org.proteinshader.structure.io
Class HelixRecord

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

public class HelixRecord
extends Object

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

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

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

Constructor Summary

HelixRecord(String chainID, String helixID, String serialNo, String startResidueID, String endResidueID, HelixEnum type)
Constructs a HelixRecord.

Method Summary

String	getChainID() Returns the Chain ID.
String	getEndResidueID() Returns the end Residue ID for the Helix.
String	getHelixID() Returns the Helix ID.
String	getSerialNo() Returns the serial number of the Helix.
String	getStartResidueID() Returns the start Residue ID for the Helix.
HelixEnum	getType() Returns the type of Helix.

Methods inherited from class java.lang.Object

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

Constructor Detail

HelixRecord

public HelixRecord(String chainID,
                   String helixID,
                   String serialNo,
                   String startResidueID,
                   String endResidueID,
                   HelixEnum type)

Constructs a HelixRecord.

Parameters:

chainID - Chain the Helix belongs to.

helixID - Helix identifier from a PDB HELIX record.

serialNo - serial number of the Helix.

startResidueID - ID of the first AminoAcid in the sequence.

endResidueID - ID of the last AminoAcid in the sequence.

type - type of Helix as a HelixEnum.

Method Detail

getChainID

public String getChainID()

Returns the Chain ID.

Returns:

The Chain ID as a String.

getHelixID

public String getHelixID()

Returns the Helix ID.

Returns:

The Helix ID as a String.

getSerialNo

public String getSerialNo()

Returns the serial number of the Helix.

Returns:

The serial number as a String.

getStartResidueID

public String getStartResidueID()

Returns the start Residue ID for the Helix.

Returns:

The start Residue ID as a String.

getEndResidueID

public String getEndResidueID()

Returns the end Residue ID for the Helix.

Returns:

The end Residue ID as a String.

getType

public HelixEnum getType()

Returns the type of Helix.

Returns:

The type as a HelixEnum.