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276 lines
12 KiB
C++
276 lines
12 KiB
C++
//
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// Copyright (C) 2007-2013 Greg Landrum
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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/*! \file AtomPairs.h
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A few quick notes about fingerprint size and the way chirality is handled in
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these functions.
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By default the atom-pair and topologic-torsion fingerprints do not include any
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information about
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chirality; the atom invariants only include information about the atomic
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number,
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number of pi electrons, and degree.
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When chirality is included, two additional bits are added to the atom
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invariants to flag R/S/no
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chirality. These additional bits change the size of the atom invariants and
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either the size
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of the final fingerprint (atom pairs) or the maximum allowed path length
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(torsions). This means
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that even fingerprints for achiral molecules are different when
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includeChirality is true.
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*/
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#include <RDGeneral/export.h>
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#ifndef __RD_ATOMPAIRS_H__
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#define __RD_ATOMPAIRS_H__
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#include <DataStructs/SparseIntVect.h>
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#include <DataStructs/BitVects.h>
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#include <cstdint>
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#include <GraphMol/Fingerprints/FingerprintUtil.h>
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namespace RDKit {
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class Atom;
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namespace AtomPairs {
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const std::string atomPairsVersion = "1.1.0";
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//! returns the atom-pair fingerprint for a molecule
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/*!
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The algorithm used is described here:
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R.E. Carhart, D.H. Smith, R. Venkataraghavan; "Atom Pairs as
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Molecular Features in Structure-Activity Studies: Definition
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and Applications" JCICS 25, 64-73 (1985).
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\param mol: the molecule to be fingerprinted
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\param minLength: minimum distance between atoms to be
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considered in a pair. Default is 1 bond.
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\param maxLength: maximum distance between atoms to be
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considered in a pair.
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Default is maxPathLen-1 bonds.
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\param fromAtoms: if provided, only atom pairs that involve
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the specified atoms will be included in the
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fingerprint
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\param ignoreAtoms: if provided, any atom pairs that include
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the specified atoms will not be included in the
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fingerprint
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\param atomInvariants: a list of invariants to use for the atom hashes
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note: only the first \c codeSize bits of each
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invariant are used.
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\param includeChirality: if set, chirality will be used in the atom invariants
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(note: this is ignored if atomInvariants are
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provided)
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\param use2D: if set, the 2D (topological) distance matrix is used.
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\param confId: the conformation to use if 3D distances are being used
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\return a pointer to the fingerprint. The client is
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responsible for calling delete on this.
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*/
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[[deprecated("please use AtomPairGenerator")]]
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RDKIT_FINGERPRINTS_EXPORT SparseIntVect<std::int32_t> *getAtomPairFingerprint(
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const ROMol &mol, unsigned int minLength, unsigned int maxLength,
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const std::vector<std::uint32_t> *fromAtoms = nullptr,
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const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
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const std::vector<std::uint32_t> *atomInvariants = nullptr,
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bool includeChirality = false, bool use2D = true, int confId = -1);
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//! \overload
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[[deprecated("please use AtomPairGenerator")]]
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RDKIT_FINGERPRINTS_EXPORT SparseIntVect<std::int32_t> *getAtomPairFingerprint(
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const ROMol &mol, const std::vector<std::uint32_t> *fromAtoms = nullptr,
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const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
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const std::vector<std::uint32_t> *atomInvariants = nullptr,
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bool includeChirality = false, bool use2D = true, int confId = -1);
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//! returns the hashed atom-pair fingerprint for a molecule
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/*!
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\param mol: the molecule to be fingerprinted
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\param nBits: the length of the fingerprint to generate
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\param minLength: minimum distance between atoms to be
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considered in a pair. Default is 1 bond.
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\param maxLength: maximum distance between atoms to be
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considered in a pair.
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Default is maxPathLen-1 bonds.
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\param fromAtoms: if provided, only atom pairs that involve
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the specified atoms will be included in the
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fingerprint
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\param ignoreAtoms: if provided, any atom pairs that include
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the specified atoms will not be included in the
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fingerprint
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\param atomInvariants: a list of invariants to use for the atom hashes
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note: only the first \c codeSize bits of each
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invariant are used.
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\param includeChirality: if set, chirality will be used in the atom invariants
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(note: this is ignored if atomInvariants are
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provided)
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\param use2D: if set, the 2D (topological) distance matrix is used.
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\return a pointer to the fingerprint. The client is
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responsible for calling delete on this.
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*/
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[[deprecated("please use AtomPairGenerator")]]
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RDKIT_FINGERPRINTS_EXPORT SparseIntVect<std::int32_t> *
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getHashedAtomPairFingerprint(
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const ROMol &mol, unsigned int nBits = 2048, unsigned int minLength = 1,
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unsigned int maxLength = maxPathLen - 1,
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const std::vector<std::uint32_t> *fromAtoms = nullptr,
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const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
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const std::vector<std::uint32_t> *atomInvariants = nullptr,
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bool includeChirality = false, bool use2D = true, int confId = -1);
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//! returns the hashed atom-pair fingerprint for a molecule as a bit vector
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/*!
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\param mol: the molecule to be fingerprinted
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\param nBits: the length of the fingerprint to generate
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\param minLength: minimum distance between atoms to be
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considered in a pair. Default is 1 bond.
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\param maxLength: maximum distance between atoms to be
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considered in a pair.
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Default is maxPathLen-1 bonds.
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\param fromAtoms: if provided, only atom pairs that involve
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the specified atoms will be included in the
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fingerprint
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\param ignoreAtoms: if provided, any atom pairs that include
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the specified atoms will not be included in the
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fingerprint
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\param atomInvariants: a list of invariants to use for the atom hashes
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note: only the first \c codeSize bits of each
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invariant are used.
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\param nBitsPerEntry: number of bits to use in simulating counts
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\param includeChirality: if set, chirality will be used in the atom invariants
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(note: this is ignored if atomInvariants are
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provided)
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\param use2D: if set, the 2D (topological) distance matrix is used.
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\param confId: the conformation to use if 3D distances are being used
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\return a pointer to the fingerprint. The client is
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responsible for calling delete on this.
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*/
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[[deprecated("please use AtomPairGenerator")]]
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RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *
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getHashedAtomPairFingerprintAsBitVect(
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const ROMol &mol, unsigned int nBits = 2048, unsigned int minLength = 1,
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unsigned int maxLength = maxPathLen - 1,
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const std::vector<std::uint32_t> *fromAtoms = nullptr,
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const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
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const std::vector<std::uint32_t> *atomInvariants = nullptr,
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unsigned int nBitsPerEntry = 4, bool includeChirality = false,
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bool use2D = true, int confId = -1);
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//! returns the topological-torsion fingerprint for a molecule
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/*!
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The algorithm used is described here:
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R. Nilakantan, N. Bauman, J. S. Dixon, R. Venkataraghavan;
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"Topological Torsion: A New Molecular Descriptor for SAR Applications.
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Comparison with Other Descriptors" JCICS 27, 82-85 (1987).
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\param mol: the molecule to be fingerprinted
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\param targetSize: the number of atoms to include in the "torsions"
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\param fromAtoms: if provided, only torsions that start or end at
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the specified atoms will be included in the
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fingerprint
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\param ignoreAtoms: if provided, any torsions that include
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the specified atoms will not be included in the
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fingerprint
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\param atomInvariants: a list of invariants to use for the atom hashes
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note: only the first \c codeSize bits of each
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invariant are used.
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\param includeChirality: if set, chirality will be used in the atom invariants
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(note: this is ignored if atomInvariants are
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provided)
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\return a pointer to the fingerprint. The client is
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responsible for calling delete on this.
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*/
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[[deprecated("please use TopologicalTorsionGenerator")]]
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RDKIT_FINGERPRINTS_EXPORT SparseIntVect<boost::int64_t> *
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getTopologicalTorsionFingerprint(
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const ROMol &mol, unsigned int targetSize = 4,
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const std::vector<std::uint32_t> *fromAtoms = nullptr,
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const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
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const std::vector<std::uint32_t> *atomInvariants = nullptr,
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bool includeChirality = false);
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//! returns a hashed topological-torsion fingerprint for a molecule
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/*!
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The algorithm used is described here:
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R. Nilakantan, N. Bauman, J. S. Dixon, R. Venkataraghavan;
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"Topological Torsion: A New Molecular Descriptor for SAR Applications.
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Comparison with Other Descriptors" JCICS 27, 82-85 (1987).
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\param mol: the molecule to be fingerprinted
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\param nBits: number of bits to include in the fingerprint
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\param targetSize: the number of atoms to include in the "torsions"
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\param fromAtoms: if provided, only torsions that start or end at
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the specified atoms will be included in the
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fingerprint
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\param ignoreAtoms: if provided, any torsions that include
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the specified atoms will not be included in the
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fingerprint
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\param atomInvariants: a list of invariants to use for the atom hashes
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note: only the first \c codeSize bits of each
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invariant are used.
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\param includeChirality: if set, chirality will be used in the atom invariants
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(note: this is ignored if atomInvariants are
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provided)
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\return a pointer to the fingerprint. The client is
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responsible for calling delete on this.
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*/
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[[deprecated("please use TopologicalTorsionGenerator")]]
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RDKIT_FINGERPRINTS_EXPORT SparseIntVect<boost::int64_t> *
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getHashedTopologicalTorsionFingerprint(
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const ROMol &mol, unsigned int nBits = 2048, unsigned int targetSize = 4,
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const std::vector<std::uint32_t> *fromAtoms = nullptr,
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const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
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const std::vector<std::uint32_t> *atomInvariants = nullptr,
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bool includeChirality = false);
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//! returns a hashed topological-torsion fingerprint for a molecule as a bit
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/// vector
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/*!
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\param mol: the molecule to be fingerprinted
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\param nBits: number of bits to include in the fingerprint
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\param targetSize: the number of atoms to include in the "torsions"
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\param fromAtoms: if provided, only torsions that start or end at
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the specified atoms will be included in the
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fingerprint
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\param ignoreAtoms: if provided, any torsions that include
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the specified atoms will not be included in the
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fingerprint
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\param atomInvariants: a list of invariants to use for the atom hashes
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note: only the first \c codeSize bits of each
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invariant are used.
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\param nBitsPerEntry: number of bits to use in simulating counts
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\param includeChirality: if set, chirality will be used in the atom invariants
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(note: this is ignored if atomInvariants are
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provided)
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\return a pointer to the fingerprint. The client is
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responsible for calling delete on this.
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*/
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[[deprecated("please use TopologicalTorsionGenerator")]]
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RDKIT_FINGERPRINTS_EXPORT ExplicitBitVect *
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getHashedTopologicalTorsionFingerprintAsBitVect(
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const ROMol &mol, unsigned int nBits = 2048, unsigned int targetSize = 4,
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const std::vector<std::uint32_t> *fromAtoms = nullptr,
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const std::vector<std::uint32_t> *ignoreAtoms = nullptr,
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const std::vector<std::uint32_t> *atomInvariants = nullptr,
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unsigned int nBitsPerEntry = 4, bool includeChirality = false);
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} // namespace AtomPairs
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} // namespace RDKit
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#endif
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