AromaticRing

Implementation Note (Oranit): There are aromatic groups that are not rings. Currently, we ignore these groups. However, in the future we may consider adding a new class called AromaticGroup that will extend Feature and the current AromaticRing class will be its subclassL: AromaticRing extends AromaticGroup extends Feature

[ ligand_pharma | Source | Keywords | Summary | Ancestors | All Members | Descendants ]

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Class Summary

class AromaticRing
: public Feature
{

public:

	// Constructors
	AromaticRing(const unsigned int id_, const FeaturedMolecule& molecule_, const vector< leda::node>& ring_);

	// Inspectors
static bool	isAromaticRing(const FeaturedMolecule& molecule, const vector< leda::node>& ring);
static bool	isAromaticRing(const Feature* feature) ;
static bool	isPlanarRing(const FeaturedMolecule& molecule, const vector< leda::node>& ring);
void	getAtoms(vector< const Mol2Atom*>& atoms) const;
void	getAtomIndices(vector< unsigned int>& atomIndices) const;
const Vector3	getNormal() const ;

	// Misc.
bool	canBeMatched(const RigidTrans3& transformation, const Feature* otherFeature) const;
bool	operator==(const Feature& otherFeature) const;

	// Output
void	dump(ostream& output) const;
void	outputMol2(ostream& output) const ;
void	outputMol2(const RigidTrans3& transformation, ostream& output) const ;
friend ostream&	operator<<(ostream& s, const AromaticRing& ring);

	// Destructors
	~AromaticRing();
protected:
float	getScoreVirtual(const Feature* otherFeature) const;
static bool	isAromaticHetero(const Mol2Atom& atom);
void	outputMol2(ostream& output, const Vector3& center) const;

}; // AromaticRing

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KEYWORD

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AUTHORS

Oranit Dror (mailto: oranit@post.tau.ac.il)

Copyright: SAMBA group, Tel-Aviv Univ. Israel, 2004.

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CHANGES LOG

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GOALS

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USAGE

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AromaticRing(const unsigned int id_, const FeaturedMolecule& molecule_, const vector< leda::node>& ring_);

  AromaticRing(const unsigned int id_, const FeaturedMolecule& molecule_, const vector< leda::node>& ring_);

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bool isAromaticRing(const FeaturedMolecule& molecule, const vector< leda::node>& ring);

Return true if the given ring is aromatic. Otherwise, return false.

  static bool isAromaticRing(const FeaturedMolecule& molecule, const vector< leda::node>& ring);

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bool isAromaticRing(const Feature* feature) ;

  static bool isAromaticRing(const Feature* feature)                                                       
;

Function is currently defined inline.

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bool isPlanarRing(const FeaturedMolecule& molecule, const vector< leda::node>& ring);

Return true if the given ring is planar. Otherwise, return false.

  static bool isPlanarRing(const FeaturedMolecule& molecule, const vector< leda::node>& ring);

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void getAtoms(vector< const Mol2Atom*>& atoms) const;

Return the atoms of the aromatic ring

  void getAtoms(vector< const Mol2Atom*>& atoms) const;

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void getAtomIndices(vector< unsigned int>& atomIndices) const;

Return the identifiers of atoms of the aromatic ring in the molecule

  void getAtomIndices(vector< unsigned int>& atomIndices) const;

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const Vector3 getNormal() const ;

Return a unit vector that is perpendicular to the aromaic ring

  const Vector3 getNormal() const                   
;

Function is currently defined inline.

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bool canBeMatched(const RigidTrans3& transformation, const Feature* otherFeature) const;

Return true if the two features can be matched after applying the given transformation on the current feature according to their type, the distance between their centers and the difference between their normals

  bool canBeMatched(const RigidTrans3& transformation, const Feature* otherFeature) const;

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bool operator==(const Feature& otherFeature) const;

Return true if the given feature is aromatic ring and the rings' centers and normals are the same.

  bool operator==(const Feature& otherFeature) const;

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void dump(ostream& output) const;

  void dump(ostream& output) const;

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void outputMol2(ostream& output) const ;

  void outputMol2(ostream& output) const                                           
;

Function is currently defined inline.

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void outputMol2(const RigidTrans3& transformation, ostream& output) const ;

output transformed feature center

  void outputMol2(const RigidTrans3& transformation, ostream& output) const                                                          
;

Function is currently defined inline.

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friend ostream& operator<<(ostream& s, const AromaticRing& ring);

Prints the atoms of the ring to the output stream

  friend ostream& operator<<(ostream& s, const AromaticRing& ring);

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~AromaticRing();

  ~AromaticRing();

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float getScoreVirtual(const Feature* otherFeature) const;

Return the score for matching the two features.

  float getScoreVirtual(const Feature* otherFeature) const;

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bool isAromaticHetero(const Mol2Atom& atom);

Return true if the type of the given atom is one of the three hetero types that can participate in an aromatic ring (N, O, or S).

  static bool isAromaticHetero(const Mol2Atom& atom);

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void outputMol2(ostream& output, const Vector3& center) const;

  void outputMol2(ostream& output, const Vector3& center) const;

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All Members

public:

	// Inspectors
FEATURE_TYPE	featureType() const ;
char*	getFeatureTypeString() const ;
unsigned int	getID() const ;
unsigned int	getRigidGroupID() const ;
const vector< unsigned int>&	getAllRigidGroups() const ;
const Vector3&	getCenter() const ;
float	getScore(const Feature* otherFeature) const ;
bool	isValid() ;
float	weight() const ;
void	getAtoms(vector< const Mol2Atom*>& atoms) const;	// pure virtual
float	getRadiusForCenterFit() const ;
float	getRadiusForCenterFit(const Feature* otherFeature) const ;
bool	canBeMatched(const RigidTrans3& transformation, const Feature* otherFeature) const;	// pure virtual
bool	operator==(const Feature& otherFeature) const;	// pure virtual

	// Setters
void	setCenter(const Vector3& center) ;
void	addRigidGroup(unsigned int groupID) ;
void	setValidity(bool valid) ;
void	setWeight(float w) ;
void	setRadiusForCenterFit(float r) ;

	// Misc.
void	resetValidityAndWeight() ;

	// Output
void	dump(ostream& output) const;	// pure virtual
void	outputMol2(ostream& output) const;	// pure virtual
void	outputMol2(const RigidTrans3& transformation, ostream& output) const;	// pure virtual
friend ostream&	operator<<(ostream& s, const Feature& feature) ;

	// Inspectors
static bool	isAromaticRing(const FeaturedMolecule& molecule, const vector< leda::node>& ring);
static bool	isAromaticRing(const Feature* feature) ;
static bool	isPlanarRing(const FeaturedMolecule& molecule, const vector< leda::node>& ring);
void	getAtomIndices(vector< unsigned int>& atomIndices) const;
const Vector3	getNormal() const ;

	// Output
void	outputMol2(ostream& output) const ;
void	outputMol2(const RigidTrans3& transformation, ostream& output) const ;
friend ostream&	operator<<(ostream& s, const AromaticRing& ring);
protected:
float	getScoreVirtual(const Feature* otherFeature) const;	// pure virtual
unsigned int	id;
vector< unsigned int>	rigidGroups;
Vector3	center_;
bool	isValidFeature_;
FEATURE_TYPE	type_;
float	weight_;
float	radiusForCenterFit_;
static bool	isAromaticHetero(const Mol2Atom& atom);
void	outputMol2(ostream& output, const Vector3& center) const;

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Ancestors

Inheritance chain for AromaticRing:

Feature

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Descendants

Class is not inherited by any others.

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