RDKit
Open-source cheminformatics and machine learning.
Reaction.h
Go to the documentation of this file.
1//
2// Copyright (c) 2007-2021, Novartis Institutes for BioMedical Research Inc.
3// and other RDKit contributors
4//
5// All rights reserved.
6//
7// Redistribution and use in source and binary forms, with or without
8// modification, are permitted provided that the following conditions are
9// met:
10//
11// * Redistributions of source code must retain the above copyright
12// notice, this list of conditions and the following disclaimer.
13// * Redistributions in binary form must reproduce the above
14// copyright notice, this list of conditions and the following
15// disclaimer in the documentation and/or other materials provided
16// with the distribution.
17// * Neither the name of Novartis Institutes for BioMedical Research Inc.
18// nor the names of its contributors may be used to endorse or promote
19// products derived from this software without specific prior written
20// permission.
21//
22// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
23// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
24// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
25// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
26// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
27// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
28// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
29// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
30// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
31// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
32// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33//
34
35#include <RDGeneral/export.h>
36#ifndef RD_REACTION_H_17Aug2006
37#define RD_REACTION_H_17Aug2006
38
39#include <GraphMol/RDKitBase.h>
40#include <RDGeneral/RDProps.h>
42#include <vector>
43
44namespace RDKit {
45class ReactionPickler;
46
47//! used to indicate an error in the chemical reaction engine
49 : public std::exception {
50 public:
51 //! construct with an error message
52 explicit ChemicalReactionException(const char *msg) : _msg(msg) {}
53 //! construct with an error message
54 explicit ChemicalReactionException(const std::string msg) : _msg(msg) {}
55 //! get the error message
56 const char *what() const noexcept override { return _msg.c_str(); }
57 ~ChemicalReactionException() noexcept override = default;
58
59 private:
60 std::string _msg;
61};
62
63//! This is a class for storing and applying general chemical reactions.
64/*!
65 basic usage will be something like:
66
67 \verbatim
68 ChemicalReaction rxn;
69 rxn.addReactantTemplate(r1);
70 rxn.addReactantTemplate(r2);
71 rxn.addProductTemplate(p1);
72 rxn.initReactantMatchers();
73
74 MOL_SPTR_VECT prods;
75 for(MOL_SPTR_VECT::const_iterator r1It=reactantSet1.begin();
76 r1It!=reactantSet1.end();++r1It;){
77 for(MOL_SPTR_VECT::const_iterator r2It=reactantSet2.begin();
78 r2It!=reactantSet2.end();++r2It;){
79 MOL_SPTR_VECT rVect(2);
80 rVect[0] = *r1It;
81 rVect[1] = *r2It;
82
83 std::vector<MOL_SPTR_VECT> lprods;
84 lprods = rxn.runReactants(rVect);
85 for(std::vector<MOL_SPTR_VECT>::const_iterator lpIt=lprods.begin();
86 lpIt!=lprods.end();++lpIt){
87 // we know this is a single-product reaction:
88 prods.push_back((*lpIt)[0]);
89 }
90 }
91 }
92 \endverbatim
93
94 NOTES:
95 - to allow more control over the reaction, it is possible to flag reactant
96 atoms as being protected by setting the common_properties::_protected
97 property on those
98 atoms. Here's an example:
99 \verbatim
100 std::string smi="[O:1]>>[N:1]";
101 ChemicalReaction *rxn = RxnSmartsToChemicalReaction(smi);
102 rxn->initReactantMatchers();
103
104 MOL_SPTR_VECT reacts;
105 reacts.clear();
106 smi = "OCO";
107 ROMol *mol = SmilesToMol(smi);
108 reacts.push_back(ROMOL_SPTR(mol));
109 std::vector<MOL_SPTR_VECT> prods;
110 prods = rxn->runReactants(reacts);
111 // here prods has two entries, because there are two Os in the
112 // reactant.
113
114 reacts[0]->getAtomWithIdx(0)->setProp(common_properties::_protected,1);
115 prods = rxn->runReactants(reacts);
116 // here prods only has one entry, the reaction at atom 0
117 // has been blocked by the _protected property
118 \endverbatim
119
120*/
122 friend class ReactionPickler;
123
124 private:
125 void copy(const ChemicalReaction &other) {
126 RDProps::operator=(other);
127 df_needsInit = other.df_needsInit;
128 df_implicitProperties = other.df_implicitProperties;
129 m_reactantTemplates.clear();
130 m_reactantTemplates.reserve(other.m_reactantTemplates.size());
131 for (ROMOL_SPTR reactant_template : other.m_reactantTemplates) {
132 m_reactantTemplates.emplace_back(new RWMol(*reactant_template));
133 }
134 m_productTemplates.clear();
135 m_productTemplates.reserve(other.m_productTemplates.size());
136 for (ROMOL_SPTR product_template : other.m_productTemplates) {
137 m_productTemplates.emplace_back(new RWMol(*product_template));
138 }
139 m_agentTemplates.clear();
140 m_agentTemplates.reserve(other.m_agentTemplates.size());
141 for (ROMOL_SPTR agent_template : other.m_agentTemplates) {
142 m_agentTemplates.emplace_back(new RWMol(*agent_template));
143 }
144 }
145
146 public:
148 //! construct a reaction from a pickle string
149 ChemicalReaction(const std::string &binStr);
151 copy(other);
152 }
154 if (this != &other) {
155 copy(other);
156 }
157 return *this;
158 }
159
160 //! Adds a new reactant template
161 /*!
162 \return the number of reactants
163
164 */
165 unsigned int addReactantTemplate(ROMOL_SPTR mol) {
166 this->df_needsInit = true;
167 this->m_reactantTemplates.push_back(mol);
168 return rdcast<unsigned int>(this->m_reactantTemplates.size());
169 }
170
171 //! Adds a new agent template
172 /*!
173 \return the number of agent
174
175 */
176 unsigned int addAgentTemplate(ROMOL_SPTR mol) {
177 this->m_agentTemplates.push_back(mol);
178 return rdcast<unsigned int>(this->m_agentTemplates.size());
179 }
180
181 //! Adds a new product template
182 /*!
183 \return the number of products
184
185 */
186 unsigned int addProductTemplate(ROMOL_SPTR mol) {
187 this->m_productTemplates.push_back(mol);
188 return rdcast<unsigned int>(this->m_productTemplates.size());
189 }
190
191 //! Removes the reactant templates from a reaction if atom mapping ratio is
192 /// below a given threshold
193 /*! By default the removed reactant templates were attached to the agent
194 templates.
195 An alternative will be to provide a pointer to a molecule vector where
196 these reactants should be saved.
197 */
198 void removeUnmappedReactantTemplates(double thresholdUnmappedAtoms = 0.2,
199 bool moveToAgentTemplates = true,
200 MOL_SPTR_VECT *targetVector = nullptr);
201
202 //! Removes the product templates from a reaction if its atom mapping ratio is
203 /// below a given threshold
204 /*! By default the removed products templates were attached to the agent
205 templates.
206 An alternative will be to provide a pointer to a molecule vector where
207 these products should be saved.
208 */
209 void removeUnmappedProductTemplates(double thresholdUnmappedAtoms = 0.2,
210 bool moveToAgentTemplates = true,
211 MOL_SPTR_VECT *targetVector = nullptr);
212
213 /*! Removes the agent templates from a reaction if a pointer to a
214 molecule vector is provided the agents are stored therein.*/
215 void removeAgentTemplates(MOL_SPTR_VECT *targetVector = nullptr);
216
217 //! Runs the reaction on a set of reactants
218 /*!
219
220 \param reactants the reactants to be used. The length of this must be equal
221 to this->getNumReactantTemplates()
222 \param maxProducts: if non zero, the maximum number of products to generate
223 before stopping. If hit a warning will be generated.
224
225 \return a vector of vectors of products. Each subvector will be
226 this->getNumProductTemplates() long.
227
228 We return a vector of vectors of products because each individual template
229 may map multiple times onto its reactant. This leads to multiple possible
230 result sets.
231 */
232 std::vector<MOL_SPTR_VECT> runReactants(
233 const MOL_SPTR_VECT reactants, unsigned int numProducts = 1000) const;
234
235 //! Runs a single reactant against a single reactant template
236 /*!
237 \param reactant The single reactant to use
238
239 \param reactantTemplateIdx the reactant template to target in the reaction
240 */
241 std::vector<MOL_SPTR_VECT> runReactant(
242 ROMOL_SPTR reactant, unsigned int reactantTemplateIdx) const;
243
244 //! Runs a single reactant in place (the reactant is modified)
245 /*!
246 This is only useable with reactions which have a single reactant and product
247 and where no atoms are added in the product.
248
249 \param reactant The single reactant to use
250
251 \return whether or not the reactant was actually modified
252 */
253 bool runReactant(RWMol &reactant) const;
254
256 return this->m_reactantTemplates;
257 }
258 const MOL_SPTR_VECT &getAgents() const { return this->m_agentTemplates; }
259 const MOL_SPTR_VECT &getProducts() const { return this->m_productTemplates; }
260
261 MOL_SPTR_VECT::const_iterator beginReactantTemplates() const {
262 return this->m_reactantTemplates.begin();
263 }
264 MOL_SPTR_VECT::const_iterator endReactantTemplates() const {
265 return this->m_reactantTemplates.end();
266 }
267
268 MOL_SPTR_VECT::const_iterator beginProductTemplates() const {
269 return this->m_productTemplates.begin();
270 }
271 MOL_SPTR_VECT::const_iterator endProductTemplates() const {
272 return this->m_productTemplates.end();
273 }
274
275 MOL_SPTR_VECT::const_iterator beginAgentTemplates() const {
276 return this->m_agentTemplates.begin();
277 }
278 MOL_SPTR_VECT::const_iterator endAgentTemplates() const {
279 return this->m_agentTemplates.end();
280 }
281
282 MOL_SPTR_VECT::iterator beginReactantTemplates() {
283 return this->m_reactantTemplates.begin();
284 }
285 MOL_SPTR_VECT::iterator endReactantTemplates() {
286 return this->m_reactantTemplates.end();
287 }
288
289 MOL_SPTR_VECT::iterator beginProductTemplates() {
290 return this->m_productTemplates.begin();
291 }
292 MOL_SPTR_VECT::iterator endProductTemplates() {
293 return this->m_productTemplates.end();
294 }
295
296 MOL_SPTR_VECT::iterator beginAgentTemplates() {
297 return this->m_agentTemplates.begin();
298 }
299 MOL_SPTR_VECT::iterator endAgentTemplates() {
300 return this->m_agentTemplates.end();
301 }
302 unsigned int getNumReactantTemplates() const {
303 return rdcast<unsigned int>(this->m_reactantTemplates.size());
304 }
305 unsigned int getNumProductTemplates() const {
306 return rdcast<unsigned int>(this->m_productTemplates.size());
307 }
308 unsigned int getNumAgentTemplates() const {
309 return rdcast<unsigned int>(this->m_agentTemplates.size());
310 }
311
312 //! initializes our internal reactant-matching datastructures.
313 /*!
314 This must be called after adding reactants and before calling
315 runReactants.
316
317 \param silent: If this bool is true, no messages will be logged during the
318 validation. By default, validation problems are reported to the warning
319 and error logs depending on their severity.
320 */
321 void initReactantMatchers(bool silent = false);
322
323 bool isInitialized() const { return !df_needsInit; }
324
325 //! validates the reactants and products to make sure the reaction seems
326 /// "reasonable"
327 /*!
328 \return true if the reaction validates without errors (warnings do not
329 stop validation)
330
331 \param numWarnings used to return the number of validation warnings
332 \param numErrors used to return the number of validation errors
333
334 \param silent: If this bool is true, no messages will be logged during the
335 validation. By default, validation problems are reported to the warning
336 and error logs depending on their severity.
337
338 */
339 bool validate(unsigned int &numWarnings, unsigned int &numErrors,
340 bool silent = false) const;
341
342 //! returns whether or not the reaction uses implicit
343 //! properties on the product atoms
344 /*!
345
346 This toggles whether or not unspecified atomic properties in the
347 products are considered to be implicit and should be copied from
348 the actual reactants. This is necessary due to a semantic difference
349 between the "reaction SMARTS" approach and the MDL RXN
350 approach:
351 In "reaction SMARTS", this reaction:
352 [C:1]-[Br:2].[O-:3]>>[C:1]-[O:3].[Br-:2]
353 applied to [CH4+]Br should yield [CH4+]O
354 Something similar drawn in an rxn file, and applied to
355 [CH4+]Br should yield [CH3]O.
356 In rxn there is no charge on the product C because nothing is
357 specified in the rxn file; in "SMARTS" the charge from the
358 actual reactants is not *removed* because no charge is
359 specified in the reaction.
360
361 */
362 bool getImplicitPropertiesFlag() const { return df_implicitProperties; }
363 //! sets the implicit properties flag. See the documentation for
364 //! getImplicitProertiesFlag() for a discussion of what this means.
365 void setImplicitPropertiesFlag(bool val) { df_implicitProperties = val; }
366
367 private:
368 bool df_needsInit{true};
369 bool df_implicitProperties{false};
370 MOL_SPTR_VECT m_reactantTemplates, m_productTemplates, m_agentTemplates;
371};
372
373//! tests whether or not the molecule has a substructure match
374//! to the reaction's reactants
375//! the \c which argument is used to return which of the reactants
376//! the molecule matches.
378 const ChemicalReaction &rxn, const ROMol &mol,
379 std::vector<unsigned int> &which, bool stopAtFirstMatch = false);
380//! \overload
382 const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which);
383//! \overload
385 const ChemicalReaction &rxn, const ROMol &mol);
386
387//! tests whether or not the molecule has a substructure match
388//! to the reaction's products
389//! the \c which argument is used to return which of the products
390//! the molecule matches.
392 const ChemicalReaction &rxn, const ROMol &mol,
393 std::vector<unsigned int> &which, bool stopAtFirstMatch = false);
394//! \overload
396 const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which);
397//! \overload
399 const ChemicalReaction &rxn, const ROMol &mol);
400
401//! tests whether or not the molecule has a substructure match
402//! to any of the reaction's agents
403//! the \c which argument is used to return which of the agents
404//! the molecule matches. If there's no match, it is equal to the number
405//! of agents on return
407 const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which);
408//! \overload
410 const ChemicalReaction &rxn, const ROMol &mol);
411
412//! returns indices of the atoms in each reactant that are changed
413//! in the reaction
414/*!
415 \param rxn the reaction we are interested in
416
417 \param mappedAtomsOnly if set, atoms that are not mapped will not be included
418 in the list of changed atoms (otherwise they are automatically included)
419
420 How are changed atoms recognized?
421 1) Atoms whose degree changes
422 2) Atoms whose bonding pattern changes
423 3) unmapped atoms (unless the mappedAtomsOnly flag is set)
424 4) Atoms connected to unmapped atoms
425 5) Atoms whose atomic number changes (unless the
426 corresponding product atom is a dummy)
427 6) Atoms with more than one atomic number query (unless the
428 corresponding product atom is a dummy)
429
430 Note that the atomic number of a query atom depends on how it's constructed.
431 When coming from SMARTS: if the first query is an atomic label/number that
432 sets the atomic number, otherwise it's zero.
433 For example [O;$(OC)] is atomic number 8 while [$(OC);O] is atomic
434 number 0.
435 When coming from RXN: the atomic number of the atom in the rxn file sets
436 the value.
437 */
439getReactingAtoms(const ChemicalReaction &rxn, bool mappedAtomsOnly = false);
440
441//! add the recursive queries to the reactants of a reaction
442/*!
443 This does its work using RDKit::addRecursiveQueries()
444
445 \param rxn the reaction we are interested in
446 \param queries - the dictionary of named queries to add
447 \param propName - the atom property to use to get query names
448 optional:
449 \param reactantLabels - to store pairs of (atom index, query string)
450 per reactant
451
452 NOTES:
453 - existing query information, if present, will be supplemented (AND logic)
454 - non-query atoms will be replaced with query atoms using only the query
455 logic
456 - query names can be present as comma separated lists, they will then
457 be combined using OR logic.
458 - throws a KeyErrorException if a particular query name is not present
459 in \c queries
460
461 */
463 ChemicalReaction &rxn, const std::map<std::string, ROMOL_SPTR> &queries,
464 const std::string &propName,
465 std::vector<std::vector<std::pair<unsigned int, std::string>>>
466 *reactantLabels = nullptr);
467
468} // namespace RDKit
469
470namespace RDDepict {
471//! \brief Generate 2D coordinates (a depiction) for a reaction
472/*!
473
474 \param rxn the reaction we are interested in
475
476 \param spacing the spacing between components of the reaction
477
478 \param updateProps if set, properties such as conjugation and
479 hybridization will be calculated for the reactant and product
480 templates before generating coordinates. This should result in
481 better depictions, but can lead to errors in some cases.
482
483 \param canonOrient canonicalize the orientation so that the long
484 axes align with the x-axis etc.
485
486 \param nFlipsPerSample - the number of rotatable bonds that are
487 flipped at random for each sample
488
489 \param nSamples - the number of samples
490
491 \param sampleSeed - seed for the random sampling process
492
493 \param permuteDeg4Nodes - try permuting the drawing order of bonds around
494 atoms with four neighbors in order to improve the depiction
495
496 for the other parameters see the documentation for compute2DCoords()
497
498*/
500 RDKit::ChemicalReaction &rxn, double spacing = 2.0, bool updateProps = true,
501 bool canonOrient = false, unsigned int nFlipsPerSample = 0,
502 unsigned int nSamples = 0, int sampleSeed = 0,
503 bool permuteDeg4Nodes = false);
504
505} // namespace RDDepict
506
507#endif
pulls in the core RDKit functionality
used to indicate an error in the chemical reaction engine
Definition: Reaction.h:49
const char * what() const noexcept override
get the error message
Definition: Reaction.h:56
ChemicalReactionException(const char *msg)
construct with an error message
Definition: Reaction.h:52
ChemicalReactionException(const std::string msg)
construct with an error message
Definition: Reaction.h:54
~ChemicalReactionException() noexcept override=default
This is a class for storing and applying general chemical reactions.
Definition: Reaction.h:121
unsigned int addProductTemplate(ROMOL_SPTR mol)
Adds a new product template.
Definition: Reaction.h:186
unsigned int addAgentTemplate(ROMOL_SPTR mol)
Adds a new agent template.
Definition: Reaction.h:176
unsigned int addReactantTemplate(ROMOL_SPTR mol)
Adds a new reactant template.
Definition: Reaction.h:165
unsigned int getNumAgentTemplates() const
Definition: Reaction.h:308
bool getImplicitPropertiesFlag() const
Definition: Reaction.h:362
unsigned int getNumReactantTemplates() const
Definition: Reaction.h:302
ChemicalReaction & operator=(const ChemicalReaction &other)
Definition: Reaction.h:153
ChemicalReaction(const std::string &binStr)
construct a reaction from a pickle string
MOL_SPTR_VECT::iterator beginProductTemplates()
Definition: Reaction.h:289
void removeUnmappedReactantTemplates(double thresholdUnmappedAtoms=0.2, bool moveToAgentTemplates=true, MOL_SPTR_VECT *targetVector=nullptr)
MOL_SPTR_VECT::const_iterator beginProductTemplates() const
Definition: Reaction.h:268
void initReactantMatchers(bool silent=false)
initializes our internal reactant-matching datastructures.
std::vector< MOL_SPTR_VECT > runReactants(const MOL_SPTR_VECT reactants, unsigned int numProducts=1000) const
Runs the reaction on a set of reactants.
const MOL_SPTR_VECT & getReactants() const
Definition: Reaction.h:255
MOL_SPTR_VECT::const_iterator endReactantTemplates() const
Definition: Reaction.h:264
void setImplicitPropertiesFlag(bool val)
Definition: Reaction.h:365
const MOL_SPTR_VECT & getAgents() const
Definition: Reaction.h:258
MOL_SPTR_VECT::iterator endProductTemplates()
Definition: Reaction.h:292
bool runReactant(RWMol &reactant) const
Runs a single reactant in place (the reactant is modified)
unsigned int getNumProductTemplates() const
Definition: Reaction.h:305
MOL_SPTR_VECT::const_iterator endProductTemplates() const
Definition: Reaction.h:271
bool isInitialized() const
Definition: Reaction.h:323
ChemicalReaction(const ChemicalReaction &other)
Definition: Reaction.h:150
MOL_SPTR_VECT::const_iterator beginAgentTemplates() const
Definition: Reaction.h:275
void removeAgentTemplates(MOL_SPTR_VECT *targetVector=nullptr)
std::vector< MOL_SPTR_VECT > runReactant(ROMOL_SPTR reactant, unsigned int reactantTemplateIdx) const
Runs a single reactant against a single reactant template.
MOL_SPTR_VECT::const_iterator beginReactantTemplates() const
Definition: Reaction.h:261
const MOL_SPTR_VECT & getProducts() const
Definition: Reaction.h:259
MOL_SPTR_VECT::iterator beginReactantTemplates()
Definition: Reaction.h:282
MOL_SPTR_VECT::iterator endAgentTemplates()
Definition: Reaction.h:299
MOL_SPTR_VECT::iterator beginAgentTemplates()
Definition: Reaction.h:296
MOL_SPTR_VECT::iterator endReactantTemplates()
Definition: Reaction.h:285
void removeUnmappedProductTemplates(double thresholdUnmappedAtoms=0.2, bool moveToAgentTemplates=true, MOL_SPTR_VECT *targetVector=nullptr)
MOL_SPTR_VECT::const_iterator endAgentTemplates() const
Definition: Reaction.h:278
bool validate(unsigned int &numWarnings, unsigned int &numErrors, bool silent=false) const
RDProps & operator=(const RDProps &rhs)
Definition: RDProps.h:24
RWMol is a molecule class that is intended to be edited.
Definition: RWMol.h:32
handles pickling (serializing) reactions
#define RDKIT_CHEMREACTIONS_EXPORT
Definition: export.h:49
RDKIT_CHEMREACTIONS_EXPORT void compute2DCoordsForReaction(RDKit::ChemicalReaction &rxn, double spacing=2.0, bool updateProps=true, bool canonOrient=false, unsigned int nFlipsPerSample=0, unsigned int nSamples=0, int sampleSeed=0, bool permuteDeg4Nodes=false)
Generate 2D coordinates (a depiction) for a reaction.
Std stuff.
Definition: Abbreviations.h:19
std::vector< INT_VECT > VECT_INT_VECT
Definition: types.h:292
RDKIT_CHEMREACTIONS_EXPORT bool isMoleculeAgentOfReaction(const ChemicalReaction &rxn, const ROMol &mol, unsigned int &which)
RDKIT_CHEMREACTIONS_EXPORT bool isMoleculeReactantOfReaction(const ChemicalReaction &rxn, const ROMol &mol, std::vector< unsigned int > &which, bool stopAtFirstMatch=false)
RDKIT_CHEMREACTIONS_EXPORT VECT_INT_VECT getReactingAtoms(const ChemicalReaction &rxn, bool mappedAtomsOnly=false)
RDKIT_CHEMREACTIONS_EXPORT bool isMoleculeProductOfReaction(const ChemicalReaction &rxn, const ROMol &mol, std::vector< unsigned int > &which, bool stopAtFirstMatch=false)
boost::shared_ptr< ROMol > ROMOL_SPTR
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
Definition: FragCatParams.h:21
RDKIT_CHEMREACTIONS_EXPORT void addRecursiveQueriesToReaction(ChemicalReaction &rxn, const std::map< std::string, ROMOL_SPTR > &queries, const std::string &propName, std::vector< std::vector< std::pair< unsigned int, std::string > > > *reactantLabels=nullptr)
add the recursive queries to the reactants of a reaction