StrandPDB

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

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AUTHORS
CHANGES LOG
GOALS
USAGE

Class Summary

class StrandPDB

{
public:
// relative parallelism between the strand in the sheets defintion
// SHEET record constants and methods
// the Strand and the Sheet infromation and methods
static bool isStrand(const char* const PDBrec);
static short strandNum(const char* const PDBrec);
static void strandSheetId(const char* const PDBrec, char id[]);
static short numOfStrandsInSheet(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 RelativeParallelism sense(const char* const PDBrec);
static char currAtom(const char* const PDBrec);
static void currResName(const char* const PDBrec, char res[]);
static char currChainId(const char* const PDBrec);
static int currResSeq(const char* const PDBrec);
static char prevAtom(const char* const PDBrec);
static void prevResName(const char* const PDBrec, char res[]);
static char prevChainId(const char* const PDBrec);
static int prevResSeq(const char* const PDBrec);
protected:
}; // StrandPDB

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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

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

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USAGE

The user is highly recommended not to use this class directly but through the Sheet 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.

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bool isStrand(const char* const PDBrec);

Returns whether the record is of the desired type 

  static bool isStrand(const char* const PDBrec);

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short strandNum(const char* const PDBrec);

Returns the strand number inside the sheet 

  static short strandNum(const char* const PDBrec);

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void strandSheetId(const char* const PDBrec, char id[]);

Copies a three chars that indicate the Sheet Id inside the molecule 

  static void strandSheetId(const char* const PDBrec, char id[]);

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short numOfStrandsInSheet(const char* const PDBrec);

Returns the number of strands in this sheet should be consistent in all the Sheet records 

  static short numOfStrandsInSheet(const char* const PDBrec);

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

Returns the name of the amino acid in the 3 letter code that begins this particular starnd. 

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

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char initChainId(const char* const PDBrec);

Returns the chain Id (if exist) of the begining of the strand. 

  static char initChainId(const char* const PDBrec);

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int initSeqNum(const char* const PDBrec);

Returns the sequence number of the starting residue of the Strand 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);

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

Returns the name of the amino acid in the 3 letter code that ends this particular strand. 

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

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char endChainId(const char* const PDBrec);

Returns the chain Id (if exist) of the ending of the strand. 

  static char endChainId(const char* const PDBrec);

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int endSeqNum(const char* const PDBrec);

Returns the sequence number of the ending residue of the Strand 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);

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RelativeParallelism sense(const char* const PDBrec);

This will return the appropriate constant on the strand's parallelism relative to the previous strand in the sheet NOTICE: the first strand has no previosu strand to realte to 

  static RelativeParallelism sense(const char* const PDBrec);

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char currAtom(const char* const PDBrec);

Returns the first atom in the current strand to create the chemical bond with the previous strand. Asuumed to be either N (the hydrogen that is connected to the nytrogen group) or O. Notice no assertion is made regarding this since in the first strand this line is empty 

  static char currAtom(const char* const PDBrec);

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

The name of the residue in which the atom making the connection reside 

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

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char currChainId(const char* const PDBrec);

The appropriate chain Id of the atom and the related resiue 

  static char currChainId(const char* const PDBrec);

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int currResSeq(const char* const PDBrec);

The residue relative number in the chain 

  static int  currResSeq(const char* const PDBrec);

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char prevAtom(const char* const PDBrec);

Returns the first atom in the previous strand to create the chemical bond with the previous strand. Asuumed to be either N (the hydrogen that is connected to the nytrogen group) or O. Notice no assertion is made regarding this since in the first strand this line is empty 

  static char prevAtom(const char* const PDBrec);

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

The name of the residue in which the atom making the connection reside 

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

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char prevChainId(const char* const PDBrec);

The appropriate chain Id of the atom and the related residue 

  static char prevChainId(const char* const PDBrec);

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int prevResSeq(const char* const PDBrec);

The residue relative number in the chain. Please notice that this number is in the range of the previous strand atom numbers 

  static int  prevResSeq(const char* const PDBrec);

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All Members

public:
// the Strand and the Sheet infromation and methods
static bool isStrand(const char* const PDBrec);
static short strandNum(const char* const PDBrec);
static void strandSheetId(const char* const PDBrec, char id[]);
static short numOfStrandsInSheet(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 RelativeParallelism sense(const char* const PDBrec);
static char currAtom(const char* const PDBrec);
static void currResName(const char* const PDBrec, char res[]);
static char currChainId(const char* const PDBrec);
static int currResSeq(const char* const PDBrec);
static char prevAtom(const char* const PDBrec);
static void prevResName(const char* const PDBrec, char res[]);
static char prevChainId(const char* const PDBrec);
static int prevResSeq(const char* const PDBrec);
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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