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* Viewmol *
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* N O D E 2 9 . H T M L *
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* Copyright (c) Joerg-R. Hill, December 2000 *
* *
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<TITLE>Data files</TITLE>
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<H1>
<BR>
Data files
</H1>
<A NAME="datafile">
V<SMALL>IEWMOL</SMALL> uses a data file named <code>viewmolrc</code> for getting informations
about atoms and available input and output filters. There may be three of these
files. V<SMALL>IEWMOL</SMALL> looks at first in the current directory for this file,
then in the users HOME directory for a file <code>.viewmolrc</code> and finally in
the directory where the environment variable <code>VIEWMOLPATH</code> points to.
In one of these three locations such a file must be found.
The file should contain the following data:
<P>
<UL>
<LI>Lines of the format:
<BR>
option <MATH CLASS=INLINE><</MATH>name of option<MATH CLASS=INLINE>></MATH>
<MATH CLASS=INLINE><</MATH>name of input filter<MATH CLASS=INLINE>></MATH>
[<MATH CLASS=INLINE><</MATH>command line options for input filter<MATH CLASS=INLINE>
></MATH>] "<MATH CLASS=INLINE><</MATH>characteristic string<MATH CLASS=INLINE>
></MATH>"
<BR>
These lines define the input filter for V<SMALL>IEWMOL</SMALL> and the command line
options connected with them (i. e. you can change the command line option if
you want). <>option> is the command line option V<SMALL>IEWMOL</SMALL> expects on its
command line or the word <code>default</code>. The input filter connected with
<code>default</code> is used if no command line option is passed to V<SMALL>IEWMOL</SMALL>.
If no default input filter is specified V<SMALL>IEWMOL</SMALL> displays a file selection
box in this case.
<name of input filter> is the path to and name of the input filter
executable. If the input filter requires command line option (e. g. a file
name) they can be specified after the name of the input filter. <code>%s</code> is
used as a placeholder for file names. The path or name of the input filter can
contain environment variables or the string <code>$OSNAME</code>. The latter is
replaced by the subdirectory name for the machine V<SMALL>IEWMOL</SMALL> is currently
running on. <characteristic string> is a string which is used to identify
the type of a particular file. The first 1024 characters of an input file passed
to V<SMALL>IEWMOL</SMALL> are scanned for this string and the input filter connected
with the string is then used to read the file. Therefore these strings have to
be unique for each input filter and have to be in every file of a certain type
within the first 1024 characters. Since most programs write their names out
at the beginning these restrictions seem to be no problem.
</LI>
<LI>Lines of the format:
<BR>
output <MATH CLASS=INLINE><</MATH>reference to resources<MATH CLASS=INLINE>>
</MATH> <MATH CLASS=INLINE><</MATH>name of output filter<MATH CLASS=INLINE>
></MATH> [<MATH CLASS=INLINE><</MATH>command line options for output filter
<MATH CLASS=INLINE>></MATH>] <code>%s</code>
<BR>
These lines define the output filter for V<SMALL>IEWMOL</SMALL>. <reference to resources>
is an arbitrary string which must refer to a resource in the Xdefaults file.
This string is used to provide the label for the output filter in the output
filter selection box. <name of output filter> is the path to and name of
the output filter executable. All output filters should at least accept the name
of the output file from their command lines. If additional parameters are required
they can also be specified after the name of the output filter. <code>%s</code> is
used as a placeholder for the output file name. Environment variables or
the string <code>$OSNAME</code> can be used in the same way as for input filters.
</LI>
<LI>Lines of the format:
<BR><MATH CLASS=INLINE><</MATH>symbol<MATH CLASS=INLINE>></MATH>
<MATH CLASS=INLINE><</MATH>rad<MATH CLASS=INLINE>></MATH> <MATH CLASS=INLINE>
<</MATH>rd<MATH CLASS=INLINE>></MATH> <MATH CLASS=INLINE><</MATH>gd
<MATH CLASS=INLINE>></MATH> <MATH CLASS=INLINE><</MATH>bd<MATH CLASS=INLINE>
></MATH><MATH CLASS=INLINE><</MATH>rl<MATH CLASS=INLINE>></MATH>
<MATH CLASS=INLINE><</MATH>gl<MATH CLASS=INLINE>></MATH> <MATH CLASS=INLINE>
<</MATH>bl<MATH CLASS=INLINE>></MATH><MATH CLASS=INLINE><</MATH>surface
<MATH CLASS=INLINE>></MATH>
<BR><symbol> is an atomic symbol, <rad> is the Van der Waals radius
of this atom in ngstrms, <rd>, <gd> and <bd> are the red,
green and blue color for the darkest part of this atom and <rl>, <gl>
and <bl> are the red, green and blue color for the lightest part of the atom.
There are four reserved strings for <symbol>. If <symbol> is <code>bd</code>
the following description describes a hydrogen bond. The <rad$> field is also
interpreted as the radius of all bond sticks. All other fields are only applied
to hydrogen bonds. <code>uc</code> specifies a unit cell corner. Radius and color
given here affect the appearance of the unit cell. <code>ps</code> and <code>ms</code>
specify the surface properties for the positive and negative isosurface,
respectively, used to draw wave function related topics. In these cases the
radius is not used. <surface> is an optional specification for the surface
used when stick, ball, or CPK drawing with surfaces is activated. <surface>
is a list of one or more of the following options
<UL>
<LI>emission <MATH CLASS=INLINE><</MATH>r<MATH CLASS=INLINE>></MATH>
<MATH CLASS=INLINE><</MATH>g<MATH CLASS=INLINE>></MATH>
<MATH CLASS=INLINE><</MATH>b<MATH CLASS=INLINE>></MATH>
<BR>
The emission color of the surface. Using this option causes the
surface to emit light. <r>, <g>, and <b> are the red,
green and blue components for the light color.
</LI>
<LI>ambient <MATH CLASS=INLINE><</MATH>r<MATH CLASS=INLINE>>
</MATH> <MATH CLASS=INLINE><</MATH>g<MATH CLASS=INLINE>></MATH>
<MATH CLASS=INLINE><</MATH>b<MATH CLASS=INLINE>></MATH>
<BR>
The ambient light which is reflected by the surface. <r>, <g>,
and <b> are the red, green and blue components for the light color.
</LI>
<LI>specular <MATH CLASS=INLINE><</MATH>r<MATH CLASS=INLINE>></MATH>
<MATH CLASS=INLINE><</MATH>g<MATH CLASS=INLINE>></MATH>
<MATH CLASS=INLINE><</MATH>b<MATH CLASS=INLINE>></MATH>
<BR>
The specular light which is reflected by the surface. <r>,
<g>, and <b> are the red, green and blue components
for the light color.
</LI>
<LI>shininess <MATH CLASS=INLINE><</MATH>n<MATH CLASS=INLINE>></MATH>
<BR>
A parameter which determines the kind of reflection. <n>
can be in the range 0 ... 128.
</LI>
<LI>alpha <MATH CLASS=INLINE><</MATH>n<MATH CLASS=INLINE>></MATH>
<BR>
This parameter determines the transparency of the surface.
</LI>
</UL>
All color specifications can be between 0.0 and 1.0. The total length
of a line specifying an atom is restricted to 132 characters. The keywords
for the surface specifications can be abbreviated with the first two letters.
</LI>
</UL>
<P>
Any line starting with '#' is treated as a comment.
<P>
<A NAME="defaults">
V<SMALL>IEWMOL</SMALL> makes extensive use of X Windows resources. All standard
search algorithms for the location of the resources apply (see e. g. O'Reilly
books on X Windows). V<SMALL>IEWMOL</SMALL> has English resources compiled in. Resources
for other languages are provided in files <code>Xdefaults.<language></code> and might
be installed as described in the installation section of this manual (p.
<A HREF="node3.html#installation"><IMG ALIGN="BOTTOM" BORDER="1" ALT="[*]"
SRC="crossref.png"></A>).
<P>
The following resources are used to specify the defaults. They can be
overwritten in the user's <code>$HOME/.Xdefaults</code> file or, in part, by
the configuration options available in the program. Defaults configurable
from within the program are marked with an asterisk (*).
<A NAME="granularity">
<A NAME="interpolation">
<A NAME="density">
<A NAME="bondtypes">
<A NAME="automatic">
<PRE>
Viewmol*geometry: 500x500+50+50 (*)
Viewmol.history.geometry: 500x250+50+590 (*)
Viewmol.spectrum.geometry: 500x250+50+590 (*)
Viewmol.MODiagram.geometry: 250x500+565+50 (*)
Viewmol.Bell: <no default>
Viewmol.model: wire (*)
Viewmol.drawingMode: surface (*)
Viewmol.bondType: conjugated (*)
Viewmol.sphereResolution: 10 (*)
Viewmol.simplifyWhileRotating: True (*)
Viewmol.interpolation: linear (*)
Viewmol.bondLength: %7.4f Ang
Viewmol.bondAngle: %7.2f deg
Viewmol.torsionAngle: %7.2f deg
Viewmol.wavenumbers: 0:5000
Viewmol.isosurface: 0.05 (*)
Viewmol.reservedColors: 0
Viewmol*spectrumForm*amplitudeSlider.decimalPoints: 2
Viewmol*spectrumForm*amplitudeSlider.minimum: -250
Viewmol*spectrumForm*amplitudeSlider.maximum: 250
Viewmol*spectrumForm*scaleSlider.decimalPoints: 2
Viewmol*spectrumForm*scaleSlider.minimum: 50
Viewmol*spectrumForm*scaleSlider.maximum: 150
Viewmol*wavefunctionForm*level.minimum: 1
Viewmol*wavefunctionForm*level.maximum: 100
Viewmol*wavefunctionForm*grid.minimum: 4
Viewmol*wavefunctionForm*grid.maximum: 20
Viewmol*wavefunctionForm*grid.value: 10
Viewmol*MODiagramForm*resolution.minimum: 1
Viewmol*MODiagramForm*resolution.maximum: 1000
Viewmol*MODiagramForm*resolution.decimalPoints: 3
Viewmol*MODiagramForm*resolution.value: 10
Viewmol.paperSize: A4 (*)
Viewmol.viewer*font: variable
Viewmol.spectrum*font: variable
Viewmol.history*font: variable
Viewmol.MODiagram*font: variable
Viewmol.viewer.background: white (*)
Viewmol.viewer.foreground: gray75 (*)
Viewmol*spectrum.spectrum.background: white (*)
Viewmol*spectrum.spectrum.foreground: black (*)
Viewmol*history.history.background: white (*)
Viewmol*history.history.foreground: blue (*)
Viewmol*MODiagram.MODiagram.background: white (*)
Viewmol*MODiagram.MODiagram.foreground: black (*)
Viewmol*foreground: black (*)
</PRE>
<P>
The <code>Viewmol.Bell</code> resource is the only resource which does not have
a default. As long as this resource is not set the standard keyboard bell
is rung as soon as a selection in one of the windows is made by mouse click.
This resource can be set to the name (and command line parameters) of any
program which shall be run instead, preferably one which produces a nicer
sound effect.
<P>
The <code>Viewmol.model</code> resource can be set to wire, stick, ball, or cpk.
The <code>Viewmol.drawingMode</code> resource can be set to dot, line, or surface.
The <code>Viewmol.bondType</code> resource can be set to single, multiple, or
conjugated. The <code>Viewmol.interpolation</code> resource can be set to none,
linear, or logarithmic. The resources for specifying formats for bond lengths,
bond angles, and torsion angles have to contain a valid C format string for
printing a floating point number. The resource for the bond lengths recognizes
Ang, pm, bohr, and au in the format string as units and converts the bond
lengths accordingly. The <code>Viewmol.reservedColors</code> resource can be used to
limited the number of colors allocated by V<SMALL>IEWMOL</SMALL> if it runs in colormap
mode. V<SMALL>IEWMOL</SMALL> tries to allocate as much colors as it can. This might
interfere with others program. In this case <code>Viewmol.reservedColors</code>
can be used to tell V<SMALL>IEWMOL</SMALL> to leave the specified number of colors
unallocated. In case of the specifications for the sliders the values given for
minimum and maximum have to be multiplied by 10<SUP>decimalPoints</SUP>.
I. e. if the number of decimals is to be changed also minimum and maximum have to be
changed. Paper sizes currently recognized are A5, A4, A3, Letter, Legal, and
<width> x <height> where <width> and <height>
are in millimeters.
<P>
The <code>Viewmol.viewer.foreground</code> resource is used for the color
of the ground if perspective drawing is enabled.
<P>
<BR><HR>
<ADDRESS>
<A HREF="mailto:joehill@users.sourceforge.net"><I>Jrg-Rdiger Hill</I></A><BR>Sun Dec 10 17:38:35 MET 2000
</ADDRESS>
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