RotamerResidue

represents residue, with one backbone and different residue conformers

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CHANGES LOG

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KEYWORD

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AUTHORS

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CHANGES LOG

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GOALS

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USAGE

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RotamerResidue(const RotamerMolecule * resMolecule, ResiduesBuildingInfo::RESIDUE_INFO resInfo, float phiAngle, float psiAngle, vector< RotamerAtom *> resBackboneAtoms, ResidueConformer * initConformer, unsigned short backboneGlobSeq);

  RotamerResidue(const RotamerMolecule * resMolecule, ResiduesBuildingInfo::RESIDUE_INFO resInfo,
		 float phiAngle, float psiAngle, vector< RotamerAtom *> resBackboneAtoms,
		 ResidueConformer * initConformer, unsigned short backboneGlobSeq);

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~RotamerResidue();

    virtual ~RotamerResidue();     

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const ResidueConformer& getCurrentConformer() const ;

  const ResidueConformer& getCurrentConformer() const                                               
;

Function is currently defined inline.

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ResidueConformer& getCurrentConformer() ;

  ResidueConformer& getCurrentConformer()                                               
;

Function is currently defined inline.

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const ResidueConformer& getNativeConformer() const ;

  const ResidueConformer& getNativeConformer() const                           
;

Function is currently defined inline.

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const ResidueConformer& getConformer(unsigned short index) const ;

  const ResidueConformer& getConformer(unsigned short index) const                                                                            
;

Function is currently defined inline.

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unsigned short getNumOfConformers() const ;

  unsigned short getNumOfConformers() const                              
;

Function is currently defined inline.

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unsigned short getCurrentConformerIndex() const ;

  unsigned short getCurrentConformerIndex() const                                  
;

Function is currently defined inline.

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bool isMovable() const ;

  bool isMovable() const                                   
;

Function is currently defined inline.

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bool isFrozen() const ;

  bool isFrozen() const                   
;

Function is currently defined inline.

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unsigned short getResidueSequence() const ;

  unsigned short getResidueSequence() const                                 
;

Function is currently defined inline.

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const RotamerMolecule& getMolecule() const ;

  const RotamerMolecule& getMolecule() const                      
;

Function is currently defined inline.

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bool isSurfaceResidue() const ;

  bool isSurfaceResidue() const                            
;

Function is currently defined inline.

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float getMaxRotamerProbability() const ;

  float getMaxRotamerProbability() const                                  
;

Function is currently defined inline.

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unsigned short backboneGlobalSequence() const ;

  unsigned short backboneGlobalSequence() const                              
;

Function is currently defined inline.

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bool isSequentialResidues(const RotamerResidue& residue) const;

  bool isSequentialResidues(const RotamerResidue& residue) const;   

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const RotamerAtom& operator[](unsigned short residueAtomIndex) const;

  const RotamerAtom& operator[](unsigned short residueAtomIndex) const;

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vector< const RotamerAtom *> getAllAtoms() const;

  vector< const RotamerAtom *> getAllAtoms() const;

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unsigned int size() const;

  unsigned int size() const;

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unsigned int backboneSize() const ;

  unsigned int backboneSize() const                                        
;

Function is currently defined inline.

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bool isMultipleConformers() const;

  bool isMultipleConformers() const;

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vector< const ResidueConformer *> getConformers() const;

  vector< const ResidueConformer *> getConformers() const;

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vector< unsigned short> getConformersSeqs() const;

  vector< unsigned short> getConformersSeqs() const;

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bool isAromatic() const ;

  bool isAromatic() const                        
;

Function is currently defined inline.

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const Vector3& getAromaticCenter() const ;

  const Vector3& getAromaticCenter() const                            
;

Function is currently defined inline.

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bool isCationic() const;

  bool isCationic() const;

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bool isAliphatic() const;

  bool isAliphatic() const;

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const RotamerAtom& getN() const;

  const RotamerAtom& getN() const;

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const RotamerAtom& getO() const;

  const RotamerAtom& getO() const;

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const RotamerAtom& getCA() const;

  const RotamerAtom& getCA() const;

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const RotamerAtom& getCB() const;

  const RotamerAtom& getCB() const;

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void chooseNearestNativeRotamer();

  void chooseNearestNativeRotamer();

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void chooseRandomRotamer();

  void chooseRandomRotamer();

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void setMolecule(const RotamerMolecule * mol) ;

  void setMolecule(const RotamerMolecule * mol)                    
;

Function is currently defined inline.

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void setIsSurfaceResidue(bool isSurfResidue) ;

  void setIsSurfaceResidue(bool isSurfResidue)                                  
;

Function is currently defined inline.

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void freeze() ;

  void freeze()                   
;

Function is currently defined inline.

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void unfreeze() ;

  void unfreeze()                    
;

Function is currently defined inline.

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void setCurrentConformer(unsigned short newCurrentConformerIndex) ;

  void setCurrentConformer(unsigned short newCurrentConformerIndex)                                                                                                                      
;

Function is currently defined inline.

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void addConformer(ResidueConformer *newConformer) ;

  void addConformer(ResidueConformer *newConformer)                                                               
;

Function is currently defined inline.

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int buildRotamers(const RotamerLibrary& rotamerLib,bool extraForChi1 , bool extraForChi2 , float nativeFavorFactor , unsigned short maxNumOfRotamers );

  int buildRotamers(const RotamerLibrary& rotamerLib,bool extraForChi1 = true, bool extraForChi2= false,
		    float nativeFavorFactor = 0.3, unsigned short maxNumOfRotamers = 44);

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vector< float> generateNearChis(const vector< float>& chis,short deltaFactorm, unsigned int chiNum);

  vector< float> generateNearChis(const vector< float>& chis,short deltaFactorm, unsigned int chiNum);

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void printConformers(ostream& s) const;

  void printConformers(ostream& s) const;

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void printDihedralAngles(ostream& s) const;

  void printDihedralAngles(ostream& s) const;

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friend ostream& operator<<(ostream& s, const RotamerResidue& r);

  friend ostream& operator<<(ostream& s, const RotamerResidue& r);

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All Members

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Ancestors

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Descendants

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