CDPL::ConfGen::RMSDConformerSelector Class Reference

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

#include <RMSDConformerSelector.hpp>

Public Member Functions
	RMSDConformerSelector ()
	Constructs the RMSDConformerSelector instance. More...
	RMSDConformerSelector (const RMSDConformerSelector &)=delete
RMSDConformerSelector &	operator= (const RMSDConformerSelector &)=delete
void	setMinRMSD (double min_rmsd)
	Sets the minimum RMSD that a candidate conformer must keep from every already-selected conformer to be accepted. More...
double	getMinRMSD () const
	Returns the currently configured minimum RMSD threshold. More...
void	setAbortCallback (const CallbackFunction &func)
	Sets the callback invoked periodically to allow the selection to be aborted by the user. More...
const CallbackFunction &	getAbortCallback () const
	Returns the currently configured abort-check callback. More...
std::size_t	getNumSymmetryMappings () const
	Returns the number of symmetry (automorphism) mappings enumerated during the last setup() call. More...
void	setMaxNumSymmetryMappings (std::size_t max_num)
	Sets the maximum number of symmetry mappings to enumerate per setup() call. More...
std::size_t	getMaxNumSymmetryMappings () const
	Returns the currently configured maximum number of symmetry mappings. More...
void	setup (const Chem::MolecularGraph &molgraph, const Util::BitSet &atom_mask)
	Sets up the selector for the subgraph of molgraph defined by atom_mask. More...
void	setup (const Chem::MolecularGraph &molgraph, const Util::BitSet &atom_mask, const Util::BitSet &stable_config_atom_mask, const 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...
bool	selected (const 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
static constexpr std::size_t	DEF_MAX_NUM_SYMMETRY_MAPPINGS = 32768
	Default maximum number of considered automorphism (symmetry) mappings per setup() call. More...

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.

Constructor & Destructor Documentation

RMSDConformerSelector() [1/2]

CDPL::ConfGen::RMSDConformerSelector::RMSDConformerSelector

(

)

Constructs the RMSDConformerSelector instance.

RMSDConformerSelector() [2/2]

CDPL::ConfGen::RMSDConformerSelector::RMSDConformerSelector ( const RMSDConformerSelector &  )

delete

Member Function Documentation

operator=()

RMSDConformerSelector& CDPL::ConfGen::RMSDConformerSelector::operator= ( const RMSDConformerSelector &  )

delete

setMinRMSD()

void CDPL::ConfGen::RMSDConformerSelector::setMinRMSD

(

double

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()

double CDPL::ConfGen::RMSDConformerSelector::getMinRMSD

(

)

const

Returns the currently configured minimum RMSD threshold.

Returns

The minimum RMSD threshold.

setAbortCallback()

void CDPL::ConfGen::RMSDConformerSelector::setAbortCallback

(

const CallbackFunction &

func

)

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

Parameters

func	The abort-check callback.

getAbortCallback()

const CallbackFunction& CDPL::ConfGen::RMSDConformerSelector::getAbortCallback

(

)

const

Returns the currently configured abort-check callback.

Returns

A const reference to the abort-check callback.

getNumSymmetryMappings()

std::size_t CDPL::ConfGen::RMSDConformerSelector::getNumSymmetryMappings

(

)

const

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

Returns

The symmetry-mapping count.

setMaxNumSymmetryMappings()

void CDPL::ConfGen::RMSDConformerSelector::setMaxNumSymmetryMappings

(

std::size_t

max_num

)

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

Parameters

max_num

The new maximum number of mappings.

getMaxNumSymmetryMappings()

std::size_t CDPL::ConfGen::RMSDConformerSelector::getMaxNumSymmetryMappings

(

)

const

Returns the currently configured maximum number of symmetry mappings.

Returns

The maximum number of mappings.

setup() [1/2]

void CDPL::ConfGen::RMSDConformerSelector::setup	(	const Chem::MolecularGraph &	molgraph,
		const 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.

setup() [2/2]

void CDPL::ConfGen::RMSDConformerSelector::setup	(	const Chem::MolecularGraph &	molgraph,
		const Util::BitSet &	atom_mask,
		const Util::BitSet &	stable_config_atom_mask,
		const 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.

selected()

bool CDPL::ConfGen::RMSDConformerSelector::selected

(

const 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.

Member Data Documentation

DEF_MAX_NUM_SYMMETRY_MAPPINGS

constexpr std::size_t CDPL::ConfGen::RMSDConformerSelector::DEF_MAX_NUM_SYMMETRY_MAPPINGS = 32768

staticconstexpr

Default maximum number of considered automorphism (symmetry) mappings per setup() call.

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The documentation for this class was generated from the following file:

• RMSDConformerSelector.hpp