org.proteinshader.structure.visitor.demos
Class ModifierVisitorDemo

java.lang.Object
  org.proteinshader.structure.visitor.demos.ModifierVisitorDemo

public class ModifierVisitorDemo
extends Object

Temporary class for testing the ModifierVisitor class.

USAGE: java -cp . path/ModifierVisitorDemo inputFilename outputFilename

where path = edu/harvard/fas/jrweber/molecular/structure/visitor/demos/

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

The Helices of the Structure are modified by changing their shape to CYLINDER, their visiblity to OPAQUE, and setting all of their Atoms and Bonds to INVISIBLE. Modifications will then be made and written to 'outputFilename-Modified.out".

Field Summary

static String	PATH
static String	usageMessage

Constructor Summary

ModifierVisitorDemo()
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	modify(Structure structure) The Helices of the Structure are modified by changing their shape to CYLINDER and setting all of their Atoms and Bonds to INVISIBLE.
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

ModifierVisitorDemo

public ModifierVisitorDemo()

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.

modify

public void modify(Structure structure)
            throws VisitorException

The Helices of the Structure are modified by changing their shape to CYLINDER and setting all of their Atoms and Bonds to INVISIBLE.

Parameters:

structure - the Structure to Modify.

Throws:

VisitorException - if an error occurs while modifying the Structure.

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.