org.proteinshader.structure.io
Class BetaStrandRecord

java.lang.Object
  org.proteinshader.structure.io.BetaStrandRecord

public class BetaStrandRecord
extends Object

This class is used by the PDBLineParser to temporarily store SHEET records.

SHEET records come before ATOM records in a PDB formatted file. However, it is better to add BetaStrands to the Structure only after all Residues in the ATOM records have been added. By adding BetaStrands last, it is possible for the constructor of a BetaStrand to verify that the BetaStrand's start Residue and end Residue are really present on the Chain the BetaStrand is added to.

The PDBLineParser will parse each SHEET record as soon as it is seen, but will store the info in a BetaStrandRecord object and then use the BetaStrandRecord objects later to add BetaStrands to the Structure.

Constructor Summary

BetaStrandRecord(String chainID, String betaStrandNumber, String sheetID, String startResidueID, String endResidueID, int sense, int strandsInSheet)
Constructs a BetaStrandRecord.

Method Summary

String	getBetaStrandNumber() Returns the BetaStrand number.
String	getChainID() Returns the Chain ID.
String	getEndResidueID() Returns the end Residue ID for the BetaStrand.
int	getSense() Returns the sense (orientation) of the BetaStrand.
String	getSheetID() Returns the ID of the sheet the BetaStrand belongs to.
String	getStartResidueID() Returns the start Residue ID for the BetaStrand.
int	getStrandsInSheet() Returns the total number of strands in the same sheet.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BetaStrandRecord

public BetaStrandRecord(String chainID,
                        String betaStrandNumber,
                        String sheetID,
                        String startResidueID,
                        String endResidueID,
                        int sense,
                        int strandsInSheet)

Constructs a BetaStrandRecord.

Parameters:

chainID - Chain the BetaStrand belongs to.

betaStrandNumber - identifier from PDB SHEET record.

sheetID - ID of the sheet the BetaStrand belongs to.

startResidueID - ID of the first AminoAcid in the sequence.

endResidueID - ID of the last AminoAcid in the sequence.

sense - orientation of the BetaStrand (0, 1, or -1).

strandsInSheet - total number of strands in the beta-sheet.

Method Detail

getChainID

public String getChainID()

Returns the Chain ID.

Returns:

The Chain ID as a String.

getBetaStrandNumber

public String getBetaStrandNumber()

Returns the BetaStrand number.

Returns:

The BetaStrand number as a String.

getSheetID

public String getSheetID()

Returns the ID of the sheet the BetaStrand belongs to.

Returns:

The sheet ID as a String.

getStartResidueID

public String getStartResidueID()

Returns the start Residue ID for the BetaStrand.

Returns:

The start Residue ID as a String.

getEndResidueID

public String getEndResidueID()

Returns the end Residue ID for the BetaStrand.

Returns:

The end Residue ID as a String.

getSense

public int getSense()

Returns the sense (orientation) of the BetaStrand.

Returns:

The sense as an int (0, 1, or -1).

getStrandsInSheet

public int getStrandsInSheet()

Returns the total number of strands in the same sheet.

Returns:

The number of strands as an int.