
System subroutines: 
<a href="#writeInput">writeInput</a> |
<a href="#writeStructure">writeStructure</a> |
<a href="#writeCSA">writeCSA</a> |
<a href="#writeDynamics">writeDynamics</a> |
<a href="#writeExp_Vol">writeExp_Vol</a> |
<a href="#writeNxyz">writeNxyz</a> |
<a href="#writeiInxyzs">writeiInxyzs</a>

<p>

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
The system YARM subroutines.  These routines are used to
prepare the input files for the various C programs that perform calculations.
Usually, the end user will not ever need to know these routines exist, although,
they are critical to understanding how YARM communicates with the C programs.
<p>

<!--------------------------------------------------------->
<a name="writeInput">
<hr>
<h4>&writeInput</h4>
<b>Summary:</b><br>
<p>

<b>Usage:</b><br>
&writeInput( $file, \%YarmModel, \%NmrParams );
<p>
Inputfile_Write creates a "YARM input file" that allows for the
PERL code to communicate with the C programs.  This file contains
all the information necessary to perform the desired calculation.
<p>

$file = Name of the file to create


<!--------------------------------------------------------->
<a name="writeStructure">
<hr>
<h4>&writeStructure</h4>
<b>Summary:</b><br>
<p>

<b>Usage:</b><br>
&writeStructure( $file, \%YarmModel );
<p>
<b>Description:</b><br>
This routine creates a YARM "structure file" from a 
supplied %YarmModel hash.
<p>
$file = name of output YARM structure file.
<p>
<b>Example:</b><br>

<!--------------------------------------------------------->
<a name="writeCSA">
<hr>
<h4>&writeCSA</h4>
<b>Summary:</b><br>
<p>

<b>Usage:</b><br>
&writeCSA( $file, \%YarmModel, \%NmrParams );
<p>

<b>Description:</b><br>
Creates a YARM CSA input file name $file.
<p>

The format for this file is:<br>
<p>
<b>Example:</b><br>

<!--------------------------------------------------------->
<a name="writeDynamics">
<hr>
<h4>&writeDynamics</h4>
<b>Summary:</b><br>
<p>

<b>Usage:</b><br>
&writeDynamics( $file, \%YarmModel );
<p>

Decsription:<br>
Creates a YARM Dynamics input file name $file.
<p>

The format for this file is:<br>
i ti Si
<p>
where i is the current atom number, ti is the current atom
internal correlation time and Si is the current atom order
parameter
<p>
<b>Example:</b><br>

<!--------------------------------------------------------->
<a name="writeExp_Vol">
<hr>
<h4>&writeExp_Vol</h4>
<b>Summary:</b><br>
<p>

<b>Usage:</b><br>
&writeExp_Vol( $file, \%xyz, \%exp_vol );
<p>

<b>Description:</b><br>
This routine creates a YARM "experimental volumes" file
that contains experimentally measured NOE volumes.

<p>
The expvol file format is "i j exp_vol\n"
<p>
<b>Example:</b><br>


<!--------------------------------------------------------->
<a name="writeNxyz">
<hr>
<h4>&writeNxyz</h4>
<b>Summary:</b><br>
<p>

<b>Usage:</b><br>
&writeNxyz( $file, \%xyz );
<p>

<b>Description:</b><br>
Builds and writes to disk the "nxyz" file
<p>

$file = file name used to write the "nxyz" file<br>
%xyz = one dimensional hash, used to get the coordinates
for the "nxyz" file.
<p>
<b>Example:</b><br>

<!--------------------------------------------------------->
<a name="writeiInxyzs">
<hr>
<h4>&writeiInxyzs</h4>
<b>Summary:</b><br>
<p>

<b>Usage:</b><br>
&writeiInxyz( $file, \%xyz );
<p>

<b>Description:</b><br>
<p>

<b>Example:</b><br>


<!--------------------------------------------------------->
<a name="writeRij_Comparison">
<hr>
<h4>&writeRij_Comparison</h4>
<b>Summary:</b><br>
<p>

<b>Usage:</b><br>
&writeRij_Comparison( \%reference_hash, \%rij_1, \%rij_2, $file);
<p>

<b>Description:</b><br>
<p>

<b>Example:</b><br>

<!--------------------------------------------------------->
<a name="writeCorrelation">
<hr>
<h4>&writeCorrelation</h4>
<b>Summary:</b><br>
<p>

<b>Usage:</b><br>
&writeCorrelation( \%reference_hash, \%hash1, \%hash2, $file );
<p>
<b>Description:</b><br>
<p>

<b>Example:</b><br>

<!--------------------------------------------------------->
<a name="writeCoordinate_Axis">
<hr>
<h4>&writeCoordinate_Axis</h4>
<b>Summary:</b><br>
<p>

<b>Usage:</b><br>
&writeCoordinate_Axis( $file, @Coordinate_Frame, $x, $y, $z );
<p>
<b>Description:</b><br>
This subroutine creates a mini-PDB file named $file that will
represent a coordinate axis system.  This is useful in viewing
reference frames.
<p>
@Coordinate_Frame is nine numbers representing 3 coordinate
axis vectors.
<p>
$x, $y, $z is the coordinate position of the origin of this
coordinate frame
<p>

<b>Example:</b><br>

