io.vmd
Class OutVMDAM

java.lang.Object
  io.TrajectoryWriter
      io.vmd.OutVMDAM

public class OutVMDAM

extends TrajectoryWriter

Author:

vincent

Field Summary

Fields inherited from class io.TrajectoryWriter

outFile

Constructor Summary

OutVMDAM(java.lang.String title)

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

Method Summary

void	writeFrame(double time, int step, double[][] positions, double[] box, java.lang.String[] atomNames, java.lang.String[] residueNames, int[] residueNumbers) Format-agnostic trajectory writer.
void	writeTitle(java.lang.String title) write more or less proper header information (author, title...)

Methods inherited from class io.TrajectoryWriter

getWriter

Methods inherited from class java.lang.Object

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

Constructor Detail

OutVMDAM

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

Parameters:

title -

Throws:

java.io.IOException

OutVMDAM

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

Parameters:

fName -

title -

Throws:

java.io.IOException

Method Detail

writeTitle

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

Description copied from class: TrajectoryWriter

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

Specified by:

writeTitle in class TrajectoryWriter

Parameters:

title - the title block

Throws:

java.io.IOException

writeFrame

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

Description copied from class: TrajectoryWriter

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.

Specified by:

writeFrame in class TrajectoryWriter

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