Package etomica.action

Class PDBWriter

java.lang.Object

etomica.action.PDBWriter

All Implemented Interfaces:

IAction

public class PDBWriter
extends java.lang.Object
implements IAction

Action that dumps a box's configuration to an PDB file. Arbitrary but unique elements are assigned to each atom type. After writing the PDB file, writeRasmolScript can be called to write a script that will properly initialize the atomic radii.

Constructor Summary

Constructors

Constructor	Description
PDBWriter()
PDBWriter(Box aBox)

Method Summary

Modifier and Type	Method	Description
void	actionPerformed()	Completes the action defined by the class implementing this interface.
void	setBox(Box newBox)
void	setFile(java.io.File newFile)	Sets the file to write to.
void	setFileName(java.lang.String fileName)	Sets the file name to write to.
void	writeRasmolScript(DiameterHashByType diameterHash)	Writes a script for rasmol that initializes the radii of each atom type.

Methods inherited from class java.lang.Object

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

Constructor Detail

PDBWriter

public PDBWriter()

PDBWriter

public PDBWriter(Box aBox)

Method Detail

setBox

public void setBox(Box newBox)

setFile

public void setFile(java.io.File newFile)

Sets the file to write to. This method (or setFileName) must be called before calling actionPerformed and again before calling writeRasmolScript.

setFileName

public void setFileName(java.lang.String fileName)

Sets the file name to write to. This method (or setFile) must be called before calling actionPerformed and again before calling writeRasmolScript.

actionPerformed

public void actionPerformed()

Description copied from interface: IAction

Completes the action defined by the class implementing this interface.

Specified by:

actionPerformed in interface IAction

writeRasmolScript

public void writeRasmolScript(DiameterHashByType diameterHash)

Writes a script for rasmol that initializes the radii of each atom type. The DiameterHashByType is used to provide radii.