RDKit: ReactionRunner.h Source File

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ReactionRunner.h
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1 //
2 // Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
3 // All rights reserved.
4 //
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12 // copyright notice, this list of conditions and the following
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16 // nor the names of its contributors may be used to endorse or promote
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32
33 #ifndef RD_REACTION_RUNNER_H
34 #define RD_REACTION_RUNNER_H
35
36 #include <GraphMol/ChemReactions/Reaction.h>
37 #include <GraphMol/ROMol.h>
38
39 namespace RDKit {
40 //! Runs the reaction on a set of reactants
41 /*!
42 \param rxn: the template reaction we are interested
43 \param reactants: the reactants to be used. The length of this must be equal
44 to
45 rxn->getNumReactantTemplates()
46 Caution: The order of the reactant templates determines the
47 order of the reactants!
48
49 \return a vector of vectors of products. Each subvector will be
50 rxn->getNumProductTemplates() long.
51
52 We return a vector of vectors of products because each individual template may
53 map multiple times onto its reactant. This leads to multiple possible result
54 sets.
55 */
56 std::vector<MOL_SPTR_VECT> run_Reactants(const ChemicalReaction& rxn,
57 const MOL_SPTR_VECT& reactants);
58
59 //! Runs a single reactant against a single reactant template
60 /*!
61 \param reactant The single reactant to use
62
63 \param reactantTemplateIdx the reactant template to target in the reaction
64
65 \return a vector of vectors of products. Each subvector will be
66 rxn->getNumProductTemplates() long.
67
68 We return a vector of vectors of products because each individual template may
69 map multiple times onto its reactant. This leads to multiple possible result
70 sets.
71
72 */
73
74 std::vector<MOL_SPTR_VECT> run_Reactant(const ChemicalReaction& rxn,
75 const ROMOL_SPTR& reactant,
76 unsigned int reactantIdx);
77
78 //! Reduce the product generated by run_Reactants or run_Reactant to
79 // the sidechains that come from the reagents
80 //
81 // n.b. molecules that might be a product of the given reaction
82 // but were not generated by run_Reactant(s) currently
83 // produce no sidechains.
84 /*!
85 \param addDummyAtoms If true, add dummy atoms to the sidechains for the
86 non-reagent parts of the sidechain. Dummy atoms are annotated with
87 the atom maps from the reaction.
88 If False, then any sidechain atom where a bond was cleaved is annotated with:
89 _rgroupAtomMaps property which indicates the scaffold atommaps that where bonded
90 _rgroupBonds property which indicates the bondtype for each atommap bonded
91 */
92
93 ROMol* reduceProductToSideChains(const ROMOL_SPTR& product,
94 bool addDummyAtoms = true);
95
96 namespace ReactionRunnerUtils {
97 MOL_SPTR_VECT generateOneProductSet(
98 const ChemicalReaction &rxn, const MOL_SPTR_VECT &reactants,
99 const std::vector<MatchVectType> &reactantsMatch);
100
101 RWMOL_SPTR convertTemplateToMol(const ROMOL_SPTR prodTemplateSptr);
102 }
103
104 } // end of RDKit namespace
105
106 #endif
RDKit::ReactionRunnerUtils::convertTemplateToMol
RWMOL_SPTR convertTemplateToMol(const ROMOL_SPTR prodTemplateSptr)
ROMol.h
Defines the primary molecule class ROMol as well as associated typedefs.
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition: Reaction.h:116
RDKit::MOL_SPTR_VECT
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
Definition: FragCatParams.h:19
RDKit::reduceProductToSideChains
ROMol * reduceProductToSideChains(const ROMOL_SPTR &product, bool addDummyAtoms=true)
Reduce the product generated by run_Reactants or run_Reactant to.
RDKit::ROMOL_SPTR
boost::shared_ptr< ROMol > ROMOL_SPTR
Definition: ChemTransforms.h:21
RDKit
Std stuff.
Definition: Atom.h:29
RDKit::run_Reactants
std::vector< MOL_SPTR_VECT > run_Reactants(const ChemicalReaction &rxn, const MOL_SPTR_VECT &reactants)
Runs the reaction on a set of reactants.
RDKit::RWMOL_SPTR
boost::shared_ptr< RWMol > RWMOL_SPTR
Definition: RWMol.h:241
Reaction.h
RDKit::run_Reactant
std::vector< MOL_SPTR_VECT > run_Reactant(const ChemicalReaction &rxn, const ROMOL_SPTR &reactant, unsigned int reactantIdx)
Runs a single reactant against a single reactant template.
RDKit::ReactionRunnerUtils::generateOneProductSet
MOL_SPTR_VECT generateOneProductSet(const ChemicalReaction &rxn, const MOL_SPTR_VECT &reactants, const std::vector< MatchVectType > &reactantsMatch)