PharmacophoreSearcher

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KEYWORD

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AUTHORS

Copyright: SAMBA group, Tel-Aviv Univ. Israel, 2003.

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CHANGES LOG

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GOALS

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USAGE

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PharmacophoreSearcher() ;

  PharmacophoreSearcher()   
;

Function is currently defined inline.

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~PharmacophoreSearcher();

  ~PharmacophoreSearcher();

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void run(const string& molsFile, const char* outputFileName, bool allPivots, bool test );

  void run(const string& molsFile, const char* outputFileName, bool allPivots, bool test=false);

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void run(const vector< string>& molFiles, const char* outputFileName, bool allPivots);

  void run(const vector< string>& molFiles, const char* outputFileName, bool allPivots);

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void run(vector< const FeaturedMolecule*>& molecules, const char* outputFileName, bool allPivots );

  void run(vector< const FeaturedMolecule*>& molecules, const char* outputFileName, bool allPivots=true);

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const Pharmacophore& getPharmacophore(unsigned int num) const ;

  const Pharmacophore& getPharmacophore(unsigned int num) const                                 
;

Function is currently defined inline.

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const vector< Pharmacophore>& getPharmacophores() const ;

  const vector< Pharmacophore>& getPharmacophores() const                            
;

Function is currently defined inline.

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unsigned int getNumOfPharmacophores() const ;

  unsigned int getNumOfPharmacophores() const                                    
;

Function is currently defined inline.

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void onePivotRun(const FeaturedMolecule* pivot, vector< const FeaturedMolecule*>& ligands, vector< MultipleResult>& multiResults, vector< PairwiseResult>& retPairwiseResults);

  void onePivotRun(const FeaturedMolecule* pivot, vector< const FeaturedMolecule*>& ligands, vector< MultipleResult>& multiResults, vector< PairwiseResult>& retPairwiseResults);

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void iteratePivots(const char* outputFileName, bool allPivots, bool test );

  void iteratePivots(const char* outputFileName, bool allPivots, bool test=false);

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void internalRun(const char* outputDirName, bool allPivots, bool test );

  void internalRun(const char* outputDirName, bool allPivots, bool test=false);

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void loadMolecules(const string& molsFile, bool test );

  void loadMolecules(const string& molsFile, bool test=false);

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void wrapPairwiseResults(vector< PairwiseResult>& results, vector< const MultipleResult*>& multipleResults);

  void wrapPairwiseResults(vector< PairwiseResult>& results, vector< const MultipleResult*>& multipleResults);

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void evaluateMultipleResults(const vector< vector< const MultipleResultCluster*> >& multipleResults, const vector< vector< const MultipleResult*> >& clusterRepresentatives, vector< vector< vector< float> > >& rmsds);

performs evaluation returns pairwise rmsds relative to pivot for each multiple result

  void evaluateMultipleResults(const vector< vector< const MultipleResultCluster*> >& multipleResults,
			       const vector< vector< const MultipleResult*> >& clusterRepresentatives,
			       vector< vector< vector< float> > >& rmsds);

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void choosePharmacophoreCandidates();

  void choosePharmacophoreCandidates(); // from the static MultipleResultCluster !!!

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void cluster(const vector< MultipleResult>& multiResults, vector< vector< const MultipleResultCluster*> >& clusteredMultiResults, vector< vector< const MultipleResult*> >& clusterRepresentatives);

  void cluster(const vector< MultipleResult>& multiResults, 
	       vector< vector< const MultipleResultCluster*> >& clusteredMultiResults, 
	       vector< vector< const MultipleResult*> >& clusterRepresentatives);

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void clusterMolecules(const vector< vector< PairwiseResult> >& results, vector< vector< PairwiseResult> >& clusteredResults) const;

  void clusterMolecules(const vector< vector< PairwiseResult> >& results,
			vector< vector< PairwiseResult> >& clusteredResults) const;

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vector< const FeaturedMolecule*> molecules_;

  vector< const FeaturedMolecule*> molecules_;

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hash_map< int, int> mapMolIDtoEntry_;

  hash_map< int, int> mapMolIDtoEntry_;

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vector< const FeaturedMolecule*> nativeMolecules_;

for evaluation

  vector< const FeaturedMolecule*> nativeMolecules_;

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vector< Pharmacophore> pharmacophores_;

output

  vector< Pharmacophore> pharmacophores_; 

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vector< const MultipleResultCluster*> chosenClusters_;

vector of chosen clusters

  vector< const MultipleResultCluster*> chosenClusters_;

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All Members

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Ancestors

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Descendants

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