CDPL.ConfGen.TorsionDriver Class Reference

Driver for the systematic enumeration of conformers obtained by rotating around rotatable bonds of a molecular graph, using preferred torsion angles taken from configured ConfGen.TorsionLibrary instances. More...

Inheritance diagram for CDPL.ConfGen.TorsionDriver:

Public Member Functions
None	__init__ ()
	Constructs the TorsionDriver instance.
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
TorsionDriverSettings	getSettings ()
	Returns the current driver settings (mutable). More...
None	clearTorsionLibraries ()
	Removes all configured torsion libraries.
None	addTorsionLibrary (TorsionLibrary lib)
	Adds lib to the list of torsion libraries consulted during torsion driving. More...
int	setup (Chem.MolecularGraph molgraph)
	Sets up the driver for molgraph with the default rotatable bond perception. More...
int	setup (Chem.MolecularGraph molgraph, Util.BitSet bond_mask)
	Sets up the driver for molgraph using only the bonds whose corresponding bit is set in bond_mask as rotatable. More...
None	clearInputCoordinates ()
	Removes all stored input coordinates.
None	clearInputCoordinates (int frag_idx)
	Removes all input coordinates of the fragment at index frag_idx. More...
None	addInputCoordinates (Math.Vector3DArray coords)
	Adds coords as a new starting conformation that the driver will torsion-drive. More...
None	addInputCoordinates (Math.Vector3DArray coords, int frag_idx)
	Adds coords as a new starting conformation restricted to the fragment at index frag_idx. More...
None	addInputCoordinates (ConformerData conf_data, int frag_idx)
	Adds the conformer data shared reference conf_data as a new starting conformation restricted to the fragment at index frag_idx. More...
None	setAbortCallback (CallbackFunction func)
	Sets the callback invoked periodically to allow the generation to be aborted by the user. 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 receiving log messages emitted by the driver. More...
LogMessageCallbackFunction	getLogMessageCallback ()
	Returns the currently configured log-message callback. More...
int	generateConformers ()
	Runs the torsion-driving conformer enumeration. More...
int	getNumConformers ()
	Returns the number of generated conformers. More...
ConformerData	getConformer (int conf_idx)
ConformerData	__getitem__ (int conf_idx)

Properties
	objectID = property(getObjectID)
	numConformers = property(getNumConformers)
	settings = property(getSettings)
	abortCallback = property(getAbortCallback, setAbortCallback)
	timeoutCallback = property(getTimeoutCallback, setTimeoutCallback)
	logMessageCallback = property(getLogMessageCallback, setLogMessageCallback)

Detailed Description

Driver for the systematic enumeration of conformers obtained by rotating around rotatable bonds of a molecular graph, using preferred torsion angles taken from configured ConfGen.TorsionLibrary instances.

Member Function Documentation

getObjectID()

int CDPL.ConfGen.TorsionDriver.getObjectID

(

)

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

Different Python TorsionDriver 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 TorsionDriver 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.

getSettings()

TorsionDriverSettings CDPL.ConfGen.TorsionDriver.getSettings

(

)

Returns the current driver settings (mutable).

Returns

A reference to the settings.

addTorsionLibrary()

None CDPL.ConfGen.TorsionDriver.addTorsionLibrary

(

TorsionLibrary

lib

)

Adds lib to the list of torsion libraries consulted during torsion driving.

Parameters

lib	The torsion library to add.

setup() [1/2]

int CDPL.ConfGen.TorsionDriver.setup

(

Chem.MolecularGraph

molgraph

)

Sets up the driver for molgraph with the default rotatable bond perception.

Parameters

molgraph

The input molecular graph.

Returns

A ConfGen.ReturnCode value reporting the outcome of the setup.

setup() [2/2]

int CDPL.ConfGen.TorsionDriver.setup	(	Chem.MolecularGraph	molgraph,
		Util.BitSet	bond_mask
	)

Sets up the driver for molgraph using only the bonds whose corresponding bit is set in bond_mask as rotatable.

Parameters

molgraph	The input molecular graph.
bond_mask	The bit mask of rotatable bonds (one bit per bond of molgraph).

Returns

A ConfGen.ReturnCode value reporting the outcome of the setup.

clearInputCoordinates()

None CDPL.ConfGen.TorsionDriver.clearInputCoordinates

(

int

frag_idx

)

Removes all input coordinates of the fragment at index frag_idx.

Parameters

frag_idx

The zero-based fragment index.

addInputCoordinates() [1/3]

None CDPL.ConfGen.TorsionDriver.addInputCoordinates

(

Math.Vector3DArray

coords

)

Adds coords as a new starting conformation that the driver will torsion-drive.

Parameters

coords

The input 3D coordinates.

addInputCoordinates() [2/3]

None CDPL.ConfGen.TorsionDriver.addInputCoordinates	(	Math.Vector3DArray	coords,
		int	frag_idx
	)

Adds coords as a new starting conformation restricted to the fragment at index frag_idx.

Parameters

coords	The input 3D coordinates of the fragment.
frag_idx	The zero-based fragment index.

addInputCoordinates() [3/3]

None CDPL.ConfGen.TorsionDriver.addInputCoordinates	(	ConformerData	conf_data,
		int	frag_idx
	)

Adds the conformer data shared reference conf_data as a new starting conformation restricted to the fragment at index frag_idx.

Parameters

conf_data	The input conformer data.
frag_idx	The zero-based fragment index.

setAbortCallback()

None CDPL.ConfGen.TorsionDriver.setAbortCallback

(

CallbackFunction

func

)

Sets the callback invoked periodically to allow the generation to be aborted by the user.

Parameters

func	The abort-check callback.

getAbortCallback()

CallbackFunction CDPL.ConfGen.TorsionDriver.getAbortCallback

(

)

Returns the currently configured abort-check callback.

Returns

A reference to the abort-check callback.

setTimeoutCallback()

None CDPL.ConfGen.TorsionDriver.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.TorsionDriver.getTimeoutCallback

(

)

Returns the currently configured timeout-check callback.

Returns

A reference to the timeout-check callback.

setLogMessageCallback()

None CDPL.ConfGen.TorsionDriver.setLogMessageCallback

(

LogMessageCallbackFunction

func

)

Sets the callback receiving log messages emitted by the driver.

Parameters

func	The log-message callback.

getLogMessageCallback()

LogMessageCallbackFunction CDPL.ConfGen.TorsionDriver.getLogMessageCallback

(

)

Returns the currently configured log-message callback.

Returns

A reference to the log-message callback.

generateConformers()

int CDPL.ConfGen.TorsionDriver.generateConformers

(

)

Runs the torsion-driving conformer enumeration.

Returns

A ConfGen.ReturnCode value reporting the outcome of the generation.

getNumConformers()

int CDPL.ConfGen.TorsionDriver.getNumConformers

(

)

Returns the number of generated conformers.

Returns

The conformer count.

getConformer()

ConformerData CDPL.ConfGen.TorsionDriver.getConformer

(

int

conf_idx

)

Parameters

conf_idx

Returns

__getitem__()

ConformerData CDPL.ConfGen.TorsionDriver.__getitem__

(

int

conf_idx

)

Parameters

conf_idx

Returns