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ReactionRunner.h
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//
// Copyright (c) 2014-2021, Novartis Institutes for BioMedical Research Inc.
// and other RDKit contributors
//
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#include <RDGeneral/export.h>
#ifndef RD_REACTION_RUNNER_H
#define RD_REACTION_RUNNER_H
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ROMol.h>
namespace RDKit {
//! Runs the reaction on a set of reactants
/*!
\param rxn: the template reaction we are interested
\param reactants: the reactants to be used. The length of this must be equal
to
rxn->getNumReactantTemplates()
Caution: The order of the reactant templates determines the
order of the reactants!
\param maxProducts: if non zero, the maximum number of products to generate
before stopping. If hit a warning will be generated.
\return a vector of vectors of products. Each subvector will be
rxn->getNumProductTemplates() long.
We return a vector of vectors of products because each individual template may
map multiple times onto its reactant. This leads to multiple possible result
sets.
*/
RDKIT_CHEMREACTIONS_EXPORT std::vector<MOL_SPTR_VECT> run_Reactants(
const ChemicalReaction &rxn, const MOL_SPTR_VECT &reactants,
unsigned int maxProducts = 1000);
//! Runs a single reactant against a single reactant template
/*!
\param reactant The single reactant to use
\param reactantTemplateIdx the reactant template to target in the reaction
\return a vector of vectors of products. Each subvector will be
rxn->getNumProductTemplates() long.
We return a vector of vectors of products because each individual template may
map multiple times onto its reactant. This leads to multiple possible result
sets.
*/
RDKIT_CHEMREACTIONS_EXPORT std::vector<MOL_SPTR_VECT> run_Reactant(
const ChemicalReaction &rxn, const ROMOL_SPTR &reactant,
unsigned int reactantIdx);
RDKIT_CHEMREACTIONS_EXPORT bool run_Reactant(const ChemicalReaction &rxn,
RWMol &reactant,
bool removeUnmatchedAtoms = true);
//! Reduce the product generated by run_Reactants or run_Reactant to
/// the sidechains that come from the reagents
//
// n.b. molecules that might be a product of the given reaction
// but were not generated by run_Reactant(s) currently
// produce no sidechains.
/*!
\param addDummyAtoms If true, add dummy atoms to the sidechains for the
non-reagent parts of the sidechain. Dummy atoms are annotated with
the atom maps from the reaction.
If False, then any sidechain atom where a bond was cleaved is annotated
with: _rgroupAtomMaps property which indicates the scaffold atommaps that
where bonded _rgroupBonds property which indicates the bondtype for each
atommap bonded
*/
RDKIT_CHEMREACTIONS_EXPORT ROMol *reduceProductToSideChains(
const ROMOL_SPTR &product, bool addDummyAtoms = true);
namespace ReactionRunnerUtils {
RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT generateOneProductSet(
const ChemicalReaction &rxn, const MOL_SPTR_VECT &reactants,
const std::vector<MatchVectType> &reactantsMatch);
RDKIT_CHEMREACTIONS_EXPORT RWMOL_SPTR
convertTemplateToMol(const ROMOL_SPTR prodTemplateSptr);
} // namespace ReactionRunnerUtils
} // namespace RDKit
#endif
ROMol.h
Defines the primary molecule class ROMol as well as associated typedefs.
Reaction.h
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition Reaction.h:122
RDKit::ROMol
Definition ROMol.h:285
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition RWMol.h:32
export.h
RDKIT_CHEMREACTIONS_EXPORT
#define RDKIT_CHEMREACTIONS_EXPORT
Definition export.h:57
RDKit::ReactionRunnerUtils
Definition ReactionRunner.h:106
RDKit::ReactionRunnerUtils::generateOneProductSet
RDKIT_CHEMREACTIONS_EXPORT MOL_SPTR_VECT generateOneProductSet(const ChemicalReaction &rxn, const MOL_SPTR_VECT &reactants, const std::vector< MatchVectType > &reactantsMatch)
RDKit::ReactionRunnerUtils::convertTemplateToMol
RDKIT_CHEMREACTIONS_EXPORT RWMOL_SPTR convertTemplateToMol(const ROMOL_SPTR prodTemplateSptr)
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::run_Reactants
RDKIT_CHEMREACTIONS_EXPORT std::vector< MOL_SPTR_VECT > run_Reactants(const ChemicalReaction &rxn, const MOL_SPTR_VECT &reactants, unsigned int maxProducts=1000)
Runs the reaction on a set of reactants.
RDKit::ROMOL_SPTR
boost::shared_ptr< ROMol > ROMOL_SPTR
Definition ChemTransforms.h:23
RDKit::run_Reactant
RDKIT_CHEMREACTIONS_EXPORT 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::reduceProductToSideChains
RDKIT_CHEMREACTIONS_EXPORT ROMol * reduceProductToSideChains(const ROMOL_SPTR &product, bool addDummyAtoms=true)
RDKit::MOL_SPTR_VECT
std::vector< boost::shared_ptr< ROMol > > MOL_SPTR_VECT
Definition FragCatParams.h:21
RDKit::RWMOL_SPTR
boost::shared_ptr< RWMol > RWMOL_SPTR
Definition RWMol.h:222