CDPL.ConfGen.RMSDConformerSelector Class Reference

Greedy RMSD-based conformer-diversity filter. More...

Inheritance diagram for CDPL.ConfGen.RMSDConformerSelector:

Public Member Functions
None	__init__ ()
	Constructs the RMSDConformerSelector instance.
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
None	setMinRMSD (float min_rmsd)
	Sets the minimum RMSD that a candidate conformer must keep from every already-selected conformer to be accepted. More...
float	getMinRMSD ()
	Returns the currently configured minimum RMSD threshold. More...
None	setAbortCallback (CallbackFunction func)
	Sets the callback invoked periodically to allow the selection to be aborted by the user. More...
CallbackFunction	getAbortCallback ()
	Returns the currently configured abort-check callback. More...
int	getNumSymmetryMappings ()
	Returns the number of symmetry (automorphism) mappings enumerated during the last setup() call. More...
None	setMaxNumSymmetryMappings (int max_num)
	Sets the maximum number of symmetry mappings to enumerate per setup() call. More...
int	getMaxNumSymmetryMappings ()
	Returns the currently configured maximum number of symmetry mappings. More...
None	setup (Chem.MolecularGraph molgraph, Util.BitSet atom_mask, Util.BitSet stable_config_atom_mask, Math.Vector3DArray coords)
	Sets up the selector for the subgraph of molgraph defined by atom_mask while restricting the enumerated automorphisms to those that preserve the chirality of atoms in stable_config_atom_mask with respect to the supplied 3D coordinates coords. More...
None	setup (Chem.MolecularGraph molgraph, Util.BitSet atom_mask)
	Sets up the selector for the subgraph of molgraph defined by atom_mask. More...
bool	selected (Math.Vector3DArray conf_coords)
	Tests whether conf_coords is sufficiently different from already-selected conformers and, if so, adds it to the selected set. More...

Static Public Attributes
int	DEF_MAX_NUM_SYMMETRY_MAPPINGS = 32768
	Default maximum number of considered automorphism (symmetry) mappings per setup() call.

Properties
	objectID = property(getObjectID)
	abortCallback = property(getAbortCallback, setAbortCallback)
	numSymmetryMappings = property(getNumSymmetryMappings)
	maxNumSymmetryMappings = property(getMaxNumSymmetryMappings, setMaxNumSymmetryMappings)
	minRMSD = property(getMinRMSD, setMinRMSD)

Detailed Description

Greedy RMSD-based conformer-diversity filter.

For each candidate conformer the selector computes the minimum symmetry-equivalent RMSD against the set of already-selected conformers. A new conformer is accepted (added to the selected set) only if its minimum RMSD exceeds the configured threshold.

Member Function Documentation

getObjectID()

int CDPL.ConfGen.RMSDConformerSelector.getObjectID

(

)

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

Different Python RMSDConformerSelector 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 RMSDConformerSelector 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.

setMinRMSD()

None CDPL.ConfGen.RMSDConformerSelector.setMinRMSD

(

float

min_rmsd

)

Sets the minimum RMSD that a candidate conformer must keep from every already-selected conformer to be accepted.

Parameters

min_rmsd

The new minimum RMSD.

getMinRMSD()

float CDPL.ConfGen.RMSDConformerSelector.getMinRMSD

(

)

Returns the currently configured minimum RMSD threshold.

Returns

The minimum RMSD threshold.

setAbortCallback()

None CDPL.ConfGen.RMSDConformerSelector.setAbortCallback

(

CallbackFunction

func

)

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

Parameters

func	The abort-check callback.

getAbortCallback()

CallbackFunction CDPL.ConfGen.RMSDConformerSelector.getAbortCallback

(

)

Returns the currently configured abort-check callback.

Returns

A reference to the abort-check callback.

getNumSymmetryMappings()

int CDPL.ConfGen.RMSDConformerSelector.getNumSymmetryMappings

(

)

Returns the number of symmetry (automorphism) mappings enumerated during the last setup() call.

Returns

The symmetry-mapping count.

setMaxNumSymmetryMappings()

None CDPL.ConfGen.RMSDConformerSelector.setMaxNumSymmetryMappings

(

int

max_num

)

Sets the maximum number of symmetry mappings to enumerate per setup() call.

Parameters

max_num

The new maximum number of mappings.

getMaxNumSymmetryMappings()

int CDPL.ConfGen.RMSDConformerSelector.getMaxNumSymmetryMappings

(

)

Returns the currently configured maximum number of symmetry mappings.

Returns

The maximum number of mappings.

setup() [1/2]

None CDPL.ConfGen.RMSDConformerSelector.setup	(	Chem.MolecularGraph	molgraph,
		Util.BitSet	atom_mask,
		Util.BitSet	stable_config_atom_mask,
		Math.Vector3DArray	coords
	)

Sets up the selector for the subgraph of molgraph defined by atom_mask while restricting the enumerated automorphisms to those that preserve the chirality of atoms in stable_config_atom_mask with respect to the supplied 3D coordinates coords.

Parameters

molgraph	The parent molecular graph.
atom_mask	The bit mask selecting atoms considered during RMSD computation.
stable_config_atom_mask	The bit mask of atoms whose stereo-configuration must be preserved.
coords	The 3D coordinates used to determine the stereo-configurations.

setup() [2/2]

None CDPL.ConfGen.RMSDConformerSelector.setup	(	Chem.MolecularGraph	molgraph,
		Util.BitSet	atom_mask
	)

Sets up the selector for the subgraph of molgraph defined by atom_mask.

Parameters

molgraph	The parent molecular graph.
atom_mask	The bit mask selecting atoms considered during RMSD computation.

selected()

bool CDPL.ConfGen.RMSDConformerSelector.selected

(

Math.Vector3DArray

conf_coords

)

Tests whether conf_coords is sufficiently different from already-selected conformers and, if so, adds it to the selected set.

Parameters

conf_coords

The candidate conformer's 3D coordinates.

Returns

True if the conformer was selected, and False otherwise.