MolHash.h
Go to the documentation of this file.
// $Id$
//
// Copyright (C) 2014 Novartis Institutes for BioMedical Research
//
// @@ 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.
//
#pragma once
#include <map>
#include <vector>
#include <string>
#include <stdexcept>
#include <boost/cstdint.hpp>
#include "../RDKitBase.h"
namespace RDKit
{
namespace MolHash
{
typedef boost::uint32_t HashCodeType;
HashCodeType generateMoleculeHashCode(const ROMol &mol,
const std::vector<unsigned> *atomsToUse=0,
const std::vector<unsigned> *bondsToUse=0, // ?? listed bonds between/to/from excluded atom(s) ??
const std::vector<boost::uint32_t> *atomCodes =0,
const std::vector<boost::uint32_t> *bondCodes =0);
enum CodeFlags // bitwise flags to combine and compute atom/bond codes
{
CF_NO_LABELS= 0x0000,
CF_ELEMENT = 0x0001,
CF_CHARGE = 0x0002,
CF_VALENCE = 0x0004,
CF_ISOTOPE = 0x0008,
CF_ATOM_CHIRALITY= 0x0010,
CF_ATOM_AROMATIC = 0x0020,
CF_ATOM_ALL = 0x00FF,
CF_BOND_ORDER = 0x0100, // ignore AROMATIZATION if corresponding flag is not specified
CF_BOND_AROMATIZATION = 0x0200,
CF_BOND_TYPE_EXACT = CF_BOND_ORDER | CF_BOND_AROMATIZATION, // exact type value with aromatic
CF_BOND_CHIRALITY = 0x0400, // include bond chirality information into bond code
CF_BOND_IN_RING = 0x0800,
CF_BOND_ALL = 0xFF00,
CF_ALL = 0xFFFF,
};
void fillAtomBondCodes(const ROMol &mol, boost::uint64_t flags // CodeFlags constants combination
, std::vector<boost::uint32_t> *atomCodes // NULL is allowed
, std::vector<boost::uint32_t> *bondCodes); // NULL is allowed
#pragma pack(push,1)
struct HashSet
{
boost::uint16_t Version;
boost::uint16_t Reserved;
boost::uint16_t NumAtoms;
boost::uint16_t NumBonds;
boost::uint32_t FormulaCRC32;
HashCodeType NonChiralAtomsHash;
HashCodeType NonChiralBondsHash;
HashCodeType ChiralAtomsHash;
HashCodeType ChiralBondsHash;
HashCodeType ChiralityHash;
public:
HashSet() { memset(this, 0, sizeof(*this));}
};
#pragma pack(pop)
void generateMoleculeHashSet(const ROMol &mol, HashSet& res,
const std::vector<unsigned> *atomsToUse=0,
const std::vector<unsigned> *bondsToUse=0);
std::string generateMoleculeHashSet(const ROMol &mol,
const std::vector<unsigned> *atomsToUse=0,
const std::vector<unsigned> *bondsToUse=0);
std::string encode(const void* bin, size_t size); // binary data to Base64 encoded string
}}
RDKit::MolHash::CF_BOND_IN_RING
Definition: MolHash.h:45
RDKit::MolHash::CF_NO_LABELS
Definition: MolHash.h:33
RDKit::MolHash::CF_ALL
Definition: MolHash.h:47
RDKit::MolHash::CF_BOND_ALL
Definition: MolHash.h:46
RDKit::MolHash::HashSet::NonChiralBondsHash
HashCodeType NonChiralBondsHash
Definition: MolHash.h:63
RDKit::MolHash::HashSet::ChiralBondsHash
HashCodeType ChiralBondsHash
Definition: MolHash.h:65
RDKit::MolHash::HashSet
Definition: MolHash.h:55
RDKit::MolHash::CF_ISOTOPE
Definition: MolHash.h:37
RDKit::MolHash::HashSet::NumBonds
boost::uint16_t NumBonds
Definition: MolHash.h:60
RDKit::MolHash::CF_BOND_CHIRALITY
Definition: MolHash.h:44
RDKit::MolHash::HashSet::FormulaCRC32
boost::uint32_t FormulaCRC32
Definition: MolHash.h:61
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:105
RDKit::MolHash::CF_ATOM_ALL
Definition: MolHash.h:40
RDKit::MolHash::HashSet::ChiralityHash
HashCodeType ChiralityHash
Definition: MolHash.h:66
RDKit::MolHash::HashSet::NonChiralAtomsHash
HashCodeType NonChiralAtomsHash
Definition: MolHash.h:62
RDKit::MolHash::CF_ATOM_CHIRALITY
Definition: MolHash.h:38
RDKit::MolHash::HashSet::HashSet
HashSet()
Definition: MolHash.h:68
RDKit::MolHash::HashSet::Reserved
boost::uint16_t Reserved
Definition: MolHash.h:58
RDKit::MolHash::generateMoleculeHashSet
void generateMoleculeHashSet(const ROMol &mol, HashSet &res, const std::vector< unsigned > *atomsToUse=0, const std::vector< unsigned > *bondsToUse=0)
RDKit::MolHash::HashSet::ChiralAtomsHash
HashCodeType ChiralAtomsHash
Definition: MolHash.h:64
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDKit::MolHash::CodeFlags
CodeFlags
Definition: MolHash.h:31
RDKit::MolHash::HashSet::NumAtoms
boost::uint16_t NumAtoms
Definition: MolHash.h:59
RDKit::MolHash::HashCodeType
boost::uint32_t HashCodeType
Definition: MolHash.h:23
RDKit::MolHash::generateMoleculeHashCode
HashCodeType generateMoleculeHashCode(const ROMol &mol, const std::vector< unsigned > *atomsToUse=0, const std::vector< unsigned > *bondsToUse=0, const std::vector< boost::uint32_t > *atomCodes=0, const std::vector< boost::uint32_t > *bondCodes=0)
RDKit::MolHash::CF_ATOM_AROMATIC
Definition: MolHash.h:39
RDKit::MolHash::fillAtomBondCodes
void fillAtomBondCodes(const ROMol &mol, boost::uint64_t flags, std::vector< boost::uint32_t > *atomCodes, std::vector< boost::uint32_t > *bondCodes)
RDKit::MolHash::CF_BOND_TYPE_EXACT
Definition: MolHash.h:43
RDKit::MolHash::CF_BOND_AROMATIZATION
Definition: MolHash.h:42
RDKit::MolHash::HashSet::Version
boost::uint16_t Version
Definition: MolHash.h:57
RDKit::MolHash::CF_CHARGE
Definition: MolHash.h:35
RDKit::MolHash::encode
std::string encode(const void *bin, size_t size)
RDKit::MolHash::CF_VALENCE
Definition: MolHash.h:36
RDKit::MolHash::CF_ELEMENT
Definition: MolHash.h:34
RDKit::MolHash::CF_BOND_ORDER
Definition: MolHash.h:41