molecularSimilarity.h

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// ----------------------------------------------------
// $Maintainer: Marcel Schumann $
// $Authors: Marcel Schumann $
// ----------------------------------------------------

// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

#ifndef BALL_STRUCTURE_MOLECULARSIMILARITY_H
#define BALL_STRUCTURE_MOLECULARSIMILARITY_H

#ifndef BALL_COMMON_H
#       include <BALL/common.h>
#endif

#include <BALL/STRUCTURE/smartsMatcher.h>
#include <BALL/KERNEL/system.h>

#ifdef BALL_HAS_OPENEYE
  #include <oechem/mol.h>
#elif defined BALL_HAS_OPENBABEL
  #include <openbabel/mol.h>
#endif


namespace BALL
{
  class BALL_EXPORT MolecularSimilarity
  {
    public:

      MolecularSimilarity(String smarts_file);

      void generateFingerprints(System& molecules, vector<vector<Size> >& fingerprints);

      void generateFingerprints(const list<Molecule*>& molecules, vector<vector<Size> >& fingerprints);

      void generateFingerprint(Molecule& molecule, vector<Size>& fingerprint);


      #ifdef BALL_HAS_OPENEYE
        static OEChem::OEMol* createOEMol(const Molecule& mol, bool ignore_hydrogen=0);

        void generateCanSmile(const Molecule& molecule, String& cansmile, OEChem::OEMol** output_oemol=0, bool ignore_hydrogen=0);

        void generateFingerprint(OEChem::OEMol& mol, vector<Size>& fingerprint);
      #elif defined BALL_HAS_OPENBABEL

        static OpenBabel::OBMol* createOBMol(const Molecule& mol, bool ignore_hydrogen=0, bool suppress_warning=0);

        static Molecule* createMolecule(OpenBabel::OBMol& obmol, bool ignore_hydrogen=0);

        void generateCanSmile(const Molecule& mol, String& cansmile, OpenBabel::OBMol** output_obmol=0, bool ignore_hydrogen=0);

        void generateFingerprint(OpenBabel::OBMol& mol, vector<Size>& fingerprint);
      #endif

      #if (defined BALL_HAS_OPENEYE | defined BALL_HAS_OPENBABEL)

        void matchSmarts(const String& usmile, const String& smarts, Size& no_matches, Size max_matches=0);
      #endif

      void generatePathFingerprint(Molecule& mol, vector<bool>& fingerprint);

      float calculateSimilarity(vector<bool>& fingerprint1, vector<bool>& fingerprint2);

      void filterRedundantMolecules(const list<Molecule*>& molecules, float similarity_threshold);

      void filterRedundantMolecules(System& molecules, float similarity_threshold);

      float calculateSimilarity(vector<Size>& fingerprint1, vector<Size>& fingerprint2, vector<float>* stddev);

      const vector<String>& getFunctionalGroupNames();


    protected:

      vector<vector<Size> > fingerprints_;
      vector<String> smarts_;
      vector<String> smart_names_;

      SmartsMatcher matcher_;

      void generatePathHash_(vector<Size>& path, Size& hash);

      bool generatePathFingerprint_(const Atom* atom, std::vector<Size>& path, std::set<const Bond*>& path_bonds, 
                                    std::vector<bool>& fingerprint);

  };
}

#endif