org.proteinshader.structure.io.demos
Class PDBStructureReaderDemo

java.lang.Object
  org.proteinshader.structure.io.demos.PDBStructureReaderDemo

public class PDBStructureReaderDemo
extends Object

Temporary class for testing the PDBStructureReader class.

USAGE: java -cp . path/PDBStructureReaderDemo inputFilename outputFilename

where path = edu/harvard/fas/jrweber/molecular/structure/io

After reading 'inputFilename' and creating a Structure, the Structure will be written as an object dump to a file named 'outputFilename.out'.

Any bad lines found while parsing the Structure will be printed to standard error. On Unix, output to standard error can be redirected to a file by placing ' 2> error_filename' as the last thing on the command line used to invoke the program.

Field Summary

static String	PATH
static String	usageMessage

Constructor Summary

PDBStructureReaderDemo()
Constructs a PDBStructureReaderDemo.

Method Summary

String	getFilenameOrDie(String[] cmdLineArgs, int index) Returns the requested command line argument if it is present.
static void	main(String[] args) Uses a PDBStructureReader to read a PDB file and create a Structure, and then uses a WriterVisitor to write the contents of the Structure to an output file.
void	printBadLines(List<String> badLines) Prints the bad lines from the PDB file to standard out.
void	writeStructure(Structure structure, String filename) Writes a Structure to a file by using a SFWriterVisitor.

Methods inherited from class java.lang.Object

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

Field Detail

PATH

public static final String PATH

See Also:

Constant Field Values

usageMessage

public static final String usageMessage

See Also:

Constant Field Values

Constructor Detail

PDBStructureReaderDemo

public PDBStructureReaderDemo()

Constructs a PDBStructureReaderDemo.

Method Detail

writeStructure

public void writeStructure(Structure structure,
                           String filename)
                    throws VisitorException

Writes a Structure to a file by using a SFWriterVisitor. If filename does not exist, it will be created. If it already exists, it will be overridden.

Parameters:

structure - the Structure to write.

filename - the name of the file to write to.

Throws:

VisitorException - if an IO error occurs.

printBadLines

public void printBadLines(List<String> badLines)

Prints the bad lines from the PDB file to standard out. To save bad lines to a file, use the redirection command for standard out, ' > filename'.

Parameters:

badLines - the bad lines to print.

getFilenameOrDie

public String getFilenameOrDie(String[] cmdLineArgs,
                               int index)

Returns the requested command line argument if it is present. Otherwise, prints a usage message to standard out and then terminates the program.

Parameters:

cmdLineArgs - the command line arguments.

index - the index position to get the filename from.

main

public static void main(String[] args)

Uses a PDBStructureReader to read a PDB file and create a Structure, and then uses a WriterVisitor to write the contents of the Structure to an output file.