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//
// Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#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);
//! 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);
}
} // end of RDKit namespace
#endif
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