.getNumGeneratedConformers

(

)

Returns the number of conformers generated during the last process() call.

Returns

The number of generated conformers.

getLibraryEntryHashCode()

int CDPL.ConfGen.FragmentLibraryGenerator.getLibraryEntryHashCode

(

)

Returns the hash code of the library entry created during the last process() call.

Returns

The hash code of the library entry.

getSettings()

FragmentConformerGeneratorSettings CDPL.ConfGen.FragmentLibraryGenerator.getSettings

(

)

Returns a reference to the fragment conformer generation settings.

Returns

A reference to the settings.