io.pdb
Class OutPDB

java.lang.Object
  io.TrajectoryWriter
      io.pdb.OutPDB

public class OutPDB

extends TrajectoryWriter

Author:

mika, vincent

Field Summary

(package private) static PrintfFormat

modelSerialFormat

Fields inherited from class io.TrajectoryWriter

outFile

Constructor Summary

OutPDB(java.lang.String title)

OutPDB(java.lang.String fileName, 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) attempt to write a reasonably correct pdb MODEL block.
void	writeFrame(int step, double[][] positions, java.lang.String[] atomNames, java.lang.String[] residueNames, int[] residueNumbers) attempt to write a reasonably correct pdb MODEL block.
void	writeTitle(java.lang.String title) write more or less proper pdb 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

Field Detail

modelSerialFormat

static final PrintfFormat modelSerialFormat

Constructor Detail

OutPDB

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

Parameters:

title -

Throws:

java.io.IOException

OutPDB

public OutPDB(java.lang.String fileName,
              java.lang.String title)
       throws java.io.IOException

Parameters:

fileName -

title -

Throws:

java.io.IOException

Method Detail

writeTitle

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

write more or less proper pdb 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

attempt to write a reasonably correct pdb MODEL block. one should in principle be able to generate a trajectory by concatenating a bunch of MODEL blocks.

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

See Also:

TrajectoryWriter.writeFrame(double, int, double[][], double[], java.lang.String[], java.lang.String[], int[])

writeFrame

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

attempt to write a reasonably correct pdb MODEL block. one should in principle be able to generate a trajectory by concatenating a bunch of MODEL blocks.

Throws:

java.io.IOException

See Also:

TrajectoryWriter.writeFrame(double, int, double[][], double[], java.lang.String[], java.lang.String[], int[])