BALL::MolecularSimilarity Class Reference

#include <BALL/STRUCTURE/molecularSimilarity.h>

Public Member Functions
	MolecularSimilarity (String smarts_file)
void	generateFingerprints (System &molecules, vector< vector< Size > > &fingerprints)
void	generateFingerprints (const list< Molecule * > &molecules, vector< vector< Size > > &fingerprints)
void	generateFingerprint (Molecule &molecule, vector< Size > &fingerprint)
void	generatePathFingerprint (Molecule &mol, vector< bool > &fingerprint)
float	calculateSimilarity (vector< bool > &fingerprint1, vector< bool > &fingerprint2)
void	filterRedundantMolecules (const list< Molecule * > &molecules, float similarity_threshold)
void	filterRedundantMolecules (System &molecules, float similarity_threshold)
float	calculateSimilarity (vector< Size > &fingerprint1, vector< Size > &fingerprint2, vector< float > *stddev)
const vector< String > &	getFunctionalGroupNames ()

Protected Member Functions
void	generatePathHash_ (vector< Size > &path, Size &hash)
bool	generatePathFingerprint_ (const Atom *atom, std::vector< Size > &path, std::set< const Bond * > &path_bonds, std::vector< bool > &fingerprint)

Protected Attributes
vector< vector< Size > >	fingerprints_
vector< String >	smarts_
vector< String >	smart_names_
SmartsMatcher	matcher_

Detailed Description

Definition at line 29 of file molecularSimilarity.h.

Constructor & Destructor Documentation

BALL::MolecularSimilarity::MolecularSimilarity

(

String

smarts_file

)

Member Function Documentation

float BALL::MolecularSimilarity::calculateSimilarity	(	vector< bool > &	fingerprint1,
		vector< bool > &	fingerprint2
	)

Calculate Tanimoto coefficient for two given binary fingerprints.

float BALL::MolecularSimilarity::calculateSimilarity	(	vector< Size > &	fingerprint1,
		vector< Size > &	fingerprint2,
		vector< float > *	stddev
	)

Calculate similarity between two fingerprints.
If stddev for function-group counts are specified, then the similarity of position i in the fingerprint-vectors is defined as zero if their absolute difference is larger than the the standard deviation, else as 1-abs(difference_i/stddev_i). If no stddev for function-group counts are given, the calculated similarity-value is equal to Tanimoto.

void BALL::MolecularSimilarity::filterRedundantMolecules	(	const list< Molecule * > &	molecules,
		float	similarity_threshold
	)

void BALL::MolecularSimilarity::filterRedundantMolecules	(	System &	molecules,
		float	similarity_threshold
	)

void BALL::MolecularSimilarity::generateFingerprint	(	Molecule &	molecule,
		vector< Size > &	fingerprint
	)

void BALL::MolecularSimilarity::generateFingerprints	(	System &	molecules,
		vector< vector< Size > > &	fingerprints
	)

void BALL::MolecularSimilarity::generateFingerprints	(	const list< Molecule * > &	molecules,
		vector< vector< Size > > &	fingerprints
	)

void BALL::MolecularSimilarity::generatePathFingerprint	(	Molecule &	mol,
		vector< bool > &	fingerprint
	)

bool BALL::MolecularSimilarity::generatePathFingerprint_ ( const Atom *  atom, std::vector< Size > &  path, std::set< const Bond * > &  path_bonds, std::vector< bool > &  fingerprint  )

protected

void BALL::MolecularSimilarity::generatePathHash_ ( vector< Size > &  path, Size &  hash  )

protected

Generate a hash-ID for a given molecule-path.
This function was adapted from OpenBabel (finger2.cpp).

const vector<String>& BALL::MolecularSimilarity::getFunctionalGroupNames

(

)

Returns the names of the functional groups that have been read from the SMARTS-file

Member Data Documentation

vector<vector<Size> > BALL::MolecularSimilarity::fingerprints_

protected

Definition at line 88 of file molecularSimilarity.h.

SmartsMatcher BALL::MolecularSimilarity::matcher_

protected

Definition at line 92 of file molecularSimilarity.h.

vector<String> BALL::MolecularSimilarity::smart_names_

protected

Definition at line 90 of file molecularSimilarity.h.

vector<String> BALL::MolecularSimilarity::smarts_

protected

Definition at line 89 of file molecularSimilarity.h.