io.g96.out
Class OutTrajG96

java.lang.Object
  io.TrajectoryWriter
      io.g96.out.OutTrajG96

public class OutTrajG96

extends TrajectoryWriter

Field Summary

(package private) G96BoxFormatter	boxFormatter
(package private) G96PositionredFormatter	positionredFormatter
(package private) G96TimestepFormatter	timestepFormatter

Fields inherited from class io.TrajectoryWriter

outFile

Constructor Summary

OutTrajG96()

OutTrajG96(java.lang.String title)

OutTrajG96(java.lang.String fName, java.lang.String title)

Method Summary

void	writeFrame(double time, int step, double[][] positions, double[] box)
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	writeFrame(G96Frame frame)
void	writeTitle(java.lang.String title) write more or less proper header information (author, title...)
void	writeTitle(java.lang.String[] 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

Field Detail

timestepFormatter

G96TimestepFormatter timestepFormatter

positionredFormatter

G96PositionredFormatter positionredFormatter

boxFormatter

G96BoxFormatter boxFormatter

Constructor Detail

OutTrajG96

public OutTrajG96()
           throws java.io.IOException

Throws:

java.io.IOException

OutTrajG96

public OutTrajG96(java.lang.String title)
           throws java.io.IOException

Parameters:

title -

Throws:

java.io.IOException

OutTrajG96

public OutTrajG96(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

writeTitle

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

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

writeFrame

public void writeFrame(double time,
                       int step,
                       double[][] positions,
                       double[] box)
                throws java.io.IOException

Throws:

java.io.IOException

writeFrame

public void writeFrame(G96Frame frame)
                throws java.io.IOException

Parameters:

frame -

Throws:

java.io.IOException