io.xplor
Class OutXPlor

java.lang.Object
  io.TrajectoryWriter
      io.xplor.OutXPlor

public class OutXPlor

extends TrajectoryWriter

Output X-PLOR crystallographic map files.

For a definition of the X-PLOR file format, see e.g. the X-PLOR 98 manual, as currently available at http://www.scripps.edu/rc/softwaredocs/msi/xplor981/formats.html

A quick repetition of the X-PLOR crystallographic map format (which we will refer to as the xplor format from now on): these files consist of a header, the density array and a footer.

The header consists of:

• Line 1: an empty line
• Line 2-5: four 80-character strings containing title information
• Line 6: a series of nine integers N_a, A_min, A_max, N_b, B_min, B_max, N_c, C_min, C_max, corresponding to the number of grid points along each cell edge and the starting/ending grid point for each dimension. The format corresponds to the FORTRAN format 9I8.
• Line 7: A series of floats corresponding to the cell dimensions a, b, c, α, β, γ. The format corresponds to the FORTRAN format 6E12.5.
• Line 8: A line that always reads "ZYX".

The density array consists of

• A line stating the section (i.e. slice along the z-axis) number KSECT, corresponding to the FORTRAN statement WRITE(OUNIT,'(I8)') KSECT.
• The contents of this section, corresponding to the FORTRAN statement WRITE(OUNIT,'(6E12.5)') ((SECTON(I,J),I=1,ISECT),J=1,JSECT).

The footer consists of

• a terminator line, containing the integer -9999 written using the FORTRAN statement (I8).
• a line containing two numbers corresponding to the average and the standard deviation of the electron density. The format corresponds to (2(E12.4,1X)).

Author:

Vincent Kraeutler

Field Summary

(package private) static PrintfFormat	xPlorDoubleFormat
(package private) static PrintfFormat	xPlorIntFormat

Fields inherited from class io.TrajectoryWriter

outFile

Constructor Summary

OutXPlor(java.lang.String title)

OutXPlor(java.lang.String fileName, java.lang.String title)

Method Summary

static java.lang.String	makeCellSpecs(double[] cellSpecs)
static java.lang.String	makeFooter(double[][][] grid)
static java.lang.String	makeGridSpecs(int[] gridSpecs)
static java.lang.String	makeHeader(int[] gridSpecs, double[] cellSpecs)
static java.lang.String	makeTitle(java.lang.String title)
void	writeDensityArray(double[][][] grid)
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	writeMap(int[] gridSpecs, double[] cellSpecs, double[][][] grid) write an X-PLOR crystallographic map
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

Field Detail

xPlorIntFormat

static final PrintfFormat xPlorIntFormat

xPlorDoubleFormat

static final PrintfFormat xPlorDoubleFormat

Constructor Detail

OutXPlor

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

OutXPlor

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

Method Detail

makeTitle

public static java.lang.String makeTitle(java.lang.String title)

makeGridSpecs

public static java.lang.String makeGridSpecs(int[] gridSpecs)

makeCellSpecs

public static java.lang.String makeCellSpecs(double[] cellSpecs)

makeHeader

public static java.lang.String makeHeader(int[] gridSpecs,
                                          double[] cellSpecs)

writeDensityArray

public void writeDensityArray(double[][][] grid)
                       throws java.lang.IllegalArgumentException,
                              java.io.IOException

Throws:

java.lang.IllegalArgumentException

java.io.IOException

makeFooter

public static java.lang.String makeFooter(double[][][] grid)

writeMap

public void writeMap(int[] gridSpecs,
                     double[] cellSpecs,
                     double[][][] grid)
              throws java.io.IOException

write an X-PLOR crystallographic map

Parameters:

gridSpecs - the grid layout (see class definition for details)

cellSpecs - the cell layout (see class definition for details)

grid - the grid values

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

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