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//
// Copyright (C) 2007-2012 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
/*! \file AtomPairs.h
*/
#ifndef __RD_ATOMPAIRS_H__
#define __RD_ATOMPAIRS_H__
#include <DataStructs/SparseIntVect.h>
#include <DataStructs/BitVects.h>
#include <boost/cstdint.hpp>
namespace RDKit {
class Atom;
namespace AtomPairs {
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;
//! returns a numeric code for the atom (the atom's hash in the
//! atom-pair scheme)
/*!
\param atom the atom to be considered
\param 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 getAtomCode(const Atom *atom,unsigned int branchSubtract=0);
//! returns an atom pair hash based on two atom hashes and the
//! distance between the atoms.
/*!
\param codeI the hash for the first atom
\param codeJ the hash for the second atom
\param dist the distance (number of bonds) between the two
atoms
*/
boost::uint32_t getAtomPairCode(boost::uint32_t codeI,boost::uint32_t codeJ,
unsigned int dist);
//! 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).
\param mol: the molecule to be fingerprinted
\param minLength: minimum distance between atoms to be
considered in a pair. Default is 1 bond.
\param maxLength: maximum distance between atoms to be
considered in a pair.
Default is maxPathLen-1 bonds.
\param fromAtoms: if provided, only atom pairs that involve
the specified atoms will be included in the
fingerprint
\param ignoreAtoms: if provided, any atom pairs that include
the specified atoms will not be included in the
fingerprint
\param atomInvariants: a list of invariants to use for the atom hashes
note: only the first \c codeSize bits of each
invariant are used.
\return a pointer to the fingerprint. The client is
responsible for calling delete on this.
*/
SparseIntVect<boost::int32_t> *
getAtomPairFingerprint(const ROMol &mol,
unsigned int minLength,unsigned int maxLength,
const std::vector<boost::uint32_t> *fromAtoms=0,
const std::vector<boost::uint32_t> *ignoreAtoms=0,
const std::vector<boost::uint32_t> *atomInvariants=0);
//! \overload
SparseIntVect<boost::int32_t> *
getAtomPairFingerprint(const ROMol &mol,
const std::vector<boost::uint32_t> *fromAtoms=0,
const std::vector<boost::uint32_t> *ignoreAtoms=0,
const std::vector<boost::uint32_t> *atomInvariants=0);
//! returns the hashed atom-pair fingerprint for a molecule
/*!
\param mol: the molecule to be fingerprinted
\param nBits: the length of the fingerprint to generate
\param minLength: minimum distance between atoms to be
considered in a pair. Default is 1 bond.
\param maxLength: maximum distance between atoms to be
considered in a pair.
Default is maxPathLen-1 bonds.
\param fromAtoms: if provided, only atom pairs that involve
the specified atoms will be included in the
fingerprint
\param ignoreAtoms: if provided, any atom pairs that include
the specified atoms will not be included in the
fingerprint
\param atomInvariants: a list of invariants to use for the atom hashes
note: only the first \c codeSize bits of each
invariant are used.
\return a pointer to the fingerprint. The client is
responsible for calling delete on this.
*/
SparseIntVect<boost::int32_t> *
getHashedAtomPairFingerprint(const ROMol &mol,
unsigned int nBits=2048,
unsigned int minLength=1,
unsigned int maxLength=maxPathLen-1,
const std::vector<boost::uint32_t> *fromAtoms=0,
const std::vector<boost::uint32_t> *ignoreAtoms=0,
const std::vector<boost::uint32_t> *atomInvariants=0);
//! returns the hashed atom-pair fingerprint for a molecule as a bit vector
/*!
\param mol: the molecule to be fingerprinted
\param nBits: the length of the fingerprint to generate
\param minLength: minimum distance between atoms to be
considered in a pair. Default is 1 bond.
\param maxLength: maximum distance between atoms to be
considered in a pair.
Default is maxPathLen-1 bonds.
\param fromAtoms: if provided, only atom pairs that involve
the specified atoms will be included in the
fingerprint
\param ignoreAtoms: if provided, any atom pairs that include
the specified atoms will not be included in the
fingerprint
\param atomInvariants: a list of invariants to use for the atom hashes
note: only the first \c codeSize bits of each
invariant are used.
\param nBitsPerEntry: number of bits to use in simulating counts
\return a pointer to the fingerprint. The client is
responsible for calling delete on this.
*/
ExplicitBitVect *
getHashedAtomPairFingerprintAsBitVect(const ROMol &mol,
unsigned int nBits=2048,
unsigned int minLength=1,
unsigned int maxLength=maxPathLen-1,
const std::vector<boost::uint32_t> *fromAtoms=0,
const std::vector<boost::uint32_t> *ignoreAtoms=0,
const std::vector<boost::uint32_t> *atomInvariants=0,
unsigned int nBitsPerEntry=4);
//! returns an topological torsion hash based on the atom hashes
//! passed in
/*!
\param atomCodes the vector of atom hashes
*/
boost::uint64_t getTopologicalTorsionCode(const std::vector<boost::uint32_t> &atomCodes);
//! 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).
\param mol: the molecule to be fingerprinted
\param targetSize: the number of atoms to include in the "torsions"
\param fromAtoms: if provided, only torsions that start or end at
the specified atoms will be included in the
fingerprint
\param ignoreAtoms: if provided, any torsions that include
the specified atoms will not be included in the
fingerprint
\param atomInvariants: a list of invariants to use for the atom hashes
note: only the first \c codeSize bits of each
invariant are used.
\return a pointer to the fingerprint. The client is
responsible for calling delete on this.
*/
SparseIntVect<boost::int64_t > *
getTopologicalTorsionFingerprint(const ROMol &mol,
unsigned int targetSize=4,
const std::vector<boost::uint32_t> *fromAtoms=0,
const std::vector<boost::uint32_t> *ignoreAtoms=0,
const std::vector<boost::uint32_t> *atomInvariants=0
);
//! returns a hashed 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).
\param mol: the molecule to be fingerprinted
\param nBits: number of bits to include in the fingerprint
\param targetSize: the number of atoms to include in the "torsions"
\param fromAtoms: if provided, only torsions that start or end at
the specified atoms will be included in the
fingerprint
\param ignoreAtoms: if provided, any torsions that include
the specified atoms will not be included in the
fingerprint
\param atomInvariants: a list of invariants to use for the atom hashes
note: only the first \c codeSize bits of each
invariant are used.
\return a pointer to the fingerprint. The client is
responsible for calling delete on this.
*/
SparseIntVect<boost::int64_t > *
getHashedTopologicalTorsionFingerprint(const ROMol &mol,
unsigned int nBits=2048,
unsigned int targetSize=4,
const std::vector<boost::uint32_t> *fromAtoms=0,
const std::vector<boost::uint32_t> *ignoreAtoms=0,
const std::vector<boost::uint32_t> *atomInvariants=0);
//! returns a hashed topological-torsion fingerprint for a molecule as a bit vector
/*!
\param mol: the molecule to be fingerprinted
\param nBits: number of bits to include in the fingerprint
\param targetSize: the number of atoms to include in the "torsions"
\param fromAtoms: if provided, only torsions that start or end at
the specified atoms will be included in the
fingerprint
\param ignoreAtoms: if provided, any torsions that include
the specified atoms will not be included in the
fingerprint
\param atomInvariants: a list of invariants to use for the atom hashes
note: only the first \c codeSize bits of each
invariant are used.
\param nBitsPerEntry: number of bits to use in simulating counts
\return a pointer to the fingerprint. The client is
responsible for calling delete on this.
*/
ExplicitBitVect *
getHashedTopologicalTorsionFingerprintAsBitVect(const ROMol &mol,
unsigned int nBits=2048,
unsigned int targetSize=4,
const std::vector<boost::uint32_t> *fromAtoms=0,
const std::vector<boost::uint32_t> *ignoreAtoms=0,
const std::vector<boost::uint32_t> *atomInvariants=0,
unsigned int nBitsPerEntry=4);
}
}
#endif
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