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5861d503e5
* Add filters to hits. * Add safeSetattr to Python wrapper. * Fix chiral centres filter. * Defaults of -1 for int max filters. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
99 lines
3.4 KiB
C++
99 lines
3.4 KiB
C++
//
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// Copyright (C) David Cosgrove 2024.
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#ifndef RDKIT_REAGENT_H
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#define RDKIT_REAGENT_H
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#include <string>
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#include <RDGeneral/export.h>
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namespace RDKit {
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class Atom;
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class ROMol;
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class RWMol;
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namespace SynthonSpaceSearch {
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// These are the numbers of bits used in the internal fingerprints.
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// The user is not restricted to these numbers for the search.
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inline constexpr unsigned int PATT_FP_NUM_BITS = 1024;
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// This class holds a Synthon that will be part of a SynthonSet.
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class RDKIT_SYNTHONSPACESEARCH_EXPORT Synthon {
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public:
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Synthon() = default;
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Synthon(const std::string &smi);
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Synthon(const Synthon &other);
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Synthon(Synthon &&other) = default;
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Synthon &operator=(const Synthon &other);
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Synthon &operator=(Synthon &&other) = default;
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const std::string &getSmiles() const { return d_smiles; }
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const std::unique_ptr<ROMol> &getOrigMol() const;
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const std::unique_ptr<ROMol> &getSearchMol() const;
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const std::unique_ptr<ExplicitBitVect> &getPattFP() const;
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const std::unique_ptr<ExplicitBitVect> &getFP() const;
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const std::vector<std::shared_ptr<ROMol>> &getConnRegions() const;
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void setSearchMol(std::unique_ptr<ROMol> mol);
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void setFP(std::unique_ptr<ExplicitBitVect> fp);
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unsigned int getNumDummies() const { return d_numDummies; }
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unsigned int getNumHeavyAtoms() const { return d_numHeavyAtoms; }
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unsigned int getNumChiralAtoms() const { return d_numChiralAtoms; }
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unsigned int getNumChiralAtomsExcDummies() const {
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return d_numChiralAtomsExcDummies;
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}
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double getMolWt() const { return d_molWt; }
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// Writes to/reads from a binary stream.
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void writeToDBStream(std::ostream &os) const;
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void readFromDBStream(std::istream &is, std::uint32_t version);
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private:
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std::string d_smiles;
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// Keep 2 copies of the molecule. The first is as passed in, which
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// will be used for building products. The second will have its
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// atoms and bonds fiddled with to make them match the product (the
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// aliphatic precursor to aromatic product issue). The search mol
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// doesn't always work with product building.
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std::unique_ptr<ROMol> dp_origMol{nullptr};
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std::unique_ptr<ROMol> dp_searchMol{nullptr};
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// The pattern fingerprint, used for substructure search screening.
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std::unique_ptr<ExplicitBitVect> dp_pattFP{nullptr};
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// The fingerprint of the dp_searchMol, used in fingerprint similarity
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// searching. Its type is known by the SynthonSpace that holds the
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// Synthon.
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std::unique_ptr<ExplicitBitVect> dp_FP{nullptr};
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// SMILES strings of any connector regions. Normally there will only
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// be 1 or 2. These are derived from the search mol.
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std::vector<std::shared_ptr<ROMol>> d_connRegions;
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unsigned int d_numDummies{0};
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unsigned int d_numHeavyAtoms{0};
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// As calculated by details::countChiralAtoms().
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unsigned int d_numChiralAtoms{0};
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// This is the number of chiral atoms excluding those that have 2 or
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// more dummies attached.
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unsigned int d_numChiralAtomsExcDummies{0};
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double d_molWt{0.0};
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// Once the search molecule has been added, get the connector regions,
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// connector fingerprint etc.
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void finishInitialization();
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// Calculate the number of dummy atoms etc.
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void calcProperties();
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};
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} // namespace SynthonSpaceSearch
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} // namespace RDKit
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#endif // RDKIT_REAGENT_H
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