LigandMolecule

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Class Summary

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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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typedef hash_map< unsigned int, RigidTrans3, hash< unsigned int> > RigidGroupTrans3Map;

  typedef hash_map< unsigned int, RigidTrans3, hash< unsigned int> > RigidGroupTrans3Map;

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LigandMolecule(unsigned int molId) ;

Constructs and empty LigandMolecule object

  LigandMolecule(unsigned int molId) ;

Function is currently defined inline.

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LigandMolecule(unsigned int molId, const string molName) ;

Constructs a LigandMolecule object according to the given Mol2 file which describes the molecule.

  LigandMolecule(unsigned int molId, const string molName) ;

Function is currently defined inline.

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void init(ifstream& mol2FileStream) ;

  void init(ifstream& mol2FileStream)                                                                                        
;

Function is currently defined inline.

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void addDummyPoints();

  void addDummyPoints();

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const Mol2Atom& getAtomById(int id) const ;

  const Mol2Atom& getAtomById(int id) const                                            ;

Function is currently defined inline.

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unsigned int getAtomIndexById(int id) const ;

  unsigned int getAtomIndexById(int id) const                                            ;

Function is currently defined inline.

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const Vector3& getDummyPoint(unsigned int dummyPointIndex) const ;

  const Vector3& getDummyPoint(unsigned int dummyPointIndex) const                                                
;

Function is currently defined inline.

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const vector< Vector3>& getDummyPoints() const ;

  const vector< Vector3>& getDummyPoints() const                         
;

Function is currently defined inline.

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

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

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unsigned int getID() const ;

  unsigned int getID() const               
;

Function is currently defined inline.

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const string& getFileName() const ;

Returns the name of the molecule (which is the name of the Mol2 file that describes the molecule)

  const string& getFileName() const                 
;

Function is currently defined inline.

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const string& getMol2Name() const ;

  const string& getMol2Name() const                      
;

Function is currently defined inline.

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const string& getName() const ;

  const string& getName() const                                          ;

Function is currently defined inline.

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HYBRIDIZATION_TYPE getHybridizationType(unsigned int atomIndex) const;

  HYBRIDIZATION_TYPE getHybridizationType(unsigned int atomIndex) const;

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const vector< RigidGroup*>& getRigidGroups() const ;

  const vector< RigidGroup*>& getRigidGroups() const                         
;

Function is currently defined inline.

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unsigned int getNumOfRigidGroups() const ;

  unsigned int getNumOfRigidGroups() 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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const RigidGroup& getRigidGroup(int groupId) const ;

  const RigidGroup& getRigidGroup(int groupId) const                                     
;

Function is currently defined inline.

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const vector< Vector3> getCoordinates(int groupId) const ;

  const vector< Vector3> getCoordinates(int groupId) const                                                          
;

Function is currently defined inline.

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int getCommonRigidGroup(unsigned int atomIndex1, unsigned int atomIndex2, unsigned int atomIndex3) const;

Return the Id of the rigid group that is common to all three atoms. Returns -1 if such a rigid group does not exist.

  int getCommonRigidGroup(unsigned int atomIndex1, unsigned int atomIndex2, unsigned int atomIndex3) const;

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void getNeighborsForAtom(unsigned int atomIndex, vector< unsigned int>& atomNeighbors) const;

Returns for atom the set of its atom neighbors

  void getNeighborsForAtom(unsigned int atomIndex, vector< unsigned int>& atomNeighbors) const;  

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unsigned int getNumOfNeighbors(unsigned int atomIndex) const;

  unsigned int getNumOfNeighbors(unsigned int atomIndex) const;

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void getNeighborsForBondAtom(unsigned int atomIndex1, unsigned int atomIndex2, vector< unsigned int>& atom1Neighbors) const;

Returns for atom1 of a given bond the set of its atom neighbors excluding the atom2 on the bond

  void getNeighborsForBondAtom(unsigned int atomIndex1, unsigned int atomIndex2,
			       vector< unsigned int>& atom1Neighbors) const;  

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int readMol2file(istream& mol2stream);

Read Mol2 file and create the graphs that represent it. Note that substructures are treated as one structure!

  int readMol2file(istream& mol2stream);

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Molecule< Mol2Atom> transformAtoms(RigidGroupTrans3Map& rigidGroupTransformations) const;

Each given transformation will be applied on the atoms of a rigid group. The atoms of a rigid group with unassigned transformation will be transfored according to the transformation of a predecessor in a BFS tree.

TODO: To modify the signature of this method so that the resulting Molecule< Mol2Atom> will be given as an argument.

  Molecule< Mol2Atom> transformAtoms(RigidGroupTrans3Map& rigidGroupTransformations) const;

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void updateTransformations(RigidGroupTrans3Map& rigidGroupTransformations) const;

  void updateTransformations(RigidGroupTrans3Map& rigidGroupTransformations) const;

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const vector< const RigidGroup*> getRigidGroups(unsigned int atomIndex) const;

Returns the rigid groups to which the given atom belongs to

  const vector< const RigidGroup*> getRigidGroups(unsigned int atomIndex) const;

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bool isClose(const Vector3& point) const;

Return true if the given atom is close (within a ball of predefined radius) to some atom of the molecule.

  bool isClose(const Vector3& point) const;    

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void outputMol2File(ostream& output) const;

Output the molecule (excluding the hydrogen atoms) to a file

  void outputMol2File(ostream& output) const;

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void outputMol2File(ostream& output, const RigidTrans3& trans) const;

transform by trans and output

  void outputMol2File(ostream& output, const RigidTrans3& trans) const;

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void outputMol2File(RigidGroupTrans3Map& transformations, ostream& output) const;

Transform the rigid groups of the molecule according to the given rigid transformations and output

  void outputMol2File(RigidGroupTrans3Map& transformations, ostream& output) const;

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void initAtomHash() ;

  void initAtomHash()                                                                                                                                                 ;

Function is currently defined inline.

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void prepareAtomIdMapping() ;

  void prepareAtomIdMapping()                                                                                                             
;

Function is currently defined inline.

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void markHinges();

Mark all flexible bonds as hinges

  void markHinges();

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void buildRigidGroups();

build all the rigid groups divided by hinges

  void buildRigidGroups();

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void orderRigidGroups();

order rigid groups according to DFS order of the tree they make

  void orderRigidGroups();

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void addHydrogensToRigidGroups();

add hydrogens

  void addHydrogensToRigidGroups();

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void markCyclicBonds();

mark all cyclic bonds (i.e. part of the ring) as not hinges

  void markCyclicBonds();

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void markPeptideBonds();

mark all peptide bonds as not hinges

  void markPeptideBonds();

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void addDummyPointsOnRings();

  void addDummyPointsOnRings();

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void addDummyPointsOnTriangles();

void addDummyPointsOnTriangles();

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bool isConnectedToElement(const leda::node u, const ELEMENT element) const;

Gets a node in the ligandGraphWithHydrogens graph and a chemical element type. Returns true if the given node represents an atom that is connected to an atom with the given element type

  bool isConnectedToElement(const leda::node u, const ELEMENT element) const;

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unsigned int numberOfNeighboursWithElement(const leda::node u, const ELEMENT element) const;

  unsigned int numberOfNeighboursWithElement(const leda::node u, const ELEMENT element) const;

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unsigned int numberOfNeighboursWithAtomType(const leda::node u, const string atomType) const;

  unsigned int numberOfNeighboursWithAtomType(const leda::node u, const string atomType) const;

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int numberOfBonds(const leda::node u) const ;

int numberOfBonds(const leda::node u) const                                               
;

Function is currently defined inline.

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bool isConnectedToAtom(const leda::node u, const string atomName) const;

Gets a node in the ligandGraphWithoutHydrogens graph and an atom name. Returns true if the given node represents an atom that is connected to atom with the given name.

  bool isConnectedToAtom(const leda::node u, const string atomName) const;

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void outputMol2Header(ostream& output) const;

Output the Mol2 header of the molecule

  void outputMol2Header(ostream& output) const;

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void outputMol2Bonds(ostream& output) const;

Output the bonds of the molecule in Mol2 format

  void outputMol2Bonds(ostream& output) const;

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vector< RigidGroup*> rigidGroups_;

Rigid Groups container

  vector< RigidGroup*> rigidGroups_;

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leda::UGRAPH< unsigned int, Bond> ligandGraphWithHydrogens;

graph representing a molecule (including all the hydrogen atoms)

  leda::UGRAPH< unsigned int, Bond> ligandGraphWithHydrogens;

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leda::UGRAPH< unsigned int, Bond> ligandGraphWithoutHydrogens;

graph representing a molecule without the hydrogen atoms

  leda::UGRAPH< unsigned int, Bond> ligandGraphWithoutHydrogens;

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map< unsigned int, leda::node> atomId2NodeWithoutHydrogens_, atomId2NodeWithHydrogens_;

These two mapping between atomId and node in the ligandGraphWithoutHydrogens and ligandGraphWithHydrogens graphs are needed to find the atoms of a bond in order to add an edge to the graph

  map< unsigned int, leda::node> atomId2NodeWithoutHydrogens_, atomId2NodeWithHydrogens_; 

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unsigned int id;

molecule id

  unsigned int id;

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string name;

molecule name

  string name;

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string mol2name_;

string mol2name_;

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hash_map< unsigned int, unsigned int> atomId2Index_;

hash_map< unsigned int, unsigned int> atomId2Index_;

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GeomHash< Vector3, const Mol2Atom*> atomHash_;

stores molecule atoms

  GeomHash< Vector3, const Mol2Atom*> atomHash_;

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vector< Vector3> dummyPoints_;

  vector< Vector3> dummyPoints_;

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float maxAtomDistance2_;

distance tolerance for hash query

  static float maxAtomDistance2_; 

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All Members

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Ancestors

• Molecule

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Descendants

• FeaturedMolecule

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