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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 {
// These are the numbers of bits used in the internal fingerprints.
// The user is not restricted to these numbers for the search.
inline constexpr unsigned int PATT_FP_NUM_BITS = 1024;
// 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);
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::unique_ptr<ROMol> &getOrigMol() const;
const std::unique_ptr<ROMol> &getSearchMol() const;
const std::unique_ptr<ExplicitBitVect> &getPattFP() const;
const std::unique_ptr<ExplicitBitVect> &getFP() const;
const std::vector<std::shared_ptr<ROMol>> &getConnRegions() const;
void setSearchMol(std::unique_ptr<ROMol> mol);
void setFP(std::unique_ptr<ExplicitBitVect> fp);
unsigned int getNumDummies() const { return d_numDummies; }
unsigned int getNumHeavyAtoms() const { return d_numHeavyAtoms; }
unsigned int getNumChiralAtoms() const { return d_numChiralAtoms; }
unsigned int getNumChiralAtomsExcDummies() const {
return d_numChiralAtomsExcDummies;
}
double getMolWt() const { return d_molWt; }
// Writes to/reads from a binary stream.
void writeToDBStream(std::ostream &os) const;
void readFromDBStream(std::istream &is, std::uint32_t version);
private:
std::string d_smiles;
// 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};
// The pattern fingerprint, used for substructure search screening.
std::unique_ptr<ExplicitBitVect> dp_pattFP{nullptr};
// The fingerprint of the dp_searchMol, used in fingerprint similarity
// searching. Its type is known by the SynthonSpace that holds the
// Synthon.
std::unique_ptr<ExplicitBitVect> dp_FP{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;
unsigned int d_numDummies{0};
unsigned int d_numHeavyAtoms{0};
// As calculated by details::countChiralAtoms().
unsigned int d_numChiralAtoms{0};
// This is the number of chiral atoms excluding those that have 2 or
// more dummies attached.
unsigned int d_numChiralAtomsExcDummies{0};
double d_molWt{0.0};
// Once the search molecule has been added, get the connector regions,
// connector fingerprint etc.
void finishInitialization();
// Calculate the number of dummy atoms etc.
void calcProperties();
};
} // namespace SynthonSpaceSearch
} // namespace RDKit
#endif // RDKIT_REAGENT_H
RDKit::Atom
The class for representing atoms.
Definition Atom.h:74
RDKit::ROMol
Definition ROMol.h:319
RDKit::RWMol
RWMol is a molecule class that is intended to be edited.
Definition RWMol.h:32
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::getMolWt
double getMolWt() const
Definition Synthon.h:53
RDKit::SynthonSpaceSearch::Synthon::Synthon
Synthon(const Synthon &other)
RDKit::SynthonSpaceSearch::Synthon::getFP
const std::unique_ptr< ExplicitBitVect > & getFP() const
RDKit::SynthonSpaceSearch::Synthon::getNumHeavyAtoms
unsigned int getNumHeavyAtoms() const
Definition Synthon.h:48
RDKit::SynthonSpaceSearch::Synthon::getSearchMol
const std::unique_ptr< ROMol > & getSearchMol() const
RDKit::SynthonSpaceSearch::Synthon::readFromDBStream
void readFromDBStream(std::istream &is, std::uint32_t version)
RDKit::SynthonSpaceSearch::Synthon::Synthon
Synthon(const std::string &smi)
RDKit::SynthonSpaceSearch::Synthon::getNumChiralAtomsExcDummies
unsigned int getNumChiralAtomsExcDummies() const
Definition Synthon.h:50
RDKit::SynthonSpaceSearch::Synthon::getNumDummies
unsigned int getNumDummies() const
Definition Synthon.h:47
RDKit::SynthonSpaceSearch::Synthon::getOrigMol
const std::unique_ptr< ROMol > & getOrigMol() const
RDKit::SynthonSpaceSearch::Synthon::getNumChiralAtoms
unsigned int getNumChiralAtoms() const
Definition Synthon.h:49
RDKit::SynthonSpaceSearch::Synthon::setFP
void setFP(std::unique_ptr< ExplicitBitVect > fp)
RDKit::SynthonSpaceSearch::Synthon::setSearchMol
void setSearchMol(std::unique_ptr< ROMol > mol)
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:39
RDKit::SynthonSpaceSearch::Synthon::getConnRegions
const std::vector< std::shared_ptr< ROMol > > & getConnRegions() const
RDKit::SynthonSpaceSearch::Synthon::Synthon
Synthon()=default
export.h
RDKIT_SYNTHONSPACESEARCH_EXPORT
#define RDKIT_SYNTHONSPACESEARCH_EXPORT
Definition export.h:585
RDKit::SynthonSpaceSearch
Definition MemoryMappedFileReader.h:19
RDKit::SynthonSpaceSearch::PATT_FP_NUM_BITS
constexpr unsigned int PATT_FP_NUM_BITS
Definition Synthon.h:27
RDKit
Std stuff.
Definition Abbreviations.h:19