CDPL.ConfGen.ConformerGenerator Class Reference

High-level driver for the generation of low-energy conformer ensembles of molecular graphs. More...

Inheritance diagram for CDPL.ConfGen.ConformerGenerator:

Public Member Functions
None	__init__ ()
	Constructs the ConformerGenerator instance.
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
ConformerGeneratorSettings	getSettings ()
	Returns the current generator settings (mutable). More...
None	clearFragmentLibraries ()
	Removes all configured fragment libraries.
None	addFragmentLibrary (FragmentLibrary lib)
	Adds lib to the list of fragment libraries consulted during fragment-based 3D structure generation. 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...
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 generator. More...
LogMessageCallbackFunction	getLogMessageCallback ()
	Returns the currently configured log-message callback. More...
int	generate (Chem.MolecularGraph molgraph)
	Generates a conformer ensemble for molgraph. More...
int	generate (Chem.MolecularGraph molgraph, Chem.MolecularGraph fixed_substr)
	Generates a conformer ensemble for molgraph while keeping the substructure fixed_substr at its current 3D coordinates. More...
int	generate (Chem.MolecularGraph molgraph, Chem.MolecularGraph fixed_substr, Math.Vector3DArray fixed_substr_coords)
	Generates a conformer ensemble for molgraph while keeping the substructure fixed_substr at the supplied 3D coordinates fixed_substr_coords. More...
None	setConformers (Chem.MolecularGraph molgraph)
	Transfers the generated conformer ensemble onto molgraph. 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

High-level driver for the generation of low-energy conformer ensembles of molecular graphs.

The generator implements two complementary sampling strategies for producing the conformer ensemble:

• a systematic strategy that performs a fragment-based 3D structure generation followed by exhaustive torsion-driving of all rotatable bonds, and
• a stochastic strategy that picks conformations randomly from the conformational space of the molecule (by default used only for flexible macrocyclic molecules).

Both strategies share a common downstream pipeline of MMFF94-based energy minimization, RMSD-based clustering and energy window filtering. Behaviour is controlled by the embedded conformer generation settings instance, the configured fragment and torsion libraries and the optional abort/timeout/log callbacks.

See also

[CFRG]

Member Function Documentation

getObjectID()

int CDPL.ConfGen.ConformerGenerator.getObjectID

(

)

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

Different Python ConformerGenerator 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 ConformerGenerator 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()

ConformerGeneratorSettings CDPL.ConfGen.ConformerGenerator.getSettings

(

)

Returns the current generator settings (mutable).

Returns

A reference to the settings.

addFragmentLibrary()

None CDPL.ConfGen.ConformerGenerator.addFragmentLibrary

(

FragmentLibrary

lib

)

Adds lib to the list of fragment libraries consulted during fragment-based 3D structure generation.

Parameters

lib	The fragment library to add.

addTorsionLibrary()

None CDPL.ConfGen.ConformerGenerator.addTorsionLibrary

(

TorsionLibrary

lib

)

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

Parameters

lib	The torsion library to add.

setAbortCallback()

None CDPL.ConfGen.ConformerGenerator.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.ConformerGenerator.getAbortCallback

(

)

Returns the currently configured abort-check callback.

Returns

A reference to the abort-check callback.

setTimeoutCallback()

None CDPL.ConfGen.ConformerGenerator.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.ConformerGenerator.getTimeoutCallback

(

)

Returns the currently configured timeout-check callback.

Returns

A reference to the timeout-check callback.

setLogMessageCallback()

None CDPL.ConfGen.ConformerGenerator.setLogMessageCallback

(

LogMessageCallbackFunction

func

)

Sets the callback receiving log messages emitted by the generator.

Parameters

func	The log-message callback.

getLogMessageCallback()

LogMessageCallbackFunction CDPL.ConfGen.ConformerGenerator.getLogMessageCallback

(

)

Returns the currently configured log-message callback.

Returns

A reference to the log-message callback.

generate() [1/3]

int CDPL.ConfGen.ConformerGenerator.generate

(

Chem.MolecularGraph

molgraph

)

Generates a conformer ensemble for molgraph.

Parameters

molgraph

The input molecular graph.

Returns

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

generate() [2/3]

int CDPL.ConfGen.ConformerGenerator.generate	(	Chem.MolecularGraph	molgraph,
		Chem.MolecularGraph	fixed_substr
	)

Generates a conformer ensemble for molgraph while keeping the substructure fixed_substr at its current 3D coordinates.

Parameters

molgraph	The input molecular graph.
fixed_substr	The substructure that must retain its current 3D coordinates.

Returns

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

Since

1.1

generate() [3/3]

int CDPL.ConfGen.ConformerGenerator.generate	(	Chem.MolecularGraph	molgraph,
		Chem.MolecularGraph	fixed_substr,
		Math.Vector3DArray	fixed_substr_coords
	)

Generates a conformer ensemble for molgraph while keeping the substructure fixed_substr at the supplied 3D coordinates fixed_substr_coords.

Parameters

molgraph	The input molecular graph.
fixed_substr	The substructure that must retain the supplied 3D coordinates.
fixed_substr_coords	The 3D coordinates assigned to fixed_substr.

Returns

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

Since

1.1

setConformers()

None CDPL.ConfGen.ConformerGenerator.setConformers

(

Chem.MolecularGraph

molgraph

)

Transfers the generated conformer ensemble onto molgraph.

The per-conformer 3D coordinates are written to each atom's 3D-coordinates array (via Chem.set3DCoordinatesArray) and the corresponding per-conformer energies are attached to the molecular graph (via Chem.setConformerEnergies).

Parameters

molgraph

The molecular graph that receives the conformer coordinates and energies.

getNumConformers()

int CDPL.ConfGen.ConformerGenerator.getNumConformers

(

)

Returns the number of generated conformers.

Returns

The conformer count.

getConformer()

ConformerData CDPL.ConfGen.ConformerGenerator.getConformer

(

int

conf_idx

)

Parameters

conf_idx

Returns

__getitem__()

ConformerData CDPL.ConfGen.ConformerGenerator.__getitem__

(

int

conf_idx

)

Parameters

conf_idx

Returns