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// $Id$
//
// 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.
//
#include <RDGeneral/export.h>
#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;
RDKIT_MOLHASH_EXPORT 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,
};
RDKIT_MOLHASH_EXPORT 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 RDKIT_MOLHASH_EXPORT 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)
RDKIT_MOLHASH_EXPORT void generateMoleculeHashSet(const ROMol &mol, HashSet &res,
const std::vector<unsigned> *atomsToUse = 0,
const std::vector<unsigned> *bondsToUse = 0);
RDKIT_MOLHASH_EXPORT std::string generateMoleculeHashSet(
const ROMol &mol, const std::vector<unsigned> *atomsToUse = 0,
const std::vector<unsigned> *bondsToUse = 0);
RDKIT_MOLHASH_EXPORT std::string encode(const void *bin,
size_t size); // binary data to Base64 encoded string
}
}
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