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108 lines
3.5 KiB
C++
108 lines
3.5 KiB
C++
//
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// Copyright (C) 2018-2021 Susan H. Leung and other RDKit contributors
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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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#include <RDGeneral/export.h>
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#ifndef RD_FRAGMENT_REMOVER_H
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#define RD_FRAGMENT_REMOVER_H
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#include <Catalogs/Catalog.h>
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#include <GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h>
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#include <GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h>
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#include <GraphMol/MolStandardize/MolStandardize.h>
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namespace RDKit {
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class ROMol;
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namespace MolStandardize {
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RDKIT_MOLSTANDARDIZE_EXPORT extern const CleanupParameters
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defaultCleanupParameters;
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typedef RDCatalog::HierarchCatalog<FragmentCatalogEntry, FragmentCatalogParams,
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int>
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FragmentCatalog;
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class RDKIT_MOLSTANDARDIZE_EXPORT FragmentRemover {
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public:
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FragmentRemover();
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FragmentRemover(const std::string fragmentFile, bool leave_last,
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bool skip_if_all_match = false);
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FragmentRemover(std::istream &fragmentStream, bool leave_last,
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bool skip_if_all_match = false);
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FragmentRemover(const std::vector<std::pair<std::string, std::string>> &data,
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bool leave_last, bool skip_if_all_match = false);
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~FragmentRemover();
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//! making FragmentRemover objects non-copyable
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FragmentRemover(const FragmentRemover &other) = delete;
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FragmentRemover &operator=(FragmentRemover const &) = delete;
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ROMol *remove(const ROMol &mol);
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void removeInPlace(RWMol &mol);
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private:
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// Setting leave_last to True will ensure at least one fragment
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// is left in the molecule, even if it is matched by a
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// FragmentPattern
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bool LEAVE_LAST;
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// If set, this causes the original molecule to be returned
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// if every fragment in it matches the salt list
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bool SKIP_IF_ALL_MATCH;
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FragmentCatalog *d_fcat;
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}; // class FragmentRemover
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// caller owns the returned pointer
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inline FragmentRemover *fragmentRemoverFromParams(
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const CleanupParameters ¶ms, bool leave_last = true,
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bool skip_if_all_match = false) {
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if (params.fragmentData.empty()) {
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return new FragmentRemover(params.fragmentFile, leave_last,
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skip_if_all_match);
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} else {
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return new FragmentRemover(params.fragmentData, leave_last,
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skip_if_all_match);
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}
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}
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class RDKIT_MOLSTANDARDIZE_EXPORT LargestFragmentChooser {
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public:
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// LargestFragmentChooser() {}
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LargestFragmentChooser(bool preferOrganic = false)
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: preferOrganic(preferOrganic) {}
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LargestFragmentChooser(const CleanupParameters ¶ms)
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: preferOrganic(params.preferOrganic),
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useAtomCount(params.largestFragmentChooserUseAtomCount),
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countHeavyAtomsOnly(params.largestFragmentChooserCountHeavyAtomsOnly) {}
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LargestFragmentChooser(const LargestFragmentChooser &other);
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~LargestFragmentChooser() = default;
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ROMol *choose(const ROMol &mol) const;
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void chooseInPlace(RWMol &mol) const;
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struct Largest {
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Largest();
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Largest(std::string &smiles, boost::shared_ptr<ROMol> fragment,
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unsigned int &numatoms, double &weight, bool &organic);
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std::string Smiles;
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boost::shared_ptr<ROMol> Fragment;
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unsigned int NumAtoms{0};
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double Weight{0};
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bool Organic{false};
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};
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private:
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bool preferOrganic;
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bool useAtomCount{true};
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bool countHeavyAtomsOnly{false};
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}; // class LargestFragmentChooser
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} // namespace MolStandardize
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} // namespace RDKit
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#endif
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