NucleicAcidAtom

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Class Summary

class NucleicAcidAtom : public Atom
{

public:

	// Constructors
	NucleicAcidAtom(const char* const PDBrec) ;

	// Query
bool	isP() const;
bool	isO3() const;
bool	isBackbone() const;
bool	isSugarAtom() const;
bool	isPhosphateAtom() const;
bool	isBaseAtom() const;
const int	getPairedAtomIndex() const ;

	// Setters
void	setPairedAtomIndex(int index) ;
protected:

}; // NucleicAcidAtom

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AUTHORS

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

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

OVERVIEW TEXT

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USAGE

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NucleicAcidAtom(const char* const PDBrec) ;

A constructor that intiate a NucleicAcidAtom object from an ATOM PDB record

  NucleicAcidAtom(const char* const PDBrec) ;

Function is currently defined inline.

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bool isP() const;

Returns true if the atom is phosphate

  bool isP() const;

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bool isO3() const;

Returns true if the atom is phosphate

  bool isO3() const;

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bool isBackbone() const;

Returns true if the atom is a backbone atom

  bool isBackbone() const;

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bool isSugarAtom() const;

Returns true if the atom belongs to the sugar group of a nucleotide

  bool isSugarAtom() const;

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bool isPhosphateAtom() const;

Returns true if the atom belongs to the phosphate group of a nucleotide

  bool isPhosphateAtom() const;

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bool isBaseAtom() const;

Returns true if the atom belongs to a nucleotide base

  bool isBaseAtom() const;

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const int getPairedAtomIndex() const ;

Return the index of the paired atom in the molecule or -1 if the atom is unpaired.

  const int getPairedAtomIndex() const                                  
;

Function is currently defined inline.

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void setPairedAtomIndex(int index) ;

Sets the index of the paired atom in the molecule or -1 if such an atom does not exist.

  void setPairedAtomIndex(int index)                                   
;

Function is currently defined inline.

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All Members

public:

	// define real type.
typedef float	real;

	// Inspection.
Vector3	position() const ;
real	x() const ;
real	x(const unsigned short coord) const ;
bool	isZero() const ;
real	norm() const ;
real	norm2() const ;
real	dist(const Vector3& p) const ;
real	dist2(const Vector3& p) const ;
const real&	operator[](const unsigned short coord) const ;
Vector3	getPerpendicularVector() const ;
Vector3	getUnitVector() const ;

	// Operators.
bool	operator==(const Vector3& v) const ;
friend Vector3	operator+(const Vector3& p1, const Vector3& p2) ;
friend Vector3	operator-(const Vector3& p1, const Vector3& p2) ;
friend Vector3	operator-(const Vector3& p) ;
friend real	operator*(const Vector3& p1, const Vector3& p2) ;
friend Vector3	operator*(const Vector3& p, const real& m) ;
friend Vector3	operator*(const real& m, const Vector3& p) ;
friend Vector3	operator/(const Vector3& p, const real& m) ;
friend Vector3	operator&(const Vector3& p1, const Vector3& p2) ;
friend real	operator\|(const Vector3& p1, const Vector3& p2) ;
friend real	operator^(const Vector3& p1, const Vector3& p2) ;
Vector3&	operator+=(const Vector3& p) ;
Vector3&	operator-=(const Vector3& p) ;
Vector3&	operator*=(const real& m) ;
Vector3&	operator/=(const real& m) ;
friend ostream&	operator<<(ostream& s, const Vector3& v) ;
friend istream&	operator>>(istream& s, Vector3& v) ;
void	output(FILE* outputFile) const ;

	// Constructors
explicit	Atom(const char* const PDBrec);

	// Inspectors
char	chainId() const;
char	altLocIndicator() const;
unsigned short	atomIndex() const;
short	residueIndex() const;
char	residueICode() const;
const char *const	type() const;
char	residueType() const;
const char *const	residueName() const;
AtomEntryType	getAtomEntryType() const;
float	getOccupancy() const;
float	getTempFactor() const;
void	setTempFactor(float ftemp);
bool	isBackbone() const;
bool	isCA() const;
bool	isCB() const;
bool	isN() const;
bool	isC() const;
bool	isO() const;
bool	isH() const;
bool	isWater() const;

	// Adaptors
void	setChainId(const char newChainId);
void	setAtomId(unsigned short newAtomId);
Atom&	operator*=(const RigidTrans3& rt) ;
	operator RESIDUE_INDEX()const ;
void	setSSE(const pair< char,short>& isseInfo) ;
pair< char,short>	getSSE()const ;
static string	parseAtomName(const char* const atomName_);
friend ostream&	operator<<(ostream& s, const Atom& at);

	// Query
bool	isP() const;
bool	isO3() const;
bool	isSugarAtom() const;
bool	isPhosphateAtom() const;
bool	isBaseAtom() const;
const int	getPairedAtomIndex() const ;

	// Setters
void	setPairedAtomIndex(int index) ;
protected:

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Ancestors

Inheritance chain for NucleicAcidAtom:

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Descendants

Class is not inherited by any others.

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