ChemRote README File
The following is a brief introduction to java, hopefully enough to
enable you to use the ChemRote applet. The text on java is an excerpt
from a short Java faq I wrote, the rest is the specifics for installing
and using ChemRote.
Table of Contents:
Java, unlike HTML, is a programming language. This means to create
something in Java, you should have a basic knowledge of Java. Java can
be used to write stand alone programs, called applications, or for
programs that run within a web page, called applets.
To run Java on a web page, the applet must be embeded within an HTLM
document. This is done with the applet tag. This tag can be used to
specify a Java applet, its size, as well as any parameters that are
specific to that applet.
The starting <applet> tag has several components. These include the
applet name (Java program to be executed), as well as the width and
height of the applet, within the HTML page. An optional codebase
(directory the applet resides in) can also be included. For an applet
named Test.class, in the java directory, with a width of 20 and height
of 10, would look like this:
<applet codebase="/java" code="Test.class" width=20 height=10>
</applet>
Notice the tag closer, </applet>. All parameter files go between the
<applet> tag and the </applet> tag. If you wanted to include an HTML
tag that would be seen on a browser that could not see your applet (a
non Java-enabled browser), then that code would also be between the
<applet> and >/applet> tags. Note that this extra code is ignored by
browsers that are Java enabled.
A parameter tag for an applet has two fields in it, the name, and the
value. Lets say our previous example had a parameter called color, and
we wanted to set it to red. Lets also assume that we want to load an
image called NoJava.gif if they can't see the applet. The code would
then look like this:
<applet codebase="/java" code="Test.class" width=20 height=10>
<param name="color" value="red">
<img src="NoJava.gif">
</applet>
This is a very simple applet, that will display a molecule as set of vectors
in a web page. It will allow a user to directly interact with the molecule
through rotating and resizing directly on the page.
The ChemRote applet comes in two distributions, at tarred, gziped
archive for Uniz platforms, and a zipped file for Windows platforms.
If you require a compressed file of another type, contact John N. Huffman
at jnhuffma@indiana.edu, and arrangements will be made.
To unpack the tarred gzipped file (ChemRote.tar.gz), go to the directory
you wish to install the files into. This must be within the directory
tree of your HTML files being served by your web server. Then use
the command:
gzip -cd ChemRote.tar.gz | tar xvf -
This will extract the files into a directory called ChemRote. If you
just wish to see the contents of the archive file, use:
gzip -cd ChemRote.tar.gz | tar tvf -
To unpack the zipped archive file (ChemRote.zip), go to the directory
you wish to install the files into. This must be within the directory
tree of your HTML files being served by your web server. Then use the
command:
pkunzip -d ChemRote.zip
This will extract the files into a directory called ChemRote. If you just
want to see the contents of the archive file, use:
pkunzip -v ChemRote.zip
To include this applet in an HTML page, use the following tag if
you unpacked the ChemRote archive in the root directory of your
web server files:
<applet codebase="/ChemRote" code="ChemRote.class" width=20 height=10>
<PARAM NAME="model" value="bucky.crt">
</applet>
Note that the tags for the applet are not case sensitive, but the
valuse are, so if the crt file were BUCKY.CRT, type it in the same
case in the value field:
<PARAM NAME="model" value="BUCKY.CRT">
For more Information on including a Java applet, see section 1.1,
Using a Java applet on a web Page.
There are several parameters that can be used to modify the way this
applet looks. Depending on which parameter you use, different parts
of the program are loaded on the clients machine when the applet is
started. Below is a list of the parameters the applet will accept,
as well as any additional information that may be needed.
| Parameter Name:
| Parameter Value:
|
|---|
|
|
| model* | crt file name
|
| background | background color
|
| border** | include a border
|
| image** | include a tiled background image
|
*This is a required parameter.
**This causes the web browser to load an extra file when the
applet is loaded, but generally won't take much longer than if
it were not use.
The model parameter gives the name of the crt file to be used for the
applet. This is the only parameter that is required. It has the
following form:
<PARAM NAME="model" VALUE="bucky.crt">
This applet came with a test file called bucky.crt. The above tag works
if the file bucky.crt is in the same directory as the ChemRote applet.
If it is in another location, specify the path relative to the web files
on your server. For example, if all your web files are in /usr/local/www,
and your data files (crt files) are in /usr/local/www/data, then the
parameter name would look like:
<PARAM NAME="model" VALUE="/data/bucky.crt">
The background parameter specifies a background color for the applet, and if it is
not specified, defaults to grey. The value uses the same form as any
other color in an HTML tag, RRGGBB, where each set of letters represents
the hexadecimal values of a red, a green, and a blue value between 0 (00)
and 255 (FF). The only difference between this and a regular color tag
is that the # must be omited. The tag for using the color red would
look like this:
<PARAM NAME="background" VALUE="FF0000">
Note: The wireframe molecule uses a shading technique that makes it look like
it is fading into the background. This is known as depth queing. To
accomplish this, the model fades from black, to the background color specified.
If you want to use a background image instead, use a background color also,
that is similar in color to the background image. That way, the molecule
will apear to fade into the background image.
This parameter will add a border around the outside of the applet. It
is a raised border, and is used to highlight the boundaries of the applet.
To use this parameter, include the tag:
<PARAM NAME="border" VALUE="true">
Note that any value in the value field will produce a border. If you
don't want a border, just leave out this tag.
This parameter will cause the applet to use the gif or jpeg image
specified to be tiled in the background behind the molecule. This
can be used to blend into a page with a background image, or just for
putting an image behind the molecule. Transparent gif images work
within the applet, so if the background parameter is used with a color,
that color will show up through the transparent gif. Note that if this
parameter is used, the image is tiled in the applet on top of the color,
so if both the background parameter and the image parameter are used,
then the background color may not be seen. To use this parameter, use
the tag:
<PARAM NAME="image" VALUE="background.gif">
The above tag works if the file background.gif is in the same directory
as the ChemRote applet. If it is in another place, use the files path
relative to the web files on your server. That means if all your web
files are in /usr/local/www, and your image files are in
/usr/local/www/images, then the parameter name would look like:
<PARAM NAME="image" VALUE="/images/background.gif">
This applet uses the crt file format, a format in use at the Indiana
University Molecular Structure Center (IUMSC) to describe crystallographic
data for molecules in Cartesian coordinates. The file consists of the xyz
coordinates of each atom followed by bond pairs. An example crt file is
provided, bucky.crt. There are three main parts to the crt file, the header,
the atom coordinates, and the bond pairs.
The header is composed of four elements: the Keyword CARTESIAN, the number
of atoms, the number of bonds, then a short, non-whitespace identification
string. The identification string is ignored in this program, but is
necessary in other programs provided by the IUMSC. An example header, for
a file with 24 atoms and 25 bonds would look lie this:
CARTESIAN 24 25 MSC96491
Each entry in the atom table has four elements: The atom identification
string, the x, y, and z coordinates, and the atomic number. The Identification
string is Composed of One or more letters (the atomic symbol) followed by an
alpha-numeric string in parenthesis. There should not be more or less lines
than specified in the crt header line. The key word ENDATOMS is used to
signify the end of the atom data. This table would look something like
this:
C(1) 0.00000 0.00000 0.00000 6
C(2) 0.22746 -1.36771 -0.19379 6
S(1) 0.79195 2.50881 0.96553 16
S(2) -0.97161 3.06715 0.12215 16
. . . . .
. . . . .
. . . . .
H(9) 1.46573 2.66531 -4.03502 1
H(10) 1.17476 2.30247 -1.75361 1
ENDATOMS
Immediately following the ENDATOMS key word, the bond table begins. This is
a list of pairs of indexes into the above atom table. Each line has two
integer numbers, representing a bond to the corresponding atoms. At the end
of the list is the key word ENDBONDS. An example bond table would look like
this:
1 2
1 6
2 3
. .
. .
. .
12 22
13 23
14 24
ENDBONDS
Using ChemRote is very simple. To rotate the molecule, click the left mouse
button in the applet, then move the mouse. The molecule should rotate in the
direction the mouse is dragged. Clicking the right mouse button
(<alt>+click for a one button mouse) within the applet and moving the
mouse will resize the image. To reset the molecule size and rotation, press
r. Pressing shift and any mouse button within the applet will take you to more
information about the applet.
| Command | Action
|
|---|
| left mouse click + move | Rotate molecule
|
Right click + move
(<alt>+mouse button) | Resize molecule
|
| <shift> + click | Take you to information on applet
|
| r key | resets molecules size and position
|