Helix

This class defines the information on the secondary structure alpha helix.

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Class Summary

class Helix

{

public:

	// Constructors
	Helix(const short helixNum , const short sseNum , const int begResidue , const int endResidue , const char beginChn , const char endChn , const unsigned short lenHelix , const HelixType htype );
explicit	Helix(const char* const pdbRec);
	Helix(const Helix& h);

	// Data members information
unsigned short	helixIdNum() const;
unsigned short	sseIdNum() const;
int	startResidue() const;
int	endResidue() const;
char	startChain() const;
char	end_Chain() const;
unsigned short	helixLength() const;
HelixType	helixType() const;
bool	isResidueInHelix(const int resNum) const;
bool	isAtomInHelix(const Atom& at) const;
friend ostream&	operator<<(ostream& s, const Helix& hel);
protected:

}; // Helix

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AUTHORS

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

Copyright: SAMBA group, Tel-Aviv Univ. Israel, 1999.

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CHANGES LOG

02.05.02 - Oranit Shem-Tov (ornit@math.tau.ac.il): - Fixing a small bug in the constructor that gets a PDB line as an input. The bug was with the length field of. It appears that this field is not always contains the length of the helix. For example, take a look at the 1ANT PDB FILE.

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GOALS

This class allows you to check and read the alpha helix lines in a PDB file or read an information on the helix on its on grounds

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USAGE

This class can be used with any relations that need the knowledge of the secondary structure in a molecule. It can be used to define a selector that will work with any kind of selectors (like selecting all the atoms that belong to the alpha helix

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Helix(const short helixNum , const short sseNum , const int begResidue , const int endResidue , const char beginChn , const char endChn , const unsigned short lenHelix , const HelixType htype );

Both the empty constructor and the regular constructor that hold all the infromation.

  Helix(const short helixNum = 0,
	const short sseNum = 0,
        const int begResidue=-1, const int endResidue=-1,
        const char beginChn='?', const char endChn='?', 
        const unsigned short lenHelix=0,
        const HelixType htype = HelixPDB::Unknown);

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explicit Helix(const char* const pdbRec);

A constructor utilizing all the methods in the HelixPDB to read the appropriate information from the helix record in the PDB.

  explicit Helix(const char* const pdbRec);

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Helix(const Helix& h);

Copy Constructor

    Helix(const Helix& h);

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unsigned short helixIdNum() const;

The helix number in the molecule

  inline unsigned short helixIdNum() const;

Function is currently defined inline.

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unsigned short sseIdNum() const;

The SSE number in the molecule

  inline unsigned short sseIdNum() const;

Function is currently defined inline.

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int startResidue() const;

The number of the start residue of the helix. The number is relative to the chain if you read the atoms through the Atom class you might find that residue num 25 in chain B has a different numbering there

  inline int startResidue() const;

Function is currently defined inline.

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int endResidue() const;

The number of the end residue of the helix. The number is relative to the chain if you read the atoms through the Atom class you might find that residue num 25 in chain B has a different numbering there

  inline int endResidue() const;

Function is currently defined inline.

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char startChain() const;

The chain char Id where the helix starts. '?' will be returned if there is no chain in this molecule

  inline char startChain() const;

Function is currently defined inline.

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char end_Chain() const;

The chain char Id where the helix ends. '?' will be returned if there is no chain in this molecule

  inline char end_Chain() const;

Function is currently defined inline.

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unsigned short helixLength() const;

The length of the helix

  inline unsigned short helixLength() const;

Function is currently defined inline.

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HelixType helixType() const;

The type of the helix if it known, the different types can be found in HelixPDB

  inline HelixType      helixType() const;

Function is currently defined inline.

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bool isResidueInHelix(const int resNum) const;

checking if a residue number is in Helix no checking on chain

  inline bool isResidueInHelix(const int resNum) const;

Function is currently defined inline.

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bool isAtomInHelix(const Atom& at) const;

checking if an Atom is in Helix with chain verification

  bool isAtomInHelix(const Atom& at) const;

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friend ostream& operator<<(ostream& s, const Helix& hel);

ostream operator allowing to print all the infromation in a special format: HELIX strat: ( , []) end : ( , []) length = Type =

  friend ostream& operator<<(ostream& s, const Helix& hel);

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All Members

public:

	// Constructors
explicit	Helix(const char* const pdbRec);

	// Data members information
unsigned short	helixIdNum() const;
unsigned short	sseIdNum() const;
int	startResidue() const;
int	endResidue() const;
char	startChain() const;
char	end_Chain() const;
unsigned short	helixLength() const;
HelixType	helixType() const;
bool	isResidueInHelix(const int resNum) const;
bool	isAtomInHelix(const Atom& at) const;
friend ostream&	operator<<(ostream& s, const Helix& hel);
protected:

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Ancestors

Class does not inherit from any other class.

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Descendants

Class is not inherited by any others.

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