RDKit::Descriptors::AtomPairs Namespace Reference

Functions
boost::uint32_t	getAtomCode (const Atom *atom, unsigned int branchSubtract=0)
boost::uint32_t	getAtomPairCode (boost::uint32_t codeI, boost::uint32_t codeJ, unsigned int dist)
SparseIntVect< boost::int32_t > *	getAtomPairFingerprint (const ROMol &mol, const std::vector< boost::uint32_t > *fromAtoms=0)
	returns the atom-pair fingerprint for a molecule
ExplicitBitVect *	getHashedAtomPairFingerprint (const ROMol &mol, unsigned int nBits=2048)
	returns the hashed atom-pair fingerprint for a molecule
boost::uint64_t	getTopologicalTorsionCode (const std::vector< boost::uint32_t > &atomCodes)
SparseIntVect< boost::int64_t > *	getTopologicalTorsionFingerprint (const ROMol &mol, unsigned int targetSize=4, const std::vector< boost::uint32_t > *fromAtoms=0)
	returns the topological-torsion fingerprint for a molecule
Variables
const std::string	atomPairsVersion = "1.1.0"
const unsigned int	numTypeBits = 4
const unsigned int	atomNumberTypes [1<< numTypeBits] = {5,6,7,8,9,14,15,16,17,33,34,35,51,52,43}
const unsigned int	numPiBits = 2
const unsigned int	maxNumPi = (1<<numPiBits)-1
const unsigned int	numBranchBits = 3
const unsigned int	maxNumBranches = (1<<numBranchBits)-1
const unsigned int	codeSize = numTypeBits+numPiBits+numBranchBits
const unsigned int	numPathBits = 5
const unsigned int	maxPathLen = (1<<numPathBits)-1
const unsigned int	numAtomPairFingerprintBits = numPathBits+2*codeSize

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Function Documentation

boost::uint32_t RDKit::Descriptors::AtomPairs::getAtomCode	(	const Atom *	atom,
		unsigned int	branchSubtract = 0
	)

returns a numeric code for the atom (the atom's hash in the atom-pair scheme)

Parameters:

	atom	the atom to be considered
	branchSubtract	(optional) a constant to subtract from the number of neighbors when the hash is calculated (used in the topological torsions code)

boost::uint32_t RDKit::Descriptors::AtomPairs::getAtomPairCode	(	boost::uint32_t	codeI,
		boost::uint32_t	codeJ,
		unsigned int	dist
	)

returns an atom pair hash based on two atom hashes and the distance between the atoms.

Parameters:

	codeI	the hash for the first atom
	codeJ	the hash for the second atom
	dist	the distance (number of bonds) between the two atoms

SparseIntVect<boost::int32_t>* RDKit::Descriptors::AtomPairs::getAtomPairFingerprint	(	const ROMol &	mol,
		const std::vector< boost::uint32_t > *	fromAtoms = 0
	)

returns the atom-pair fingerprint for a molecule

The algorithm used is described here: R.E. Carhart, D.H. Smith, R. Venkataraghavan; "Atom Pairs as Molecular Features in Structure-Activity Studies: Definition and Applications" JCICS 25, 64-73 (1985).

Parameters:

	mol,:	the molecule to be fingerprinted
	fromAtoms,:	if provided, only atom pairs that involve the specified atoms will be included in the fingerprint

Returns:

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

ExplicitBitVect* RDKit::Descriptors::AtomPairs::getHashedAtomPairFingerprint	(	const ROMol &	mol,
		unsigned int	nBits = 2048
	)

returns the hashed atom-pair fingerprint for a molecule

Parameters:

	mol,:	the molecule to be fingerprinted
	nBits,:	the length of the fingerprint to generate

Returns:

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

boost::uint64_t RDKit::Descriptors::AtomPairs::getTopologicalTorsionCode

(

const std::vector< boost::uint32_t > &

atomCodes

)

returns an topological torsion hash based on the atom hashes passed in

Parameters:

atomCodes

the vector of atom hashes

SparseIntVect<boost::int64_t >* RDKit::Descriptors::AtomPairs::getTopologicalTorsionFingerprint	(	const ROMol &	mol,
		unsigned int	targetSize = 4,
		const std::vector< boost::uint32_t > *	fromAtoms = 0
	)

returns the topological-torsion fingerprint for a molecule

The algorithm used is described here: R. Nilakantan, N. Bauman, J. S. Dixon, R. Venkataraghavan; "Topological Torsion: A New Molecular Descriptor for SAR Applications. Comparison with Other Descriptors" JCICS 27, 82-85 (1987).

Parameters:

	mol,:	the molecule to be fingerprinted
	targetSize,:	the number of atoms to include in the torsions
	fromAtoms,:	if provided, only torsions that start or end at the specified atoms will be included in the fingerprint

Returns:

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

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Variable Documentation

const unsigned int RDKit::Descriptors::AtomPairs::atomNumberTypes[1<< numTypeBits] = {5,6,7,8,9,14,15,16,17,33,34,35,51,52,43}

Definition at line 25 of file AtomPairs.h.

const std::string RDKit::Descriptors::AtomPairs::atomPairsVersion = "1.1.0"

Definition at line 23 of file AtomPairs.h.

const unsigned int RDKit::Descriptors::AtomPairs::codeSize = numTypeBits+numPiBits+numBranchBits

Definition at line 30 of file AtomPairs.h.

const unsigned int RDKit::Descriptors::AtomPairs::maxNumBranches = (1<<numBranchBits)-1

Definition at line 29 of file AtomPairs.h.

const unsigned int RDKit::Descriptors::AtomPairs::maxNumPi = (1<<numPiBits)-1

Definition at line 27 of file AtomPairs.h.

const unsigned int RDKit::Descriptors::AtomPairs::maxPathLen = (1<<numPathBits)-1

Definition at line 32 of file AtomPairs.h.

const unsigned int RDKit::Descriptors::AtomPairs::numAtomPairFingerprintBits = numPathBits+2*codeSize

Definition at line 33 of file AtomPairs.h.

const unsigned int RDKit::Descriptors::AtomPairs::numBranchBits = 3

Definition at line 28 of file AtomPairs.h.

const unsigned int RDKit::Descriptors::AtomPairs::numPathBits = 5

Definition at line 31 of file AtomPairs.h.

const unsigned int RDKit::Descriptors::AtomPairs::numPiBits = 2

Definition at line 26 of file AtomPairs.h.

const unsigned int RDKit::Descriptors::AtomPairs::numTypeBits = 4

Definition at line 24 of file AtomPairs.h.