SecondStruct

This class encapsulate all the reading of the secondary structure from the PDB file and gives various methods of verification on them

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KEWORDS
AUTHORS
CHANGES LOG
GOALS
USAGE

Class Summary

class SecondStruct

{
public:
// Constructors
SecondStruct();
explicit SecondStruct(const char* const PDBFileName);
SecondStruct(const SecondStruct& ss);
// Data members infromation
const Helices& AlphaHelices() const;
const Sheets& BetaSheets() const;
static void readSSFromPDBFile(const char* const pdbFileName, vector< Helix>& helices, vector< Strand>& strands);
static void readSSFromPDBFile(ifstream& pdbStream, vector< Helix>& helices, vector< Strand>& strands);
static void readSSFromDsspFile(const char* const dsspFileName, vector< Helix>& helices, vector< Strand>& strands);
static void readSSFromDsspFile(ifstream& dsspStream, vector< Helix>& helices, vector< Strand>& strands);
static bool isDsspHelix(char dsspSSType) ;
SecondStruct& operator=(const SecondStruct& rhs);
// Inspecting particular information
Helix& operator[](const int helixId);
Sheet& operator[](const char sheetId);
// Adding information
void addAHelix(const Helix& helix);
void addBSheet(const Sheet& sheet);
// Atoms belogning inspections
bool isResInAHelix(const short helixNum, const int resNum) const;
bool isInBSheet(const char sheetId[], const int resNum) const;
bool isFromSameSS(const vector< short>& indices);
bool isFromSameSS(const short indices[], int len);
SSType residueInSS(const int resNum) const;
short numOfAHelix(const int resNum) const;
const char* numOfBSheet(const int resNum) const;
pair< const char *,short> sheetAndStrandId(const int resNum) const;
friend ostream& operator<<(ostream& s, const SecondStruct& sst);
protected:
}; // SecondStruct

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KEWORDS

secondary, structure, alpha, helix, beta, strand, sheet, connection, molecule, atom, PDB

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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

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GOALS

The goals of this class is save for the user the need to anderstand all the particulars of the representaion of the secondary structures in the PDB and yet allow him to use its infromation. The class has various quering methods

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USAGE

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SecondStruct();

Empty Constructor 

  SecondStruct();

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explicit SecondStruct(const char* const PDBFileName);

A constructor that will read all the relevand infromation from the PDB file and then close it 

  explicit SecondStruct(const char* const PDBFileName);

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SecondStruct(const SecondStruct& ss);

Copy constructor 

  SecondStruct(const SecondStruct& ss);

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const Helices& AlphaHelices() const;

The small array of Helices 

  inline const Helices& AlphaHelices() const;

Function is currently defined inline.


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const Sheets& BetaSheets() const;

The small array of BetaSheets 

  inline const Sheets&  BetaSheets() const;

Function is currently defined inline.


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void readSSFromPDBFile(const char* const pdbFileName, vector< Helix>& helices, vector< Strand>& strands);

Read all the relevant information about the helices and the strands of the molecule, descibed in the givan PDB file and then close it author: Oranit Shem-Tov (ornit@math.tau.ac.il) 

  static void readSSFromPDBFile(const char* const pdbFileName,
				vector< Helix>& helices,
				vector< Strand>& strands);

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void readSSFromPDBFile(ifstream& pdbStream, vector< Helix>& helices, vector< Strand>& strands);

Read all the relevant information about the helices and the strands of the molecule, descibed in the givan PDB stream. Note: After invoking the method, the stream stays open. Author: Oranit Shem-Tov (ornit@math.tau.ac.il) 

  static void readSSFromPDBFile(ifstream& pdbStream,
				vector< Helix>& helices,
				vector< Strand>& strands);

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void readSSFromDsspFile(const char* const dsspFileName, vector< Helix>& helices, vector< Strand>& strands);

Read all the relevant information about the helices and the strands of the molecule, descibed in the givan DSSP file and then close it author: Oranit Shem-Tov (ornit@math.tau.ac.il) 

  static void readSSFromDsspFile(const char* const dsspFileName,
				 vector< Helix>& helices,
				 vector< Strand>& strands);

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void readSSFromDsspFile(ifstream& dsspStream, vector< Helix>& helices, vector< Strand>& strands);

Read all the relevant information about the helices and the strands of the molecule, descibed in the givan DSSP stream. Note: After invoking the method, the stream stays open. Author: Oranit Shem-Tov (ornit@math.tau.ac.il) Implementation Note: The format of the DSSP format is described in the following URL: http://www.cmbi.kun.nl/gv/dssp/descrip.html 

  static void readSSFromDsspFile(ifstream& dsspStream,
                                 vector< Helix>& helices,
                                 vector< Strand>& strands);

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bool isDsspHelix(char dsspSSType) ;

Gets a char which represents a secondary structure assignment and determines if it a helix. Author: Oranit Shem-Tov (ornit@math.tau.ac.il) 

  static bool isDsspHelix(char dsspSSType)                                                                                                                                                       
;

Function is currently defined inline.


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SecondStruct& operator=(const SecondStruct& rhs);

a safe assignment operator 

    SecondStruct& operator=(const SecondStruct& rhs);

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Helix& operator[](const int helixId);

Requesting a certain helix by its id. 

    Helix& operator[](const int helixId);

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Sheet& operator[](const char sheetId);

Requesting a certain sheet by its letter id. If it not found the end of the vector is returned The user need to check this out before proceeding A particular strand can afterwood be requested since the BetaSheet class inherits from SmallArray where a operator[] is defined 

    Sheet& operator[](const char sheetId);

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void addAHelix(const Helix& helix);

Adding a new Helix 

    void addAHelix(const Helix& helix);

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void addBSheet(const Sheet& sheet);

Adding a new Beta sheet 

    void addBSheet(const Sheet& sheet);

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bool isResInAHelix(const short helixNum, const int resNum) const;

Checking whether a certain residue in a certain chain is located in a particular alpha helix 

    bool isResInAHelix(const short helixNum, const int resNum) const;

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bool isInBSheet(const char sheetId[], const int resNum) const;

Checking whether a certain residue in a certain chain is located in a particular beta sheet Since this is done by checking all the strands until finding the strand that the residue is in it, this act might be computationally expensive 

    bool isInBSheet(const char sheetId[],  const int resNum) const;

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bool isFromSameSS(const vector< short>& indices);

given a vector of indecises will return true if the indices come from the same SS structure or not at the moment atoms that come from the same sheet but not from the same strand are considered as from different SS 

    bool isFromSameSS(const vector< short>& indices);

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bool isFromSameSS(const short indices[], int len);

same as above only with a regular array. 

    bool isFromSameSS(const short indices[], int len);

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SSType residueInSS(const int resNum) const;

Making a general search on all the secondary structures returning the type if the residue was found in one of them and known if not 

    SSType residueInSS(const int resNum) const;

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short numOfAHelix(const int resNum) const;

Looking for the residue in all the helices and returning the helix number if found, and -1 if not. 

    short numOfAHelix(const int resNum) const;

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const char* numOfBSheet(const int resNum) const;

Looking for the residue in all the sheets and returning the char id of the sheet if found, and '\0' if not 

    const char* numOfBSheet(const int resNum) const;

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pair< const char *,short> sheetAndStrandId(const int resNum) const;

Looking for the residue in all the sheets and returning a pair the pointer to the char[3] id of the sheet if found, and NULL if not, as the first argument. The strand number in case there is a sheet and -1 if not. 

    pair< const char *,short> sheetAndStrandId(const int resNum) const;

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friend ostream& operator<<(ostream& s, const SecondStruct& sst);

Listing of all the secondary structure in the printing format defined inside Helix, Strand and BetaSheet classes 

  friend ostream& operator<<(ostream& s, const SecondStruct& sst);

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All Members

public:
// Constructors
explicit SecondStruct(const char* const PDBFileName);
// Data members infromation
const Helices& AlphaHelices() const;
const Sheets& BetaSheets() const;
static void readSSFromPDBFile(const char* const pdbFileName, vector< Helix>& helices, vector< Strand>& strands);
static void readSSFromPDBFile(ifstream& pdbStream, vector< Helix>& helices, vector< Strand>& strands);
static void readSSFromDsspFile(const char* const dsspFileName, vector< Helix>& helices, vector< Strand>& strands);
static void readSSFromDsspFile(ifstream& dsspStream, vector< Helix>& helices, vector< Strand>& strands);
static bool isDsspHelix(char dsspSSType) ;
SecondStruct& operator=(const SecondStruct& rhs);
// Inspecting particular information
Helix& operator[](const int helixId);
Sheet& operator[](const char sheetId);
// Adding information
void addAHelix(const Helix& helix);
void addBSheet(const Sheet& sheet);
// Atoms belogning inspections
bool isResInAHelix(const short helixNum, const int resNum) const;
bool isInBSheet(const char sheetId[], const int resNum) const;
bool isFromSameSS(const vector< short>& indices);
bool isFromSameSS(const short indices[], int len);
SSType residueInSS(const int resNum) const;
short numOfAHelix(const int resNum) const;
const char* numOfBSheet(const int resNum) const;
pair< const char *,short> sheetAndStrandId(const int resNum) const;
friend ostream& operator<<(ostream& s, const SecondStruct& sst);
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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