io
Class TrajectoryWriter

java.lang.Object
  io.TrajectoryWriter

Direct Known Subclasses:

OutPDB, OutPosG96, OutTrajG96, OutVMDAM, OutXPlor

public abstract class TrajectoryWriter

extends java.lang.Object

Author:

vincent

Field Summary

(package private) java.lang.String	fileName
protected java.io.OutputStreamWriter	outFile

Constructor Summary

TrajectoryWriter(java.lang.String title)

TrajectoryWriter(java.lang.String fName, java.lang.String title)

Method Summary

static TrajectoryWriter	getWriter(java.lang.String format, java.lang.String title) Get a trajectory writer for a given output format.
abstract void	writeFrame(double time, int step, double[][] positions, double[] box, java.lang.String[] atomNames, java.lang.String[] residueNames, int[] residueNumbers) Format-agnostic trajectory writer.
abstract void	writeTitle(java.lang.String title) write more or less proper header information (author, title...)

Methods inherited from class java.lang.Object

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

Field Detail

fileName

java.lang.String fileName

outFile

protected java.io.OutputStreamWriter outFile

Constructor Detail

TrajectoryWriter

public TrajectoryWriter(java.lang.String title)
                 throws java.io.IOException

Parameters:

title - the pdb title block

Throws:

java.io.IOException

TrajectoryWriter

public TrajectoryWriter(java.lang.String fName,
                        java.lang.String title)
                 throws java.io.IOException

Parameters:

fName - the file name

title - the pdb title block

Throws:

java.io.IOException

Method Detail

writeTitle

public abstract void writeTitle(java.lang.String title)
                         throws java.io.IOException

write more or less proper header information (author, title...)

Parameters:

title - the title block

Throws:

java.io.IOException

writeFrame

public abstract void writeFrame(double time,
                                int step,
                                double[][] positions,
                                double[] box,
                                java.lang.String[] atomNames,
                                java.lang.String[] residueNames,
                                int[] residueNumbers)
                         throws java.io.IOException

Format-agnostic trajectory writer. Since every format actually writes different things, we have to supply all information that might be required by any format... the implementation of simpler custom interfaces is up to the respective writer implementations.

Parameters:

time - the time of the frame

step - corresponds to a given time step (g96, vmd) or model serial (pdb)

positions - the 3N coordinates

box - the 3 box dimensions (ignored by pdb)

atomNames - the N atom names

residueNames - the N residue names of the atoms

residueNumbers - the N residue numbers of the atoms

Throws:

java.io.IOException

getWriter

public static TrajectoryWriter getWriter(java.lang.String format,
                                         java.lang.String title)
                                  throws java.io.IOException

Get a trajectory writer for a given output format.

Parameters:

format - the desired output format.

title - title to be written.

Returns:

appropriate trajectoryWriter

Throws:

java.io.IOException