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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.
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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
45class 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.
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.
66
67//! Adjusts the reactant templates to properly match reagents
69 const MOL_SPTR_VECT &templates,
70 const MolOps::AdjustQueryParameters &params);
71
72//! merge query Hs if appropriate
74
75// Default adjustment parameters for matching reagents
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
92 << " deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead"
93 << std::endl;
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
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
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
160 ChemicalReaction &rxn, unsigned int &operationsThatFailed,
161 unsigned int sanitizeOps = SANITIZE_ALL,
163//! \overload
165 ChemicalReaction &rxn,
167
168//! Does the usual molecular sanitization on each reactant, agent, and product
169/// of the reaction
171 ChemicalReaction &rxn,
172 unsigned int sanitizeOps = MolOps::SanitizeFlags::SANITIZE_ALL);
173
174} // namespace RxnOps
175} // namespace RDKit
176
177#endif
#define BOOST_LOG(__arg__)
Definition RDLog.h:110
RDKIT_RDGENERAL_EXPORT RDLogger rdWarningLog
This is a class for storing and applying general chemical reactions.
Definition Reaction.h:121
class for flagging sanitization errors
Definition SanitizeRxn.h:45
const char * what() const noexcept override
Definition SanitizeRxn.h:49
RxnSanitizeException(std::string msg)
Definition SanitizeRxn.h:48
~RxnSanitizeException() noexcept override=default
RxnSanitizeException(const char *msg)
Definition SanitizeRxn.h:47
#define RDKIT_CHEMREACTIONS_EXPORT
Definition export.h:49
RDKIT_CHEMREACTIONS_EXPORT void fixAtomMaps(ChemicalReaction &rxn)
const MolOps::AdjustQueryParameters DefaultRxnAdjustParams()
Definition SanitizeRxn.h:76
const MolOps::AdjustQueryParameters ChemDrawRxnAdjustParams()
Definition SanitizeRxn.h:90
RDKIT_CHEMREACTIONS_EXPORT void sanitizeRxnAsMols(ChemicalReaction &rxn, unsigned int sanitizeOps=MolOps::SanitizeFlags::SANITIZE_ALL)
const MolOps::AdjustQueryParameters MatchOnlyAtRgroupsAdjustParams()
@ SANITIZE_ADJUST_REACTANTS
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_CHEMREACTIONS_EXPORT void adjustTemplates(const MOL_SPTR_VECT &templates, const MolOps::AdjustQueryParameters &params)
Adjusts the reactant templates to properly match reagents.
RDKIT_CHEMREACTIONS_EXPORT void fixRGroups(ChemicalReaction &rxn)
RDKIT_CHEMREACTIONS_EXPORT void fixHs(ChemicalReaction &rxn)
merge query Hs if appropriate
Std stuff.
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
Parameters controlling the behavior of MolOps::adjustQueryProperties.
Definition MolOps.h:344