HelixPDB

This class defines a set of tools to be used when trying to read alpha helix secondary structure from the Protein Data Bank file format.

Quick Index

AUTHORS

CHANGES LOG

GOALS

USAGE

Class Summary

class HelixPDB

{

public:
static bool	isHelix(const char* const PDBrec);

	// the Strand and the Sheet infromation and methods
static short	helixID(const char* const PDBrec);
static void	initResName(const char* const PDBrec, char res[]);
static char	initChainID(const char* const PDBrec);
static int	initSeqNum(const char* const PDBrec);
static void	endResName(const char* const PDBrec, char res[]);
static char	endChainID(const char* const PDBrec);
static int	endSeqNum(const char* const PDBrec);
static HelixType	helixClass(const char* const PDBrec);
static unsigned short	length(const char* const PDBrec);
protected:

}; // HelixPDB

Back to the top of HelixPDB

AUTHORS

Zipi Fligelamn (zipo@math.tau.ac.il)

Back to the top of HelixPDB

CHANGES LOG

2.09.01 All PDB indices are shifted, minus one.

Back to the top of HelixPDB

GOALS

Class HelixPDB is designed to serve as an encapsulation to reading secondary structure of the alpha helix kind from the PDB file format. Methods are static requiring no object instantiation before their use.

Back to the top of HelixPDB

USAGE

The user is highly recommended not to use this class directly but through the Helix or SecondStruct class. Though regarding that a line in the PDB record has a length of 80 chars. Acoording to the latest submittion manual the differnt fields and their charechteristic type were defined.

Back to the top of HelixPDB

bool isHelix(const char* const PDBrec);

Returns whether the record is a helix

  static bool isHelix(const char* const PDBrec);

Back to the top of HelixPDB

short helixID(const char* const PDBrec);

Returns the helix number

  static short helixID(const char* const PDBrec);

Back to the top of HelixPDB

void initResName(const char* const PDBrec, char res[]);

Enters into res the 3 letter code of the residue strating the helix

  static void initResName(const char* const PDBrec, char res[]);

Back to the top of HelixPDB

char initChainID(const char* const PDBrec);

Returns the chain Id where the beginning residue resides. if there is no such chain it will return '?' if there is no chain.

  static char initChainID(const char* const PDBrec);

Back to the top of HelixPDB

int initSeqNum(const char* const PDBrec);

Returns the relative sequence number of the starting residue of the helix. Please Notice! that this residue is relative to the chain if you read the atoms through the Atom class you might find that atom 25 in chain B has a different numbering there

  static int initSeqNum(const char* const PDBrec);

Back to the top of HelixPDB

void endResName(const char* const PDBrec, char res[]);

Enters into res the 3 letter code of the residue ending the helix

  static void endResName(const char* const PDBrec, char res[]);

Back to the top of HelixPDB

char endChainID(const char* const PDBrec);

Returns the chain Id where the ending residue resides. if there is no such chain it will return '?' if there is no chain.

  static char endChainID(const char* const PDBrec);

Back to the top of HelixPDB

int endSeqNum(const char* const PDBrec);

Returns the relative sequence number of the ending residue of the helix. Please Notice! that this residue is relative to the chain if you read the atoms through the Atom class you might find that atom 25 in chain B has a different numbering there

  static int endSeqNum(const char* const PDBrec);

Back to the top of HelixPDB

HelixType helixClass(const char* const PDBrec);

Returns the number characteristic to the helix type. this might have mo meaning if you have a very old version of the pdb file. Please make sure you have downloaded the most recent version that comply with the contents guide version 2.1 from October 1996

  static HelixType helixClass(const char* const PDBrec);

Back to the top of HelixPDB

unsigned short length(const char* const PDBrec);

returns the number of amino acids that participate in this helix

  static unsigned short length(const char* const PDBrec);

Back to the top of HelixPDB

All Members

public:
static bool	isHelix(const char* const PDBrec);

	// the Strand and the Sheet infromation and methods
static short	helixID(const char* const PDBrec);
static void	initResName(const char* const PDBrec, char res[]);
static char	initChainID(const char* const PDBrec);
static int	initSeqNum(const char* const PDBrec);
static void	endResName(const char* const PDBrec, char res[]);
static char	endChainID(const char* const PDBrec);
static int	endSeqNum(const char* const PDBrec);
static HelixType	helixClass(const char* const PDBrec);
static unsigned short	length(const char* const PDBrec);
protected:

Back to the top of HelixPDB

Ancestors

Class does not inherit from any other class.

Back to the top of HelixPDB

Descendants

Class is not inherited by any others.

Back to the top of HelixPDB

Generated from source by the Cocoon utilities on Sun Nov 15 13:35:25 2009 .

Report problems to jkotula@unimax.com