org.proteinshader.structure.io
Class PDBStructureReader

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

All Implemented Interfaces:

StructureReader

public class PDBStructureReader
extends Object
implements StructureReader

This concrete implementation of interface StructureReader reads a protein structure entry from a '.pdb' file formated according to the PDB Contents Guide (Version 2.2, 20 Dec 1996) and creates a Structure.

The first line of the file must start with 'HEADER' to indicate a PDB header record, and a complete list of the record types that need to be recognized are specified in the RecordEnum enumeration of package io.enums. A PDBLineParser is used to assist the readFile() method.

Currently, PDBStructureReader only reads protein (amino acids and heterogens). It does not read DNA, but that capability will be added at a later time (beyond the scope of this thesis).

Field Summary

static int

MIN_CHAR_IN_HEADER The minimum number of columns in a HEADER record.

Constructor Summary

PDBStructureReader()
Creates a PDBStructureReader.

Method Summary

List<String>	getBadLines() Returns a list with any bad lines that were found the last time readStructure() was called.
Structure	readStructure(File file) Reads a protein structure from a ".pdb" file and returns a Structure object.
Structure	readStructure(String filename) Reads a protein structure from a ".pdb" file and returns a Structure object.

Methods inherited from class java.lang.Object

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

Field Detail

MIN_CHAR_IN_HEADER

public static final int MIN_CHAR_IN_HEADER

The minimum number of columns in a HEADER record.

See Also:

Constant Field Values

Constructor Detail

PDBStructureReader

public PDBStructureReader()

Creates a PDBStructureReader.

Method Detail

readStructure

public Structure readStructure(String filename)
                        throws StructureReaderException

Reads a protein structure from a ".pdb" file and returns a Structure object.

The first line of a PDB formatted file must be a HEADER record with a PDB ID code. A StructureReaderException will be thrown if a problem occurs.

Serious errors which prevent obtaining a Structure will result in a StructureReaderException (e.g., The file cannot be found or does not appear to be a PDB formatted file). Errors such as a bad individual record (a single line) will be recorded in a list of bad lines that can be obtained with the getBadLines() method.

Specified by:

readStructure in interface StructureReader

Parameters:

filename - the name of the PDB formatted file to read.

Returns:

The newly created Structure.

Throws:

StructureReaderException - if a serious error occurs while parsing the PDB file.

readStructure

public Structure readStructure(File file)
                        throws StructureReaderException

Reads a protein structure from a ".pdb" file and returns a Structure object.

The first line of a PDB formatted file must be a HEADER record with a PDB ID code. A StructureReaderException will be thrown if a problem occurs.

Serious errors which prevent obtaining a Structure will result in a StructureReaderException (e.g., The file cannot be found or does not appear to be a PDB formatted file). Errors such as a bad individual record (a single line) will be recorded in a list of bad lines that can be obtained with the getBadLines() method.

Specified by:

readStructure in interface StructureReader

Parameters:

file - the PDB formatted file to read.

Returns:

The newly created Structure.

Throws:

StructureReaderException - if a serious error occurs while parsing the PDB file.

getBadLines

public List<String> getBadLines()

Returns a list with any bad lines that were found the last time readStructure() was called.

Specified by:

getBadLines in interface StructureReader

Returns:

A list of invalid lines from a PDB formatted file.