org.proteinshader.structure.io
Class PDBHelixFieldExtractor

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

public class PDBHelixFieldExtractor
extends Object

Extracts fields from a PDB HELIX record.

The line must be a PDB HELIX record as specified in the the PDB Contents Guide (Version 2.2, 20 Dec 1996).

The column numbers specified in the PDB guide start at 1 rather than at 0, so a field written as (helixID field: 12-14) would be in columns 11-13 in a String.

Constructor Summary

PDBHelixFieldExtractor()
Constructs a PDBHelixFieldExtractor.

Method Summary

String	extractChainID(String line) Obtains the chainID from (initChainID field: 20).
String	extractEndResidueID(String line) Obtains the endResidueID by combining (endResName field: 28-30), (endSeqNum field: 34-37), and the optional (endICode field: 38).
String	extractHelixID(String line) Obtains the helixID from (helixID field: 12-14).
String	extractSerialNo(String line) Obtains the helix serial number from (serial field: 8-10).
String	extractStartResidueID(String line) Obtains the startResidueID by combining (initResName field: 16-18), (initSeqNum field: 22-25), and the optional (initICode field: 26).
HelixEnum	extractType(String line) Extracts the helix type from (helixClass field: 39-40).

Methods inherited from class java.lang.Object

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

Constructor Detail

PDBHelixFieldExtractor

public PDBHelixFieldExtractor()

Constructs a PDBHelixFieldExtractor.

Method Detail

extractSerialNo

public String extractSerialNo(String line)
                       throws PDBFieldExtractorException

Obtains the helix serial number from (serial field: 8-10).

Parameters:

line - a HELIX record at least 80 characters in length.

Returns:

The helix serial number as a String

Throws:

PDBFieldExtractorException - if the helix serial number field cannot be converted to an integer.

extractHelixID

public String extractHelixID(String line)
                      throws PDBFieldExtractorException

Obtains the helixID from (helixID field: 12-14). Leading and trailing whitespace are removed.

Parameters:

line - a HELIX record at least 80 characters in length.

Returns:

The helixID as a String.

Throws:

PDBFieldExtractorException - if a helixID cannot be obtained.

extractChainID

public String extractChainID(String line)
                      throws PDBFieldExtractorException

Obtains the chainID from (initChainID field: 20). If the chainID field is blank, the default chainID from PDBLineParser will be used.

Parameters:

line - a HELIX record at least 80 characters in length.

Returns:

The chainID as a String.

Throws:

PDBFieldExtractorException - if a chainID cannot be obtained.

extractStartResidueID

public String extractStartResidueID(String line)
                             throws PDBFieldExtractorException

Obtains the startResidueID by combining (initResName field: 16-18), (initSeqNum field: 22-25), and the optional (initICode field: 26). A blank space is placed between these fields, and leading and trailing whitespace are removed.

Parameters:

line - a HELIX record at least 80 characters in length.

Returns:

The startResidueID as a String.

Throws:

PDBFieldExtractorException - if the line is too short or either the initResName field or the initSeqNum field is blank.

extractEndResidueID

public String extractEndResidueID(String line)
                           throws PDBFieldExtractorException

Obtains the endResidueID by combining (endResName field: 28-30), (endSeqNum field: 34-37), and the optional (endICode field: 38). A blank space is placed between these fields, and leading and trailing whitespace are removed.

Parameters:

line - a HELIX record at least 80 characters in length.

Returns:

The startResidueID as a String.

Throws:

PDBFieldExtractorException - if the line is too short or either the endResName field or the endSeqNum field is blank.

extractType

public HelixEnum extractType(String line)
                      throws PDBFieldExtractorException

Extracts the helix type from (helixClass field: 39-40). If the field is blank, null will be returned (the Helix constructor will use a default HelixEnum if given null as the type). Otherwise, the number in the helixClass field will be converted to a HelixEnum type.

Parameters:

line - a HELIX record at least 80 characters in length.

Returns:

The helix type as a HelixEnum.

Throws:

PDBFieldExtractorException - if the char in the helixClass field cannot be matched to a known type or if the record is too short.