CDPL.ConfGen.FragmentConformerGenerator Class Reference

Driver for the generation of low-energy conformer ensembles for single molecular fragments (chain, small ring system or macrocycle) More...

Inheritance diagram for CDPL.ConfGen.FragmentConformerGenerator:

Public Member Functions
None	__init__ ()
	Constructs the FragmentConformerGenerator instance.
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
None	setAbortCallback (CallbackFunction func)
	Sets the callback invoked periodically to allow conformer 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 that receives log messages produced during conformer generation. More...
LogMessageCallbackFunction	getLogMessageCallback ()
	Returns the currently configured log-message callback. More...
int	generate (Chem.MolecularGraph molgraph)
	Generates a conformer ensemble for the fragment molgraph (the fragment type is perceived automatically). More...
int	generate (Chem.MolecularGraph molgraph, Chem.MolecularGraph fixed_substr, Math.Vector3DArray fixed_substr_coords)
	Generates a conformer ensemble for the fragment molgraph while keeping the substructure fixed_substr at the supplied 3D coordinates. More...
int	generate (Chem.MolecularGraph molgraph, int frag_type)
	Generates a conformer ensemble for the fragment molgraph using the fragment-type-specific settings selected by frag_type. More...
int	generate (Chem.MolecularGraph molgraph, int frag_type, Chem.MolecularGraph fixed_substr, Math.Vector3DArray fixed_substr_coords)
	Generates a conformer ensemble for the fragment molgraph using the fragment-type-specific settings selected by frag_type while keeping the substructure fixed_substr at the supplied 3D coordinates. 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)
FragmentConformerGeneratorSettings	getSettings ()
	Returns the current generator settings. More...
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 generation of low-energy conformer ensembles for single molecular fragments (chain, small ring system or macrocycle)

Conformer sampling is done in a stochastic manner using distance-geometry-based raw coordinates generation, MMFF94 energy minimization and conformer RMSD clustering.

See also

[CFRG]

Member Function Documentation

getObjectID()

int CDPL.ConfGen.FragmentConformerGenerator.getObjectID

(

)

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

Different Python FragmentConformerGenerator 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 FragmentConformerGenerator 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.

setAbortCallback()

None CDPL.ConfGen.FragmentConformerGenerator.setAbortCallback

(

CallbackFunction

func

)

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

Parameters

func	The abort-check callback.

getAbortCallback()

CallbackFunction CDPL.ConfGen.FragmentConformerGenerator.getAbortCallback

(

)

Returns the currently configured abort-check callback.

Returns

A reference to the abort-check callback.

setTimeoutCallback()

None CDPL.ConfGen.FragmentConformerGenerator.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.FragmentConformerGenerator.getTimeoutCallback

(

)

Returns the currently configured timeout-check callback.

Returns

A reference to the timeout-check callback.

setLogMessageCallback()

None CDPL.ConfGen.FragmentConformerGenerator.setLogMessageCallback

(

LogMessageCallbackFunction

func

)

Sets the callback that receives log messages produced during conformer generation.

Parameters

func	The log-message callback.

getLogMessageCallback()

LogMessageCallbackFunction CDPL.ConfGen.FragmentConformerGenerator.getLogMessageCallback

(

)

Returns the currently configured log-message callback.

Returns

A reference to the log-message callback.

generate() [1/4]

int CDPL.ConfGen.FragmentConformerGenerator.generate

(

Chem.MolecularGraph

molgraph

)

Generates a conformer ensemble for the fragment molgraph (the fragment type is perceived automatically).

Parameters

molgraph

The fragment to process.

Returns

A status code defined in ConfGen.ReturnCode.

generate() [2/4]

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

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

Parameters

molgraph	The fragment to process.
fixed_substr	The substructure that must retain the supplied 3D coordinates.
fixed_substr_coords	The 3D coordinates assigned to fixed_substr.

Returns

A status code defined in ConfGen.ReturnCode.

Since

1.1

generate() [3/4]

int CDPL.ConfGen.FragmentConformerGenerator.generate	(	Chem.MolecularGraph	molgraph,
		int	frag_type
	)

Generates a conformer ensemble for the fragment molgraph using the fragment-type-specific settings selected by frag_type.

Parameters

molgraph	The fragment to process.
frag_type	One of the ConfGen.FragmentType values selecting the per-fragment-class settings.

Returns

A status code defined in ConfGen.ReturnCode.

generate() [4/4]

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

Generates a conformer ensemble for the fragment molgraph using the fragment-type-specific settings selected by frag_type while keeping the substructure fixed_substr at the supplied 3D coordinates.

Parameters

molgraph	The fragment to process.
frag_type	One of the ConfGen.FragmentType values selecting the per-fragment-class settings.
fixed_substr	The substructure that must retain the supplied 3D coordinates.
fixed_substr_coords	The 3D coordinates assigned to fixed_substr.

Returns

A status code defined in ConfGen.ReturnCode.

Since

1.1

setConformers()

None CDPL.ConfGen.FragmentConformerGenerator.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.FragmentConformerGenerator.getNumConformers

(

)

Returns the number of generated conformers.

Returns

The conformer count.

getConformer()

ConformerData CDPL.ConfGen.FragmentConformerGenerator.getConformer

(

int

conf_idx

)

Parameters

conf_idx

Returns

getSettings()

FragmentConformerGeneratorSettings CDPL.ConfGen.FragmentConformerGenerator.getSettings

(

)

Returns the current generator settings.

Returns

A reference to the settings.

__getitem__()

ConformerData CDPL.ConfGen.FragmentConformerGenerator.__getitem__

(

int

conf_idx

)

Parameters

conf_idx

Returns