FilterCatalog.h

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//  Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
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#ifndef _RD_FILTER_CATALOG_PARAMS_
#define _RD_FILTER_CATALOG_PARAMS_

#include <Catalogs/Catalog.h>
#include <Catalogs/CatalogParams.h>
#include "FilterCatalogEntry.h"

namespace RDKit {
class FilterCatalog;
class FilterCatalogParams : public RDCatalog::CatalogParams {
 public:
  enum FilterCatalogs {
    PAINS_A = (1u << 1),
    PAINS_B = (1u << 2),
    PAINS_C = (1u << 3),
    PAINS = PAINS_A | PAINS_B | PAINS_C,

    BRENK = (1u << 4),
    NIH = (1u << 5),
    ZINC = (1u << 6),

    ALL = PAINS | BRENK | NIH | ZINC
  };

  FilterCatalogParams() : RDCatalog::CatalogParams() {
    setTypeStr("Filter Catalog Parameters");
  }

  FilterCatalogParams(FilterCatalogs catalogs) : RDCatalog::CatalogParams() {
    setTypeStr("Filter Catalog Parameters");
    addCatalog(catalogs);
  }

  FilterCatalogParams(const FilterCatalogParams &other)
      : RDCatalog::CatalogParams(other), d_catalogs(other.d_catalogs) {}

  virtual ~FilterCatalogParams() {}

  //------------------------------------
  //! Adds an existing FilterCatalog specification to be used in the
  // FilterCatalog
  //
  /*!
    Specifies an existing filter catalog to be used.

      \param catalogs One of the enumerated known FilterCatalogs
    */
  virtual bool addCatalog(FilterCatalogs catalogs);

  //------------------------------------
  //! Returns the existing list of FilterCatalogs to be used.
  const std::vector<FilterCatalogs> &getCatalogs() const { return d_catalogs; }
  //! Fill a catalog with the appropriate entries
  virtual void fillCatalog(FilterCatalog &catalog);

  //! serializes (pickles) to a stream
  virtual void toStream(std::ostream &ss) const;
  //! returns a string with a serialized (pickled) representation
  virtual std::string Serialize() const;
  //! initializes from a stream pickle
  virtual void initFromStream(std::istream &ss);
  //! initializes from a string pickle
  virtual void initFromString(const std::string &text);

 private:
  std::vector<FilterCatalogs> d_catalogs;

#ifdef RDK_USE_BOOST_SERIALIZATION
  friend class boost::serialization::access;
  template <class Archive>
  void serialize(Archive &ar, const unsigned int version) {
    RDUNUSED_PARAM(version);
    ar &d_catalogs;
  }
#endif
};

typedef RDCatalog::Catalog<FilterCatalogEntry, FilterCatalogParams> FCatalog;
class FilterCatalog : public FCatalog {
 public:
  // syntactic sugar for getMatch(es) return values.
  typedef boost::shared_ptr<FilterCatalogEntry> SENTRY;

#if BOOST_VERSION / 100000 >= 1 && (BOOST_VERSION / 100 % 1000) > 44
#define BOOST_PYTHON_SUPPORT_SHARED_CONST
#endif

#ifdef BOOST_PYTHON_SUPPORT_SHARED_CONST
  // If boost::python can support shared_ptr of const objects
  //  we can enable support for this feature
  typedef boost::shared_ptr<const entryType_t> CONST_SENTRY;
#else
  typedef boost::shared_ptr<entryType_t> CONST_SENTRY;
#endif

  FilterCatalog() : FCatalog(), d_entries() {}

  FilterCatalog(FilterCatalogParams::FilterCatalogs catalogs)
      : FCatalog(), d_entries() {
    setCatalogParams(new paramType_t(catalogs));
  }

  FilterCatalog(const FilterCatalogParams &params) : FCatalog(), d_entries() {
    setCatalogParams(new paramType_t(params));
  }

  FilterCatalog(const FilterCatalog &rhs)
      : FCatalog(rhs), d_entries(rhs.d_entries) {}

  FilterCatalog(const std::string &binStr);

  ~FilterCatalog();

  virtual std::string Serialize() const;

  // Adds a new FilterCatalogEntry to the catalog
  /*!
    Adds a new FilterCatalogEntry to the catalog  The catalog
    owns the entry

    \param entry          The FilterCatalogEntry to add.
    \param updateFPLength unused in the FilterCatalog object.
  */

  virtual unsigned int addEntry(FilterCatalogEntry *entry,
                                bool updateFPLength = true);

  // Adds a new FilterCatalogEntry to the catalog
  /*!
    Adds a new FilterCatalogEntry to the catalog  The catalog
    owns the entry

    \param entry          The shared_ptr of the FilterCatalogEntry to add.
    \param updateFPLength unused in the FilterCatalog object.
  */

  virtual unsigned int addEntry(SENTRY entry, bool updateFPLength = true);

  // Removes a FilterCatalogEntry to the catalog by description
  /*!
    Removes a FilterCatalogEntry from the catalog.

    \param idx          The FilterCatalogEntry index for the entry to remove.
     n.b. removing an entry may change the indicies of other entries.
          To safely remove entries, remove entries with the highest idx
           first.
  */
  bool removeEntry(unsigned int idx);
  bool removeEntry(CONST_SENTRY entry);

  //------------------------------------
  //! returns a particular FilterCatalogEntry in the Catalog
  //!  required by Catalog.h API
  virtual const FilterCatalogEntry *getEntryWithIdx(unsigned int idx) const;

  //------------------------------------
  //! returns a particular FilterCatalogEntry in the Catalog
  //!  memory safe version of getEntryWithIdx
  CONST_SENTRY getEntry(unsigned int idx) const;

  //------------------------------------
  //! returns the idx of the given entry, UINT_MAX if not found.

  unsigned int getIdxForEntry(const FilterCatalogEntry *entry) const;
  unsigned int getIdxForEntry(CONST_SENTRY entry) const;

  //------------------------------------
  //! returns the number of entries in the catalog
  virtual unsigned int getNumEntries() const { return d_entries.size(); }

  //------------------------------------
  //! Reset the current catalog to match the specified FilterCatalogParameters
  /*
    \param params  The new FilterCatalogParams specifying the new state of the
    catalog
  */
  virtual void setCatalogParams(FilterCatalogParams *params);

  //------------------------------------
  //! Returns true if the molecule matches any entry in the catalog
  /*
    \param mol  ROMol to match against the catalog
  */
  bool hasMatch(const ROMol &mol) const;

  //------------------------------------
  //! Returns the first match against the catalog
  /*
    \param mol  ROMol to match against the catalog
  */
  CONST_SENTRY getFirstMatch(const ROMol &mol) const;

  //------------------------------------
  //! Returns all matches to the molecule
  /*
    \param mol  ROMol to match against the catalog
  */
  const std::vector<CONST_SENTRY> getMatches(const ROMol &mol) const;

 private:
  void Clear();
  std::vector<SENTRY> d_entries;
};

bool FilterCatalogCanSerialize();
}

#endif