ChemAtom

This is a class that addes additional atrributes to Atom

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KEYWORD

Class Summary

class ChemAtom
: public Atom, public EnergyAtom
{

public:

	// Constructors
	ChemAtom();
	ChemAtom(const Vector3& p, const char ch, const unsigned short aid, const unsigned short resid, const char* const t, const char resTp, const int chem_type , const float rad , const float charge );

	// modifiers
void	setChemType(const int chem_type) ;
void	setRadius(const float r) ;
void	setEpsilon(const float e) ;
void	setCharge(const float c) ;
void	setHBData(const HB_TYPE hbType, const Vector3& hbDirection);
void	setSteadyProb(const float p) ;
void	setASA(const float ASA) ;
void	setPosition(const Vector3& v) ;

	// Inspectors
int	getChemType() const ;
float	getRadius() const ;
float	getEpsilon() const ;
bool	isHydrogen() const ;
float	getCharge() const ;
bool	isDonor() const ;
bool	isAcceptor() const ;
const Vector3&	getHBDirection() const ;
float	getSteadyProb() const ;
float	getASA() const ;
bool	isNonPolar() const ;
static const float	maxRadius;
protected:

}; // ChemAtom

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KEYWORD

ChemAtom, radius, charge, type, ASA, solvation

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AUTHORS

Dina Schneidman (duhovka@tau.ac.il)

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GOALS

ChemAtom extends Atom and has 4 additional attributes: chemical type, radius, charge and probability of the atom of being steady.

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CHANGES LOG

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USAGE

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ChemAtom();

empty atom

  ChemAtom();

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ChemAtom(const Vector3& p, const char ch, const unsigned short aid, const unsigned short resid, const char* const t, const char resTp, const int chem_type , const float rad , const float charge );

construction with atom data

  ChemAtom(const Vector3& p, const char ch, const unsigned short aid,
	   const unsigned short resid, const char* const t, const char resTp,
	   const int chem_type=0, const float rad=1.5, const float charge=0);

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void setChemType(const int chem_type) ;

set chemical type

  void setChemType(const int chem_type)                                                                                                                                                               
;

Function is currently defined inline.

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void setRadius(const float r) ;

set radius

  void setRadius(const float r)                 
;

Function is currently defined inline.

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void setEpsilon(const float e) ;

set epsilon

  void setEpsilon(const float e)                  
;

Function is currently defined inline.

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void setCharge(const float c) ;

set charge

  void setCharge(const float c)                 
;

Function is currently defined inline.

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void setHBData(const HB_TYPE hbType, const Vector3& hbDirection);

set HB data

  void setHBData(const HB_TYPE hbType, const Vector3& hbDirection);

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void setSteadyProb(const float p) ;

set probability of being steady

  void setSteadyProb(const float p)                     
;

Function is currently defined inline.

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void setASA(const float ASA) ;

set ASA

  void setASA(const float ASA)                
;

Function is currently defined inline.

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void setPosition(const Vector3& v) ;

set atom position

  void setPosition(const Vector3& v)               
;

Function is currently defined inline.

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int getChemType() const ;

get atom chemical type for ACE computation

  int getChemType() const                                                                               
;

Function is currently defined inline.

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float getRadius() const ;

get atom radius

  float getRadius() const                    
;

Function is currently defined inline.

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float getEpsilon() const ;

get epsilon value

  float getEpsilon() const                     
;

Function is currently defined inline.

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bool isHydrogen() const ;

  bool isHydrogen() const                  
;

Function is currently defined inline.

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float getCharge() const ;

get atom charge

  float getCharge() const                    
;

Function is currently defined inline.

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bool isDonor() const ;

  bool isDonor() const                                                     
;

Function is currently defined inline.

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bool isAcceptor() const ;

  bool isAcceptor() const                                                        
;

Function is currently defined inline.

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const Vector3& getHBDirection() const ;

returns direction of h-donor/acceptor, in case of undefined direction zero vector is returned

  const Vector3& getHBDirection() const                         
;

Function is currently defined inline.

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float getSteadyProb() const ;

get probability of being steady

  float getSteadyProb() const                        
;

Function is currently defined inline.

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float getASA() const ;

get ASA

  float getASA() const                 
;

Function is currently defined inline.

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bool isNonPolar() const ;

  bool isNonPolar() const                        
;

Function is currently defined inline.

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const float maxRadius;

maximal atom radius

  static const float maxRadius;

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All Members

public:

	// 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;
bool	isP() const;
bool	isRNABackbone() const;
bool	isSugarAtom() 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);
float	getRadius() const;	// pure virtual
float	getEpsilon() const;	// pure virtual
bool	isHydrogen() const;	// pure virtual
float	getCharge() const;	// pure virtual
bool	isDonor() const;	// pure virtual
bool	isAcceptor() const;	// pure virtual
const Vector3&	getHBDirection() const;	// pure virtual
Vector3	position() const;	// pure virtual

	// modifiers
void	setChemType(const int chem_type) ;
void	setRadius(const float r) ;
void	setEpsilon(const float e) ;
void	setCharge(const float c) ;
void	setHBData(const HB_TYPE hbType, const Vector3& hbDirection);
void	setSteadyProb(const float p) ;
void	setASA(const float ASA) ;
void	setPosition(const Vector3& v) ;

	// Inspectors
int	getChemType() const ;
float	getRadius() const ;
float	getEpsilon() const ;
bool	isHydrogen() const ;
float	getCharge() const ;
bool	isDonor() const ;
bool	isAcceptor() const ;
const Vector3&	getHBDirection() const ;
float	getSteadyProb() const ;
float	getASA() const ;
bool	isNonPolar() const ;
static const float	maxRadius;
protected:

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Ancestors

Inheritance chain for ChemAtom:

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Descendants

Class is not inherited by any others.

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