Atom

This is a general class to hold an atom as it appears in a PDB file.

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KEYWORD

AUTHORS

CHANGES LOG

USAGE

Class Summary

class Atom : public Vector3

{

public:

	// Constructors
	Atom();
	Atom(const Vector3& p, const char ch, const unsigned short aid, const unsigned short resid, const char* const t, const char resTp, const char resICode );
	Atom(const Vector3& p, const AtomEntryType atp, const char ch, const unsigned short aid, const unsigned short resid, const char* const t, const char resTp, const char* const res, const char resICode );
	Atom(const Vector3& p, const AtomEntryType atp, const char ch, const unsigned short aid, const unsigned short resid, const char* const atomName_, const char resTp, const char* const res, const float occup, const float tmp, const char resICode );
	Atom(const Vector3& p, unsigned short aid);
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);
protected:

}; // Atom

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KEYWORD

atom, PDB, particle

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AUTHORS

Meir Fuchs (meirfux@math.tau.ac.il), Zipi Fligelman (zipo@math.tau.ac.il)

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CHANGES LOG

13.11.07 Elad Donsky Adding alternate location field <\LI>
2.08.07 Efrat Adding isCB method <\LI>
10.05.05 Nelly Bluvshtein 1. String data member for residueSeqID ( = "45A") was replaced by residueSeqICode ( = 'A'). The residue number is stored in residueId (as it was). Atom constructors were changed to get resICode (with default = ' '). residueSequenceID() returns concatenation of residueId and residueSeqICode. 2. isH(),isWater() added for Molecule::WaterHydrogenUnSelector <\LI>
10.10.04 Dina Schneidman Residue name is stored in a 3-characters string instead of char[3] <\LI>
16.07.04 Oranit Dror A small update in the << operator <\LI>
17.3.04 pair(char,short) sseInfo added.
13.01.04 Dina and Oranit Atom name is stored in a 4-characters string instead of char[4]. If the name length is shorter than 4 characters then blanks are appended. The "type" method is now returns a terminated char[] ('\0' at the end).
15.01.03 Max
class Atom : public Particle -> class Atom : public Vector3
All functions are changed accordingly. <\LI>
Occupancy and temperature factor were added. 8.01.03 Alex <\LI>
getAtomEntryType() - function that tells if an atom is ATOM or HETATM record in PDB file. 8.01.03 Alex <\LI>
isBackbone() - function that returns true for backbone atoms 8.01.03 Dina <\LI>
Added: operator RESIDUE_INDEX()const (14.12.03 Max) <\LI>

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USAGE

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Atom();

An empty constructor that gives the atom members null values

  Atom();

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Atom(const Vector3& p, const char ch, const unsigned short aid, const unsigned short resid, const char* const t, const char resTp, const char resICode );

An explicit constructor

  Atom(const Vector3& p, const char ch, const unsigned short aid, 
       const unsigned short resid, 
       const char* const t,
       const char resTp,
       const char resICode = ' ');

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Atom(const Vector3& p, const AtomEntryType atp, const char ch, const unsigned short aid, const unsigned short resid, const char* const t, const char resTp, const char* const res, const char resICode );

  Atom(const Vector3& p, const AtomEntryType atp, const char ch,
       const unsigned short aid, const unsigned short resid,
       const char* const t, const char resTp, const char* const res, const char resICode = ' ');

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Atom(const Vector3& p, const AtomEntryType atp, const char ch, const unsigned short aid, const unsigned short resid, const char* const atomName_, const char resTp, const char* const res, const float occup, const float tmp, const char resICode );

  Atom(const Vector3& p, const AtomEntryType atp, const char ch,
       const unsigned short aid, const unsigned short resid,
       const char* const atomName_, const char resTp, const char* const res,
       const float occup, const float tmp, const char resICode = ' ');

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Atom(const Vector3& p, unsigned short aid);

  Atom(const Vector3& p, unsigned short aid);

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explicit Atom(const char* const PDBrec);

A constructor that intiate an atom type from a line of a PDB record

  explicit Atom(const char* const PDBrec);

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char chainId() const;

Returns the chainId - important for working with complexes

  char chainId() const;

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char altLocIndicator() const;

Returns the alternative location indicator.

  char altLocIndicator() const;

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unsigned short atomIndex() const;

returns the atom index in the PDB file

  unsigned short atomIndex() const;

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short residueIndex() const;

returns the residue (thas the atom belongs to) index in the PDB file

  short residueIndex() const;

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char residueICode() const;

returns space if there are no alternatives for this atom, column 26 in PDB format

  char residueICode() const;

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const char *const type() const;

Returns the atom type

  const char *const type() const;

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char residueType() const;

Returns the residue type in one letter code.

  char residueType() const;

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const char *const residueName() const;

Returns the residue type in 3-letter mnemonic. If no matching mnemonic is found a NULL pointer is returned.

  const char *const residueName() const;

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AtomEntryType getAtomEntryType() const;

Return the type of the PDB entry, currently only ATOM and HETATM are identified.

  AtomEntryType getAtomEntryType() const;

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float getOccupancy() const;

Returns the occupancy, which is a measure of the fraction of molecules in the crystal in which the current atom actually occupies the specified position

  float getOccupancy() const;

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float getTempFactor() const;

Returns the temperature factor, which is a measure of how much an atom oscillates or vibrates around the specified position

  float getTempFactor() const;

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void setTempFactor(float ftemp);

Sets new temperature factor

  void setTempFactor(float ftemp);

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bool isBackbone() const;

Returns true if the atom is backbone atom: N, Ca, C, O

  bool isBackbone() const;

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bool isCA() const;

Returns true if the atom is CA atom

  bool isCA() const;

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bool isCB() const;

Returns true if the atom is CB atom

  bool isCB() const;

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bool isN() const;

Returns true if the atom is N atom

  bool isN() const;

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bool isC() const;

Returns true if the atom is C atom

  bool isC() const;

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bool isO() const;

Returns true if the atom is O atom

  bool isO() const;

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bool isH() const;

Returns true if the atom is H atom

  bool isH() const;

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bool isWater() const;

Returns true if the atom is water's atom

  bool isWater() const;

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void setChainId(const char newChainId);

Sets the chain ID for various implementation like the VMD coloring scheme, or RasMol web assignment. Please make sure you use it with accordance to the appropriate software util.

  void setChainId(const char newChainId);

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void setAtomId(unsigned short newAtomId);

Set atomId

  void setAtomId(unsigned short newAtomId);

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Atom& operator*=(const RigidTrans3& rt) ;

applies transformation on Atom coordinates

  Atom& operator*=(const RigidTrans3& rt)                                                        
;

Function is currently defined inline.

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operator RESIDUE_INDEX()const ;

Converts Atom into RESIDUE_INDEX (atoms of the same residue type will have the same RESIDUE_INDEX)

  operator RESIDUE_INDEX()const                        ;

Function is currently defined inline.

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void setSSE(const pair< char,short>& isseInfo) ;

Updates SSE information

  void setSSE(const pair< char,short>& isseInfo)                   
;

Function is currently defined inline.

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pair< char,short> getSSE()const ;

Updates SSE information

  pair< char,short> getSSE()const                 
;

Function is currently defined inline.

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string parseAtomName(const char* const atomName_);

  static string parseAtomName(const char* const atomName_);

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friend ostream& operator<<(ostream& s, const Atom& at);

Writing back the PBD line - without the endline

  friend ostream& operator<<(ostream& s, const Atom& at);

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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);
protected:

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Ancestors

Inheritance chain for Atom:

Vector3

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Descendants

NucleicAcidAtom

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