CDPL.ConfGen.FragmentAssembler Class Reference

Driver for the fragment-based generation of 3D starting conformers. More...

Inheritance diagram for CDPL.ConfGen.FragmentAssembler:

Public Member Functions
None	__init__ ()
	Constructs the FragmentAssembler instance.
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
FragmentAssemblerSettings	getSettings ()
	Returns the current assembler settings (mutable). More...
None	clearFragmentLibraries ()
	Removes all configured fragment libraries.
None	addFragmentLibrary (FragmentLibrary lib)
	Adds lib to the list of fragment libraries consulted during assembly. More...
None	setAbortCallback (CallbackFunction func)
	Sets the callback invoked periodically to allow the processing 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 assembler. More...
LogMessageCallbackFunction	getLogMessageCallback ()
	Returns the currently configured log-message callback. More...
int	assemble (Chem.MolecularGraph molgraph)
	Assembles 3D conformer(s) for molgraph from fragment building blocks. More...
int	assemble (Chem.MolecularGraph molgraph, Chem.MolecularGraph fixed_substr, Math.Vector3DArray fixed_substr_coords)
	Assembles 3D conformer(s) for molgraph while keeping the substructure fixed_substr at the supplied 3D coordinates. More...
int	getNumConformers ()
	Returns the number of assembled 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 fragment-based generation of 3D starting conformers.

The assembler decomposes a molecular graph into chain and ring fragments, looks up pre-built conformers from a ConfGen.FragmentLibrary for each fragment (generating them on the fly when no library entry is available) and reassembles them into full 3D structures. The conformers produced this way are intended to serve as starting conformers for subsequent torsion driving — they are not (in general) a final conformer ensemble.

See also

ConfGen.TorsionDriver, ConfGen.ConformerGenerator

Member Function Documentation

getObjectID()

int CDPL.ConfGen.FragmentAssembler.getObjectID

(

)

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

Different Python FragmentAssembler 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 FragmentAssembler 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()

FragmentAssemblerSettings CDPL.ConfGen.FragmentAssembler.getSettings

(

)

Returns the current assembler settings (mutable).

Returns

A reference to the settings.

addFragmentLibrary()

None CDPL.ConfGen.FragmentAssembler.addFragmentLibrary

(

FragmentLibrary

lib

)

Adds lib to the list of fragment libraries consulted during assembly.

Parameters

lib	The fragment library to add.

setAbortCallback()

None CDPL.ConfGen.FragmentAssembler.setAbortCallback

(

CallbackFunction

func

)

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

Parameters

func	The abort-check callback.

getAbortCallback()

CallbackFunction CDPL.ConfGen.FragmentAssembler.getAbortCallback

(

)

Returns the currently configured abort-check callback.

Returns

A reference to the abort-check callback.

setTimeoutCallback()

None CDPL.ConfGen.FragmentAssembler.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.FragmentAssembler.getTimeoutCallback

(

)

Returns the currently configured timeout-check callback.

Returns

A reference to the timeout-check callback.

setLogMessageCallback()

None CDPL.ConfGen.FragmentAssembler.setLogMessageCallback

(

LogMessageCallbackFunction

func

)

Sets the callback receiving log messages emitted by the assembler.

Parameters

func	The log-message callback.

getLogMessageCallback()

LogMessageCallbackFunction CDPL.ConfGen.FragmentAssembler.getLogMessageCallback

(

)

Returns the currently configured log-message callback.

Returns

A reference to the log-message callback.

assemble() [1/2]

int CDPL.ConfGen.FragmentAssembler.assemble

(

Chem.MolecularGraph

molgraph

)

Assembles 3D conformer(s) for molgraph from fragment building blocks.

Parameters

molgraph

The input molecular graph.

Returns

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

assemble() [2/2]

int CDPL.ConfGen.FragmentAssembler.assemble	(	Chem.MolecularGraph	molgraph,
		Chem.MolecularGraph	fixed_substr,
		Math.Vector3DArray	fixed_substr_coords
	)

Assembles 3D conformer(s) for molgraph while keeping the substructure fixed_substr at the supplied 3D coordinates.

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 assembly.

Since

1.1

getNumConformers()

int CDPL.ConfGen.FragmentAssembler.getNumConformers

(

)

Returns the number of assembled conformers.

Returns

The conformer count.

getConformer()

ConformerData CDPL.ConfGen.FragmentAssembler.getConformer

(

int

conf_idx

)

Parameters

conf_idx

Returns

__getitem__()

ConformerData CDPL.ConfGen.FragmentAssembler.__getitem__

(

int

conf_idx

)

Parameters

conf_idx

Returns