RDKit: SanitizeRxn.h Source File

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SanitizeRxn.h
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1//
2// Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
3// All rights reserved.
4//
5// Redistribution and use in source and binary forms, with or without
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32#include <RDGeneral/export.h>
33#ifndef RDKIT_SANITIZERXN_H
34#define RDKIT_SANITIZERXN_H
35
36#include "Reaction.h"
37#include <GraphMol/MolOps.h>
38#include <string>
39#include <exception>
40#include <utility>
41
42namespace RDKit {
43
44//! class for flagging sanitization errors
45 class RDKIT_CHEMREACTIONS_EXPORT RxnSanitizeException : public std::exception {
46 public:
47 RxnSanitizeException(const char *msg) : _msg(msg) {}
48 RxnSanitizeException(std::string msg) : _msg(std::move(msg)) {}
49 const char *what() const noexcept override { return _msg.c_str(); }
50 ~RxnSanitizeException() noexcept override = default;
51
52 private:
53 std::string _msg;
54};
55
56namespace RxnOps {
57//! Any dummy atom with a map but no RGroup label, should be an RGroup
58//! in RDKit's view of a reaction.
59//! See if these atoms can be salvaged into RGroups.
60 RDKIT_CHEMREACTIONS_EXPORT void fixRGroups(ChemicalReaction &rxn);
61
62//! If atom maps are not defined on rgroups, attempt to deduce them from the
63//! RGroup
64//! labels, or add new ones if possible.
65 RDKIT_CHEMREACTIONS_EXPORT void fixAtomMaps(ChemicalReaction &rxn);
66
67//! Adjusts the reactant templates to properly match reagents
68 RDKIT_CHEMREACTIONS_EXPORT void adjustTemplates(
69 const MOL_SPTR_VECT &templates,
70 const MolOps::AdjustQueryParameters &params);
71
72//! merge query Hs if appropriate
73 RDKIT_CHEMREACTIONS_EXPORT void fixHs(ChemicalReaction &rxn);
74
75// Default adjustment parameters for matching reagents
76 inline const MolOps::AdjustQueryParameters DefaultRxnAdjustParams() {
77 MolOps::AdjustQueryParameters params;
78 params.adjustDegree = false;
79 params.adjustDegreeFlags = MolOps::ADJUST_IGNOREALL;
80 params.adjustRingCount = false;
81 params.adjustRingCountFlags = MolOps::ADJUST_IGNOREALL;
82 params.makeDummiesQueries = false;
83 params.aromatizeIfPossible = true;
84 return params;
85}
86
87// Default adjustment parameters for ChemDraw style matching of reagents
88// -- deprecated - renamed MatchOnlyAtRgroupsAdjustParams
89// -- this doesn't match sciquest style searching
90 inline const MolOps::AdjustQueryParameters ChemDrawRxnAdjustParams() {
91 BOOST_LOG(rdWarningLog)
92 << " deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead"
93 << std::endl;
94 MolOps::AdjustQueryParameters params;
95 params.adjustDegree = true;
96 params.adjustDegreeFlags = MolOps::ADJUST_IGNOREDUMMIES;
97 params.adjustRingCount = false;
98 params.adjustRingCountFlags = MolOps::ADJUST_IGNORENONE;
99 params.makeDummiesQueries = false;
100 params.aromatizeIfPossible = true;
101 return params;
102}
103
104 inline const MolOps::AdjustQueryParameters MatchOnlyAtRgroupsAdjustParams() {
105 MolOps::AdjustQueryParameters params;
106 params.adjustDegree = true;
107 params.adjustDegreeFlags = MolOps::ADJUST_IGNOREDUMMIES;
108 params.adjustRingCount = false;
109 params.adjustRingCountFlags = MolOps::ADJUST_IGNORENONE;
110 params.makeDummiesQueries = false;
111 params.aromatizeIfPossible = true;
112 return params;
113}
114
115 typedef enum {
116 SANITIZE_NONE = 0x0,
117 SANITIZE_RGROUP_NAMES = 0x1,
118 SANITIZE_ATOM_MAPS = 0x2,
119 SANITIZE_ADJUST_REACTANTS = 0x4,
120 SANITIZE_MERGEHS = 0x8,
121 SANITIZE_ADJUST_PRODUCTS = 0x10,
122 SANITIZE_ALL = 0xFFFFFFFF
123} SanitizeRxnFlags;
124
125//! \brief carries out a collection of tasks for cleaning up a reaction and
126/// ensuring
127//! that it makes "chemical sense" in the context of RDKit reacitons
128/*!
129 This functions calls the following in sequence
130 -# RxnOps::fixRGroups()
131 -# RxnOps::fixupAtomMaps()
132 -# RxnOps::fixupTemplateAromaticity()
133 -# RxnOps::mergeHs()
134
135 \param rxn : the ChemicalReaction to be cleaned
136
137 \param operationThatFailed : the first (if any) sanitization operation that
138 fails is set here.
139 The values are taken from the \c SanitizeFlags
140 enum.
141 On success, the value is \c
142 SanitizeFlags::SANITIZE_NONE
143
144 \param sanitizeOps : the bits here are used to set which sanitization
145 operations are carried
146 out. The elements of the \c SanitizeFlags enum define
147 the operations.
148
149 <b>Notes:</b>
150 - This attempts to fix known issues with certain reaction drawers.
151 HOWEVER, if any flag is returned in operationsPerformed,
152 the reaction may still be suspect to its validity.
153 - Aromaticity can be tricky when starting with Kekule structures that
154 have query features, aromaticity works well for non-query rings, however
155 certain structures (substitutions on Kekule rings that should really be
156 aromatic) may not have enough information.
157*/
158
159 RDKIT_CHEMREACTIONS_EXPORT void sanitizeRxn(
160 ChemicalReaction &rxn, unsigned int &operationsThatFailed,
161 unsigned int sanitizeOps = SANITIZE_ALL,
162 const MolOps::AdjustQueryParameters &params = DefaultRxnAdjustParams());
163//! \overload
164 RDKIT_CHEMREACTIONS_EXPORT void sanitizeRxn(
165 ChemicalReaction &rxn,
166 const MolOps::AdjustQueryParameters &params = DefaultRxnAdjustParams());
167
168//! Does the usual molecular sanitization on each reactant, agent, and product
169/// of the reaction
170 RDKIT_CHEMREACTIONS_EXPORT void sanitizeRxnAsMols(
171 ChemicalReaction &rxn,
172 unsigned int sanitizeOps = MolOps::SanitizeFlags::SANITIZE_ALL);
173
174} // namespace RxnOps
175} // namespace RDKit
176
177#endif
MolOps.h
BOOST_LOG
#define BOOST_LOG(__arg__)
Definition RDLog.h:109
rdWarningLog
RDKIT_RDGENERAL_EXPORT RDLogger rdWarningLog
Reaction.h
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition Reaction.h:121
RDKit::RxnSanitizeException::what
const char * what() const noexcept override
Definition SanitizeRxn.h:49
RDKit::RxnSanitizeException::RxnSanitizeException
RxnSanitizeException(std::string msg)
Definition SanitizeRxn.h:48
RDKit::RxnSanitizeException::~RxnSanitizeException
~RxnSanitizeException() noexcept override=default
RDKit::RxnSanitizeException::RxnSanitizeException
RxnSanitizeException(const char *msg)
Definition SanitizeRxn.h:47
export.h
RDKIT_CHEMREACTIONS_EXPORT
#define RDKIT_CHEMREACTIONS_EXPORT
Definition export.h:57
RDKit::MolOps::ADJUST_IGNORENONE
@ ADJUST_IGNORENONE
Definition MolOps.h:399
RDKit::MolOps::ADJUST_IGNOREDUMMIES
@ ADJUST_IGNOREDUMMIES
Definition MolOps.h:402
RDKit::MolOps::ADJUST_IGNOREALL
@ ADJUST_IGNOREALL
Definition MolOps.h:405
RDKit::RxnOps
Definition SanitizeRxn.h:56
RDKit::RxnOps::fixAtomMaps
RDKIT_CHEMREACTIONS_EXPORT void fixAtomMaps(ChemicalReaction &rxn)
RDKit::RxnOps::DefaultRxnAdjustParams
const MolOps::AdjustQueryParameters DefaultRxnAdjustParams()
Definition SanitizeRxn.h:76
RDKit::RxnOps::ChemDrawRxnAdjustParams
const MolOps::AdjustQueryParameters ChemDrawRxnAdjustParams()
Definition SanitizeRxn.h:90
RDKit::RxnOps::sanitizeRxnAsMols
RDKIT_CHEMREACTIONS_EXPORT void sanitizeRxnAsMols(ChemicalReaction &rxn, unsigned int sanitizeOps=MolOps::SanitizeFlags::SANITIZE_ALL)
RDKit::RxnOps::MatchOnlyAtRgroupsAdjustParams
const MolOps::AdjustQueryParameters MatchOnlyAtRgroupsAdjustParams()
Definition SanitizeRxn.h:104
RDKit::RxnOps::SANITIZE_ADJUST_REACTANTS
@ SANITIZE_ADJUST_REACTANTS
Definition SanitizeRxn.h:119
RDKit::RxnOps::SANITIZE_MERGEHS
@ SANITIZE_MERGEHS
Definition SanitizeRxn.h:120
RDKit::RxnOps::SANITIZE_ALL
@ SANITIZE_ALL
Definition SanitizeRxn.h:122
RDKit::RxnOps::SANITIZE_ATOM_MAPS
@ SANITIZE_ATOM_MAPS
Definition SanitizeRxn.h:118
RDKit::RxnOps::SANITIZE_ADJUST_PRODUCTS
@ SANITIZE_ADJUST_PRODUCTS
Definition SanitizeRxn.h:121
RDKit::RxnOps::SANITIZE_NONE
@ SANITIZE_NONE
Definition SanitizeRxn.h:116
RDKit::RxnOps::SANITIZE_RGROUP_NAMES
@ SANITIZE_RGROUP_NAMES
Definition SanitizeRxn.h:117
RDKit::RxnOps::sanitizeRxn
RDKIT_CHEMREACTIONS_EXPORT void sanitizeRxn(ChemicalReaction &rxn, unsigned int &operationsThatFailed, unsigned int sanitizeOps=SANITIZE_ALL, const MolOps::AdjustQueryParameters &params=DefaultRxnAdjustParams())
carries out a collection of tasks for cleaning up a reaction and ensuring that it makes "chemical sen...
RDKit::RxnOps::adjustTemplates
RDKIT_CHEMREACTIONS_EXPORT void adjustTemplates(const MOL_SPTR_VECT &templates, const MolOps::AdjustQueryParameters &params)
Adjusts the reactant templates to properly match reagents.
RDKit::RxnOps::fixRGroups
RDKIT_CHEMREACTIONS_EXPORT void fixRGroups(ChemicalReaction &rxn)
RDKit::RxnOps::fixHs
RDKIT_CHEMREACTIONS_EXPORT void fixHs(ChemicalReaction &rxn)
merge query Hs if appropriate
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::MOL_SPTR_VECT
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
Definition FragCatParams.h:21
RDKit::MolOps::AdjustQueryParameters
Parameters controlling the behavior of MolOps::adjustQueryProperties.
Definition MolOps.h:417
RDKit::MolOps::AdjustQueryParameters::adjustDegreeFlags
std::uint32_t adjustDegreeFlags
Definition MolOps.h:419
RDKit::MolOps::AdjustQueryParameters::makeDummiesQueries
bool makeDummiesQueries
Definition MolOps.h:425
RDKit::MolOps::AdjustQueryParameters::adjustRingCountFlags
std::uint32_t adjustRingCountFlags
Definition MolOps.h:422
RDKit::MolOps::AdjustQueryParameters::adjustDegree
bool adjustDegree
Definition MolOps.h:418
RDKit::MolOps::AdjustQueryParameters::aromatizeIfPossible
bool aromatizeIfPossible
Definition MolOps.h:428
RDKit::MolOps::AdjustQueryParameters::adjustRingCount
bool adjustRingCount
Definition MolOps.h:421