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https://github.com/rdkit/rdkit.git
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5dfd67a22a
* copy in, get building, add some basic tests * complete the testing Except for regiosiomers, which do not work * regioisomers work now * backup commit; things work * remove last of NM macros from hashfunctions.cpp * remove last of NM macros from hashfunctions.cpp * remove dependency on the abstraction layer * typo * start using namespaces clang-format * switch to using enums for the HashFunctions and StripTypes * Add initial python wrapper (and tests) * move the new hashing code to the MolHash library still may want to revise the naming of this * Setup deprecation of the older hashing code * better release notes text * change in response to review
96 lines
3.1 KiB
C++
96 lines
3.1 KiB
C++
//
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// Copyright (C) 2014 Novartis Institutes for BioMedical Research
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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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#include <RDGeneral/export.h>
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#pragma once
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#include <map>
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#include <vector>
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#include <string>
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#include <stdexcept>
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#include <cstdint>
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#include "../RDKitBase.h"
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#include "nmmolhash.h"
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namespace RDKit {
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namespace MolHash {
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typedef std::uint32_t HashCodeType;
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// \deprecated This function will go away in a future release.
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// please use the MolHash() function instead
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RDKIT_MOLHASH_EXPORT HashCodeType generateMoleculeHashCode(
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const ROMol &mol, const std::vector<unsigned> *atomsToUse = 0,
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const std::vector<unsigned> *bondsToUse =
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0, // ?? listed bonds between/to/from excluded atom(s) ??
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const std::vector<std::uint32_t> *atomCodes = 0,
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const std::vector<std::uint32_t> *bondCodes = 0);
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enum CodeFlags // bitwise flags to combine and compute atom/bond codes
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{ CF_NO_LABELS = 0x0000,
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CF_ELEMENT = 0x0001,
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CF_CHARGE = 0x0002,
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CF_VALENCE = 0x0004,
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CF_ISOTOPE = 0x0008,
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CF_ATOM_CHIRALITY = 0x0010,
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CF_ATOM_AROMATIC = 0x0020,
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CF_ATOM_ALL = 0x00FF,
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CF_BOND_ORDER =
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0x0100, // ignore AROMATIZATION if corresponding flag is not specified
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CF_BOND_AROMATIZATION = 0x0200,
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CF_BOND_TYPE_EXACT =
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CF_BOND_ORDER | CF_BOND_AROMATIZATION, // exact type value with aromatic
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CF_BOND_CHIRALITY =
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0x0400, // include bond chirality information into bond code
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CF_BOND_IN_RING = 0x0800,
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CF_BOND_ALL = 0xFF00,
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CF_ALL = 0xFFFF,
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};
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// \deprecated This function will go away in a future release.
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RDKIT_MOLHASH_EXPORT void fillAtomBondCodes(
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const ROMol &mol, boost::uint64_t flags // CodeFlags constants combination
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,
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std::vector<std::uint32_t> *atomCodes // NULL is allowed
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,
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std::vector<std::uint32_t> *bondCodes); // NULL is allowed
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#pragma pack(push, 1)
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struct RDKIT_MOLHASH_EXPORT HashSet {
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std::uint16_t Version;
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std::uint16_t Reserved;
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std::uint16_t NumAtoms;
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std::uint16_t NumBonds;
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std::uint32_t FormulaCRC32;
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HashCodeType NonChiralAtomsHash;
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HashCodeType NonChiralBondsHash;
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HashCodeType ChiralAtomsHash;
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HashCodeType ChiralBondsHash;
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HashCodeType ChiralityHash;
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public:
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HashSet() { memset(this, 0, sizeof(*this)); }
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};
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#pragma pack(pop)
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// \deprecated This function will go away in a future release.
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RDKIT_MOLHASH_EXPORT void generateMoleculeHashSet(
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const ROMol &mol, HashSet &res, const std::vector<unsigned> *atomsToUse = 0,
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const std::vector<unsigned> *bondsToUse = 0);
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// \deprecated This function will go away in a future release.
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RDKIT_MOLHASH_EXPORT std::string generateMoleculeHashSet(
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const ROMol &mol, const std::vector<unsigned> *atomsToUse = 0,
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const std::vector<unsigned> *bondsToUse = 0);
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// \deprecated This function will go away in a future release.
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RDKIT_MOLHASH_EXPORT std::string encode(
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const void *bin,
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size_t size); // binary data to Base64 encoded string
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} // namespace MolHash
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} // namespace RDKit
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