DBEvaluator

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DBEvaluator(const string& ligandFileName);

  DBEvaluator(const string& ligandFileName);

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DBEvaluator(const string& ligandFileName, const string& decoysFileName);

  DBEvaluator(const string& ligandFileName, const string& decoysFileName);

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void detectAndSearch(const string& outDir, unsigned int batchSize, unsigned int batchNumber);

  void detectAndSearch(const string& outDir, unsigned int batchSize, unsigned int batchNumber);

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void pharmacophoreDetection(const string& outDir, unsigned int batchSize , unsigned int batchNumber );

runs Pharmacophores detection and save to files (+ random ligand selection) outDir = outDir_batchSize_batchNumber, one file per detected pharmacophore

  void pharmacophoreDetection(const string& outDir, unsigned int batchSize=5, unsigned int batchNumber=0);

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void screen(const string& decoyFileName, const string& outDir, const string& phaFile);

outFileName =~ decoyFileName_batchNum_phaNumber

  void screen(const string& decoyFileName, const string& outDir, const string& phaFile);

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void iterate(const char* outDir);

the training set is selected randomly from ligands_

  void iterate(const char* outDir);

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void singleRun(const char* outDir, const string& trainFileName);

the training set is taken from trainFileName, all ligands_ are used as testSet

  void singleRun(const char* outDir, const string& trainFileName);

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void singleRun(const char* outDir, unsigned int batchSize , unsigned int runNumber );

the training set of size = batchSize is selected randomly from ligands_

  void singleRun(const char* outDir, unsigned int batchSize=5, unsigned int runNumber=0);

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void normalizeScore( multimap< float, PairwiseResult*>& setResults, const multimap< float, PairwiseResult*>& setResultsIn);

  static void normalizeScore( multimap< float, PairwiseResult*>& setResults, const multimap< float, PairwiseResult*>& setResultsIn);

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void prepareEnrichmentGraphData(const string& activeScoreFileName, const string& decoyScoreFileName, const string& outFileName);

  static void prepareEnrichmentGraphData(const string& activeScoreFileName,
					 const string& decoyScoreFileName, 
					 const string& outFileName);

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void prepareEFData(const string& activeScoreFileName, const string& decoyScoreFileName, const string& outFileName);

  static void prepareEFData(const string& activeScoreFileName,
			    const string& decoyScoreFileName, 
			    const string& outFileName);

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void singleRun(PharmacophoreSearcher& phaSearcher, unsigned int batchNum, vector< const FeaturedMolecule*>& trainingSet, vector< const FeaturedMolecule*>& testSet, const char* outDir);

  void singleRun(PharmacophoreSearcher& phaSearcher, unsigned int batchNum, vector< const FeaturedMolecule*>& trainingSet, vector< const FeaturedMolecule*>& testSet, const char* outDir);

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void prepareEnrichmentGraphData(const multimap< float, PairwiseResult*>& activeResults, const multimap< float, PairwiseResult*>& decoyResults, unsigned int batchSize, const string& outFileName) const;

  void prepareEnrichmentGraphData(const multimap< float, PairwiseResult*>& activeResults,
				  const multimap< float, PairwiseResult*>& decoyResults,
				  unsigned int batchSize, const string& outFileName) const;

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void prepareEnrichmentGraphData(const multimap< float, bool>& scoreMap, unsigned int numOfActives, const string& outFileName);

@param scoreMap Holds for each molecule the score and a boolean flag that indicates if the molecule is a active (true) or a decoy (false) @param numOfActives The number of actives for which records are available in the scoreMap.

  static void prepareEnrichmentGraphData(const multimap< float, bool>& scoreMap, 
					 unsigned int numOfActives,
					 const string& outFileName);

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void insert(const string& scoreFileName, multimap< float, bool>& scoreMap, bool isActive);

  static void insert(const string& scoreFileName, multimap< float, bool>& scoreMap, bool isActive);

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void prepareEFData(const multimap< float, PairwiseResult*>& decoyResults, const multimap< float, PairwiseResult*>& testSetResults, unsigned int batchSize, const string& outFileName) const;

  void prepareEFData(const multimap< float, PairwiseResult*>& decoyResults,
		     const multimap< float, PairwiseResult*>& testSetResults,
		     unsigned int batchSize, const string& outFileName) const;

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void prepareEFData(const multimap< float, bool>& scoreMap, unsigned int numOfActives, const string& outFileName);

@param scoreMap Holds for each molecule the score and a boolean flag that indicates if the molecule is a active (true) or a decoy (false) @param numOfActives The number of actives for which records are available in the scoreMap.

  static void prepareEFData(const multimap< float, bool>& scoreMap, 
			    unsigned int numOfActives,
			    const string& outFileName);

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void outputScores(const multimap< float, PairwiseResult*>& trainingSetResults, const multimap< float, PairwiseResult*>& testSetResults, const multimap< float, PairwiseResult*>& decoyResults, const string& outFileName, const Pharmacophore& pharmacophore) const;

  void outputScores(const multimap< float, PairwiseResult*>& trainingSetResults,
		    const multimap< float, PairwiseResult*>& testSetResults,
		    const multimap< float, PairwiseResult*>& decoyResults,
		    const string& outFileName, const Pharmacophore& pharmacophore) const;

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void randomSelectTrainingSetMolecules(unsigned int numOfMols, set< unsigned int>& selectedMolecules) const;

  void randomSelectTrainingSetMolecules(unsigned int numOfMols, set< unsigned int>& selectedMolecules) const;

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string getBatchID(unsigned int batchSize, unsigned int batchNumber) ;

  string getBatchID(unsigned int batchSize, unsigned int batchNumber)                           ;

Function is currently defined inline.

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void trainingSetSelection(vector< const FeaturedMolecule*>& trainingSet, vector< const FeaturedMolecule*>& otherLigandSet, unsigned int batchSize);

  void trainingSetSelection(vector< const FeaturedMolecule*>& trainingSet, 
			    vector< const FeaturedMolecule*>& otherLigandSet, 
			    unsigned int batchSize);

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void trainingSetSelection(vector< const FeaturedMolecule*>& trainingSet, unsigned int batchSize);

  void trainingSetSelection(vector< const FeaturedMolecule*>& trainingSet, 
			    unsigned int batchSize);

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vector< const FeaturedMolecule*> ligands_;

  vector< const FeaturedMolecule*> ligands_;

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vector< const FeaturedMolecule*> decoys_;

  vector< const FeaturedMolecule*> decoys_;

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