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Synthon.h
Go to the documentation of this file.
//
// Copyright (C) David Cosgrove 2024.
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#ifndef RDKIT_REAGENT_H
#define RDKIT_REAGENT_H
#include <string>
#include <RDGeneral/export.h>
namespace RDKit {
class Atom;
class ROMol;
class RWMol;
namespace SynthonSpaceSearch {
// This class holds a Synthon that will be part of a SynthonSet.
class RDKIT_SYNTHONSPACESEARCH_EXPORT Synthon {
public:
Synthon() = default;
Synthon(const std::string &smi, const std::string &id);
Synthon(const Synthon &other);
Synthon(Synthon &&other) = default;
Synthon &operator=(const Synthon &other);
Synthon &operator=(Synthon &&other) = default;
const std::string &getSmiles() const { return d_smiles; }
const std::string &getId() const { return d_id; }
const std::unique_ptr<ROMol> &getOrigMol() const;
const std::unique_ptr<ROMol> &getSearchMol() const;
const std::unique_ptr<ExplicitBitVect> &getPattFP() const;
const std::vector<std::shared_ptr<ROMol>> &getConnRegions() const;
void setSearchMol(std::unique_ptr<RWMol> mol);
// Writes to/reads from a binary stream.
void writeToDBStream(std::ostream &os) const;
void readFromDBStream(std::istream &is);
// Tag each atom and bond with the given molecule number and its index,
// so we can find them again in a product if necessary.
void tagAtomsAndBonds(int molNum) const;
private:
std::string d_smiles;
std::string d_id;
// Keep 2 copies of the molecule. The first is as passed in, which
// will be used for building products. The second will have its
// atoms and bonds fiddled with to make them match the product (the
// aliphatic precursor to aromatic product issue). The search mol
// doesn't always work with product building.
std::unique_ptr<ROMol> dp_origMol{nullptr};
std::unique_ptr<ROMol> dp_searchMol{nullptr};
std::unique_ptr<ExplicitBitVect> dp_pattFP{nullptr};
// SMILES strings of any connector regions. Normally there will only
// be 1 or 2. These are derived from the search mol.
std::vector<std::shared_ptr<ROMol>> d_connRegions;
// One the search molecule has been added, get the connector regions,
// connector fingerprint etc.
void finishInitialization();
};
// Return a molecule containing the portions of the molecule starting at
// each dummy atom and going out up to 3 bonds. There may be more than
// 1 fragment if there are dummy atoms more than 3 bonds apart, and there
// may be fragments with more than 1 dummy atom if their fragments fall
// within 3 bonds of each other. E.g. the molecule [1*]CN(C[2*])Cc1ccccc1
// will give [1*]CN(C)C[1*]. The 2 dummy atoms are 4 bonds apart, but the
// fragments overlap. All dummy atoms given isotope 1 whatever they had before.
RDKIT_SYNTHONSPACESEARCH_EXPORT std::unique_ptr<ROMol> getConnRegion(
const ROMol &mol);
} // namespace SynthonSpaceSearch
} // namespace RDKit
#endif // RDKIT_REAGENT_H
RDKit::ROMol
Definition ROMol.h:199
RDKit::SynthonSpaceSearch::Synthon
Definition Synthon.h:26
RDKit::SynthonSpaceSearch::Synthon::setSearchMol
void setSearchMol(std::unique_ptr< RWMol > mol)
RDKit::SynthonSpaceSearch::Synthon::writeToDBStream
void writeToDBStream(std::ostream &os) const
RDKit::SynthonSpaceSearch::Synthon::operator=
Synthon & operator=(const Synthon &other)
RDKit::SynthonSpaceSearch::Synthon::getPattFP
const std::unique_ptr< ExplicitBitVect > & getPattFP() const
RDKit::SynthonSpaceSearch::Synthon::getId
const std::string & getId() const
Definition Synthon.h:36
RDKit::SynthonSpaceSearch::Synthon::Synthon
Synthon(const Synthon &other)
RDKit::SynthonSpaceSearch::Synthon::getSearchMol
const std::unique_ptr< ROMol > & getSearchMol() const
RDKit::SynthonSpaceSearch::Synthon::getOrigMol
const std::unique_ptr< ROMol > & getOrigMol() const
RDKit::SynthonSpaceSearch::Synthon::operator=
Synthon & operator=(Synthon &&other)=default
RDKit::SynthonSpaceSearch::Synthon::Synthon
Synthon(Synthon &&other)=default
RDKit::SynthonSpaceSearch::Synthon::getSmiles
const std::string & getSmiles() const
Definition Synthon.h:35
RDKit::SynthonSpaceSearch::Synthon::Synthon
Synthon(const std::string &smi, const std::string &id)
RDKit::SynthonSpaceSearch::Synthon::tagAtomsAndBonds
void tagAtomsAndBonds(int molNum) const
RDKit::SynthonSpaceSearch::Synthon::getConnRegions
const std::vector< std::shared_ptr< ROMol > > & getConnRegions() const
RDKit::SynthonSpaceSearch::Synthon::Synthon
Synthon()=default
RDKit::SynthonSpaceSearch::Synthon::readFromDBStream
void readFromDBStream(std::istream &is)
export.h
RDKIT_SYNTHONSPACESEARCH_EXPORT
#define RDKIT_SYNTHONSPACESEARCH_EXPORT
Definition export.h:545
RDKit::SynthonSpaceSearch::getConnRegion
RDKIT_SYNTHONSPACESEARCH_EXPORT std::unique_ptr< ROMol > getConnRegion(const ROMol &mol)
RDKit
Std stuff.
Definition Abbreviations.h:19