RDKit::MorganFingerprints Namespace Reference

Typedefs
typedef std::map < boost::uint32_t, std::vector < std::pair< boost::uint32_t, boost::uint32_t > > >	BitInfoMap
Functions
SparseIntVect< boost::uint32_t > *	getFingerprint (const ROMol &mol, unsigned int radius, std::vector< boost::uint32_t > *invariants=0, const std::vector< boost::uint32_t > *fromAtoms=0, bool useChirality=false, bool useBondTypes=true, bool onlyNonzeroInvariants=false, BitInfoMap *atomsSettingBits=0)
	returns the Morgan fingerprint for a molecule
ExplicitBitVect *	getFingerprintAsBitVect (const ROMol &mol, unsigned int radius, unsigned int nBits, std::vector< boost::uint32_t > *invariants=0, const std::vector< boost::uint32_t > *fromAtoms=0, bool useChirality=false, bool useBondTypes=true, bool onlyNonzeroInvariants=false, BitInfoMap *atomsSettingBits=0)
	returns the Morgan fingerprint for a molecule as a bit vector
void	getConnectivityInvariants (const ROMol &mol, std::vector< boost::uint32_t > &invars, bool includeRingMembership=true)
	returns the connectivity invariants for a molecule
void	getFeatureInvariants (const ROMol &mol, std::vector< boost::uint32_t > &invars, std::vector< ROMOL_SPTR > *patterns=0)
	returns the feature invariants for a molecule
Variables
std::vector< std::string >	defaultFeatureSmarts
std::vector< ROMOL_SPTR >	defaultFeatureMatchers
const std::string	morganFingerprintVersion = "1.0.0"
const std::string	morganConnectivityInvariantVersion = "1.0.0"
const std::string	morganFeatureInvariantVersion = "0.1.0"

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Typedef Documentation

typedef std::map<boost::uint32_t,std::vector<std::pair<boost::uint32_t,boost::uint32_t> > > RDKit::MorganFingerprints::BitInfoMap

Definition at line 54 of file MorganFingerprints.h.

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Function Documentation

void RDKit::MorganFingerprints::getConnectivityInvariants	(	const ROMol &	mol,
		std::vector< boost::uint32_t > &	invars,
		bool	includeRingMembership = true
	)

returns the connectivity invariants for a molecule

Parameters:

	mol	: the molecule to be considered
	invars	: used to return the results
	includeRingMembership	: if set, whether or not the atom is in a ring will be used in the invariant list.

void RDKit::MorganFingerprints::getFeatureInvariants	(	const ROMol &	mol,
		std::vector< boost::uint32_t > &	invars,
		std::vector< ROMOL_SPTR > *	patterns = 0
	)

returns the feature invariants for a molecule

Parameters:

	mol,:	the molecule to be considered
	invars	: used to return the results
	patterns,:	if provided should contain the queries used to assign atom-types. if not provided, feature definitions adapted from reference: Gobbi and Poppinger, Biotech. Bioeng. _61_ 47-54 (1998) will be used for Donor, Acceptor, Aromatic, Halogen, Basic, Acidic

SparseIntVect<boost::uint32_t>* RDKit::MorganFingerprints::getFingerprint	(	const ROMol &	mol,
		unsigned int	radius,
		std::vector< boost::uint32_t > *	invariants = 0,
		const std::vector< boost::uint32_t > *	fromAtoms = 0,
		bool	useChirality = false,
		bool	useBondTypes = true,
		bool	onlyNonzeroInvariants = false,
		BitInfoMap *	atomsSettingBits = 0
	)

returns the Morgan fingerprint for a molecule

These fingerprints are similar to the well-known ECFP or FCFP fingerprints, depending on which invariants are used.

The algorithm used is described in the paper Rogers, D. & Hahn, M. Extended-Connectivity Fingerprints. JCIM 50:742-54 (2010) http://dx.doi.org/10.1021/ci100050t

The original implementation was done using this paper: D. Rogers, R.D. Brown, M. Hahn J. Biomol. Screen. 10:682-6 (2005) and an unpublished technical report: http://www.ics.uci.edu/~welling/teaching/ICS274Bspring06/David%20Rogers%20-%20ECFP%20Manuscript.doc

Parameters:

	mol,:	the molecule to be fingerprinted
	radius,:	the number of iterations to grow the fingerprint
	invariants	: optional pointer to a set of atom invariants to be used. By default ECFP-type invariants are used (calculated by getConnectivityInvariants())
	fromAtoms	: if this is provided, only the atoms in the vector will be used as centers in the fingerprint
	useChirality	: if set, additional information will be added to the fingerprint when chiral atoms are discovered. This will cause C[C@H](F)Cl, C[C@@H](F)Cl, and CC(F)Cl to generate different fingerprints.
	useBondTypes	: if set, bond types will be included as part of the hash for calculating bits
	onlyNonzeroInvariants	: if set, bits will only be set from atoms that have a nonzero invariant.
	atomsSettingBits	: if nonzero, this will be used to return information about the atoms that set each particular bit. The keys are the map are bit ids, the values are lists of (atomId, radius) pairs.

Returns:

a pointer to the fingerprint. The client is responsible for calling delete on this.

ExplicitBitVect* RDKit::MorganFingerprints::getFingerprintAsBitVect	(	const ROMol &	mol,
		unsigned int	radius,
		unsigned int	nBits,
		std::vector< boost::uint32_t > *	invariants = 0,
		const std::vector< boost::uint32_t > *	fromAtoms = 0,
		bool	useChirality = false,
		bool	useBondTypes = true,
		bool	onlyNonzeroInvariants = false,
		BitInfoMap *	atomsSettingBits = 0
	)

returns the Morgan fingerprint for a molecule as a bit vector

see documentation for getFingerprint() for theory/references

Parameters:

	mol,:	the molecule to be fingerprinted
	radius,:	the number of iterations to grow the fingerprint
	nBits,:	the number of bits in the final fingerprint
	invariants	: optional pointer to a set of atom invariants to be used. By default ECFP-type invariants are used (calculated by getConnectivityInvariants())
	fromAtoms	: if this is provided, only the atoms in the vector will be used as centers in the fingerprint
	useChirality	: if set, additional information will be added to the fingerprint when chiral atoms are discovered. This will cause C[C@H](F)Cl, C[C@@H](F)Cl, and CC(F)Cl to generate different fingerprints.
	useBondTypes	: if set, bond types will be included as part of the hash for calculating bits
	onlyNonzeroInvariants	: if set, bits will only be set from atoms that have a nonzero invariant.
	atomsSettingBits	: if nonzero, this will be used to return information about the atoms that set each particular bit. The keys are the map are bit ids, the values are lists of (atomId, radius) pairs.

Returns:

a pointer to the fingerprint. The client is responsible for calling delete on this.

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Variable Documentation

std::vector<ROMOL_SPTR> RDKit::MorganFingerprints::defaultFeatureMatchers

std::vector<std::string> RDKit::MorganFingerprints::defaultFeatureSmarts

const std::string RDKit::MorganFingerprints::morganConnectivityInvariantVersion = "1.0.0"

Definition at line 156 of file MorganFingerprints.h.

const std::string RDKit::MorganFingerprints::morganFeatureInvariantVersion = "0.1.0"

Definition at line 172 of file MorganFingerprints.h.

const std::string RDKit::MorganFingerprints::morganFingerprintVersion = "1.0.0"

Definition at line 56 of file MorganFingerprints.h.