molDB.h

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// ----------------------------------------------------
// $Maintainer: Marcel Schumann $
// $Authors: Marcel Schumann, Marc Röttig $
// ----------------------------------------------------

#ifndef MOLDB_H
#define MOLDB_H

#include <QtSql/QtSql>
#include <BALL/COMMON/exception.h>
#include <BALL/KERNEL/bond.h>
#include <BALL/KERNEL/atom.h>
#include <BALL/KERNEL/molecule.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/DATATYPE/string.h>

#include <BALL/KERNEL/forEach.h>
#include <BALL/DOCKING/COMMON/result.h>
#include <set>
#include <BALL/STRUCTURE/molecularSimilarity.h>

#if defined BALL_HAS_OPENBABEL || defined BALL_HAS_OPENEYE
  #include <BALL/STRUCTURE/logP.h>
  #ifdef BALL_HAS_OPENEYE
    #include <oechem/graphmol.h>
  #endif
#endif


namespace BALL
{
    class BALL_EXPORT MolDB
    {
      public:

        struct VendorInfo
        {
          String database_compound_ID;
          String vendor_name;
          String vendors_compound_ID;
          double molecular_weight;
        };

        // static function for creating a new database
        static void createNewDatabase(String& host, String& user, String& password, String& db_name, int port=0);

        int getVersion();

        MolDB(String hostname,String user, String password, String db, int port=3306);

        virtual ~MolDB();

        void getDatasetSummary(vector<String>& dataset_names, vector<Size>& no_isomers, vector<Size>& no_conformations);

        void searchMoleculesByUCK(String uck, list<LongSize>& conformation_IDs);

        Molecule* fetchMoleculeById(LongSize conformation_id);

        vector<Molecule*> fetchMoleculeById(vector<LongSize>& conformation_ids);

        LongSize storeMolecule(Molecule *mol, String* conformation_hash);

        LongSize storeMolecule(Molecule *mol)
        {
          return storeMolecule(mol,0);
        };

        void deleteIsomer(LongSize isomer_id);

        void deleteConformation(LongSize conformation_id);

        void storeResult(Result* result, String& target_name);

        vector<Result*> fetchResults(list<String>& conformation_hashs, String target_name="");

        void searchMoleculesByLogP(const double& min_logP, const double& max_logP, list<LongSize>& conformation_IDs, const list<LongSize>* conformation_IDs_to_check, bool input_isomer_IDs=0, bool output_isomer_IDs=0);

        void searchMoleculesByMW(const double& min_MW, const double& max_MW, list<LongSize>& conformation_IDs, const list<LongSize>* conformation_IDs_to_check, bool input_isomer_IDs, bool output_isomer_IDs);

        void fetchDatasetConformationIDs(String& target_name, list<LongSize>& conformation_IDs, const list<LongSize>* conformation_IDs_to_check=0, bool input_isomer_IDs=0, bool output_isomer_IDs=0);

        void searchSimilarMoleculesByFingerprint(list<vector<bool> >& query_fingerprints, const float& minimal_similarity, const float& maximal_similarity, list<LongSize>& conformation_IDs, const list<LongSize>* conformation_IDs_to_check=0, bool input_isomer_IDs=0, bool output_isomer_IDs=0);

        #if defined BALL_HAS_OPENBABEL || defined BALL_HAS_OPENEYE

        void searchMoleculesBySmarts(const list<String>& smarts, list<LongSize>& conformation_IDs, const list<LongSize>* conformation_IDs_to_check=0, const list<Size>* no_of_matches=0, bool intersection=1, bool input_isomer_IDs=0, bool output_isomer_IDs=0);
        #endif

        void fetchVendorInformation(Molecule* mol, list<VendorInfo>& vendor_info);

        bool hasResults();

        void disableFunctionalGroupCounting();

        void setVendorPropertyNames(String vendor_name, String vendors_compound_id_tag, bool fetch_vendorname_from_prop, String vendor_version, String url);


      private:
        MolDB(const MolDB& /*tc*/){};

        static const Size VERSION;
        QSqlDatabase database_;
        String dbtype_;
        String hostname_;
        String user_;
        String password_;
        String db_name_;
        bool fg_counting_disabled_;

        bool save_vendor_information_;
        bool fetch_vendorname_from_prop_;
        String property_vendorname_;
        String vendorname_;
        String vendorversion_;
        String vendorurl_;
        String property_vendorID_;

        void searchMoleculesByIsomerColumn_(const String prop_name, const double& min_value, const double& max_value, list<LongSize>& conformation_IDs, const list<LongSize>* conformation_IDs_to_check, bool input_isomer_IDs, bool output_isomer_IDs);

        void buildProperties(Molecule* mol, LongSize ID, list<String>& property_columns);

        MolecularSimilarity* molecular_similarity_;

        #if defined BALL_HAS_OPENBABEL || defined BALL_HAS_OPENEYE
          LogP logP_;
        #endif

        void bitvectorToBytearray_(const vector<bool>& bitvector, QByteArray& bytearray);

        void bytearrayToBitvector_(const QByteArray& bytearray, vector<bool>& bitvector);

      public:
        static void buildTopology(Molecule& mol, QByteArray &data);

        static void getTopology(Molecule& mol, QDataStream &ds);

        static void buildCoordinates(Molecule& mol, QByteArray &data);

        static void getCoordinates(Molecule& mol, QDataStream &ds);

        static void buildCharges(Molecule& mol, QByteArray &data);

        static void getCharges(Molecule& mol, QDataStream &ds);
    };
}

#endif /* MOLDB_H */