RigidGroup

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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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RigidGroup(LigandMolecule* mol, unsigned int groupId) ;

  RigidGroup(LigandMolecule* mol, unsigned int groupId) ;

Function is currently defined inline.

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const vector< unsigned int>& getAtoms() const ;

Return the indices (and not the Mol2 Atom IDs) of the atoms in the molecule

  const vector< unsigned int>& getAtoms() const                  
;

Function is currently defined inline.

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const vector< Vector3> getCoordinates() const;

Return the 3D coordinates of the rigid group's atoms

  const vector< Vector3> getCoordinates() const;

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const vector< unsigned int>& getDummyPoints() const ;

Returns a vector with the indices of the dummy points in the molecule

  const vector< unsigned int>& getDummyPoints() const                         
;

Function is currently defined inline.

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void getCriticalPoints(vector< Vector3>& criticalPoints) const;

atoms + dummy

  void getCriticalPoints(vector< Vector3>& criticalPoints) const;

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const vector< RotatableBond>& getRotatableBonds() const ;

  const vector< RotatableBond>& getRotatableBonds() const                            
;

Function is currently defined inline.

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const RotatableBond& getRotatableBond(unsigned int rbondID) const;

  const RotatableBond& getRotatableBond(unsigned int rbondID) const;

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unsigned int getID() const ;

  unsigned int getID() const               
;

Function is currently defined inline.

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unsigned int numberOfHeavyAtoms() const ;

  unsigned int numberOfHeavyAtoms() const                         
;

Function is currently defined inline.

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bool isAtomInRigidGroup(unsigned int atomIndex) const;

  bool isAtomInRigidGroup(unsigned int atomIndex) const;  

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void addAtom(unsigned int atom) ;

  void addAtom(unsigned int atom)                           
;

Function is currently defined inline.

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void addHydrogen(unsigned int atom) ;

  void addHydrogen(unsigned int atom)                                
;

Function is currently defined inline.

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void addDummyPoint(unsigned int dummyPoint) ;

@param dummyPoint is an index of a dummy point in the molecule

  void addDummyPoint(unsigned int dummyPoint)                                        
;

Function is currently defined inline.

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void addAtoms(const vector< unsigned int>& newAtoms) ;

  void addAtoms(const vector< unsigned int>& newAtoms)                                                                                
;

Function is currently defined inline.

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void addRotatableBond(RotatableBond& rbond);

  void addRotatableBond(RotatableBond& rbond);

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void rigidTrans(const RigidTrans3& trans, Molecule< Mol2Atom>& mol) const;

Gets a copy of the molecule and transform the atoms of the rigid group according to the given rigid transformation.

  void rigidTrans(const RigidTrans3& trans, Molecule< Mol2Atom>& mol) const;

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friend ostream& operator<<(ostream& s, const RigidGroup& group);

print for debug purposes

  friend ostream& operator<<(ostream& s, const RigidGroup& group);

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LigandMolecule* molecule;

  LigandMolecule* molecule;

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vector< unsigned int> atoms;

  vector< unsigned int> atoms; // Holds the indices (and not the Mol2 Atom IDs) of the atoms in the molecule 

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vector< unsigned int> hydrogens_;

  vector< unsigned int> hydrogens_;

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vector< unsigned int> dummyPoints_;

  vector< unsigned int> dummyPoints_; // Holds the indices of the dummy points in the molecule

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vector< RotatableBond> rotatableBonds_;

  vector< RotatableBond> rotatableBonds_;

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unsigned int id;

  unsigned int id;

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vector< bool> transformedAtoms_;

atoms that are transformed by transformation, which is all atoms, except hinge second atom

  vector< bool> transformedAtoms_;

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bool isTransformedAtomsUpdated_;

  bool isTransformedAtomsUpdated_;

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All Members

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Ancestors

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Descendants

• FeaturedRigidGroup

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