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Chemesthetics V2.0
Manual
(C) 1990 by Joerg Fenin
1 What is Chemesthetics
Chemesthetics, a symbiose of the words chemistry and esthetics is
a program that displays molecules as a calotte model. This kind of
display contains a certain esthetic attitude, even extremely
poisonous molecules like nicotine or dioxine look quite nice.
In June 89 a program that did exactly what was described above,
called CDCHEM has been published in the c't computer magazine. It
was written by Robert Kaufmann in TurboPascal for an IBM PC.
Unfortunately it had two great disadvantages: the input of new
data was extremly uncomfortable, and of course, it was written for
an IBM PC. So I decided to re-write the program for the Amiga.
But it wasn't as easy as I had expected. Function calls in Pascal
are being done by 'call by reference' where as in C they are
processed by 'call by value'. I didn't like pointer-arithmetic at
this time very much, so I had some difficulty in working this
over.
Finally I was given the deciding kick by a program called P2C that
translates Pascal into C automatically. A totaly confusing but
*RUNNING* program was generated, but it was even more
uncomfortable than the original. So it took me another couple of
months and a lot of work to write a resonable user interface and
to make the program readable again.
2 Copyright, Distribution etc.
Chemesthetics V2.00 is copyrighted (C) 1990 Joerg Fenin / Metalworx
The routines of the Arp-library are copyrighted AmigaDos Resource
Project.
The routines of the IFF-library are copyrighted Christian A.
Weber.
The palette requester is copyrighted (C) 1989 Jonathan Potter.
Chemesthetics is Freeware, that means it may be copied or
distributed freely as long as the following rules are obeyed:
- The copyright-information remain unchanged
- The following files are distributed *TOGETHER*:
Chemesthetics (English version)
Chem_E.dat
Chemesthetics.doc
or
Chemesthetics (German version)
Chem_G.dat
Chemesthetics.doc
- The copying fee may not be more than DM 5,- rsp. not more
than $ 5 in the current currency in foreign (out of Germany)
countries.
- None of the files listed above or the source file may be
part of a commercial product without the (written)
permission of the author.
Copying and/or distributing is forbidden on PD-series of Stefan
Ossowski PD-Versand, Rainer Wolf PD-Versand (OASE), Markt &
Technik Verlag AG, Karstadt AG and all other PD-distributors that
charge more than DM 5,- / $ 5,- for one disk. I don't see why they
should make the big money with my work.
As I am very lazy concerning donating money for freeware myself,
I don't expect to receive any donation for this program. However
I won't reject it; especially not from chemistry teachers.
For sending me DM 30,- / $ 20 you can become a registered user.
After sending me the money you will recieve the latest version
(including serial number) and a *PRINTED* manual.
The program may be ordered at:
Joerg Fenin
Zum Jaegerfeld 19
2100 Hamburg 90
Germany
3 Installation
Copy the Arp- and the IFF-Library into your LIBS: drawer.
That's it!
4 How to use Chemesthetics
The basis for each molecule are atoms. A watermolecule for example
consists of one oxygen and two hydrogen atoms. The position of the
atoms must be told to the program as well as the position of the
light source, the twisting and the reflection of the molecule.
Out of this data a calotte model of the molecule is calculated.
Entered data may be saved and restored for later use. A completed
picture can be saved as an IFF graphics file.
4.1 The entering of data
Select 'Molecule data' from the input menu.
A new window opens where you can enter the data. To do this switch
the edit gadget to ADD. The cursor appears in the first of the
input gadgets. Enter here the short sign of the atom, for example
O for oxygen. Press <RETURN> and the cursor jumps to the next
string gadget, the position field for the x-coordinate. Enter 160
for example. Do this analogly for the coordinates for Y and Z.
Finally enter the radius for the atom. The radius describes the
size of the atom. The higher the radius the bigger the atom. Size
relationships of the atoms can be found in a usual chemistry book.
The axises lay in space as follows:
^ _
z | /|
| / y
| /
|/
------> x
You'll find some examples in the .cdm-files.
Enter all atoms of a molecule one after another. The locations of
the atoms to each other can be also found in chemistry books. In
addition you'll find some examples on the disk. With "Project -
Load molecule" they may be loaded.
After entering all atoms, Chemesthetics needs some data concerning
the molecule as a whole:
The magnifiction factor (MagnFactor) expresses the magnification
of the whole molecule. A magnification facter of 1.0 leaves the
molecule unchanged, a magnification factor < 1.0 shrinks, a
magnification factor > 1.0 expands the molecule.
The following three values express the twisting of the molecule in
space. It may be twisted around any of the three axises. Therefore
enter the desired values in the string gadgets.
Now follow the values for the light source. Chemesthetics uses a
kind of ray tracing algorithm to create a three dimensional
appearance for the calotte model. Even shadowing is taken into
consideration. To do this a vector of the light source has to be
entered. A resanoble value is for example X=20000, Y=-100000,
Z=20000. All example molecules on the disk use this vector.
The last value that has to be entered declares the relexion of the
atoms. The higher the reflection the stronger will the light
source be reflected in each atom. A value of 100 will reflect the
light like a mirror.
Is everything correct click on the OK-gadget, to cancel all inputs
click the CANCEL-gadget or the closegadget.
4.2 Display a molecule
You'll find two menuitems in the menu "Paint", i.e. 'Outline' and
'Calottes'. If you select 'Outline' just a circle will be painted
for each molecule. It gives you a quick survey how the molecoule
will look like. This mode gives you the chance to experiment with
different data (mostly twists) without having to wait for hours
just to see it's not what you wanted. Certainly the stereoscopic
effect may be lost.
If you are satisfied with all the values select 'Calottes'. The
molecule will be drawn considering all the data including light
and reflection. Because of the mass of data large molecules like
dioxine can take up to one hour until they are finished. But the
result compensates the efforts.
A calotte painting may be interrupted anytime by clicking on the
left mouse button.
4.3 Save a molecule
In the "Project" menu you'll find, among others, two 'save'-
menuitems, i.e. 'Save molecule' and 'Save IFF'. Use the first to
save the molecule as a Chemsthetics datafile, it will get, if not
changed, the extension .cdm.
With 'Save IFF' the screen will be saved as an IFF graphics file.
With the menuitem 'IFF compression' you select wether the file
will be compressed using the CmpByteRun1 compression algorithm
(default) (see the documentation of the IFF-library) or not.
Compression can reduce the size of the IFF-file dramatically so it
is recommended you do not change the compression default. As far
as I know all graphic programs like DPaint or Butcher can read
these files. However you can switch compression off.
5 Short menu overview
5.1 Copyright
Copyright-Information
5.1.1 Credits
Information about who supported the completion of this programm
(and who didn't :-( )
5.2 Project
Input and output functions
5.2.1 Load Mol (Amiga-L)
Opens the file requester and loads, after selecting the name, the
corresponding molecule file. If Chemesthetics detects an error in
the data it will display a warning. In this case it is highly
recommended that you check the data by selecting
"Input...molecular data".
5.2.2 Save Mol (Amiga-S)
Opens the file requester and saves, after entering or selecting
the name, the current data as a Chemesthetics data file (.cdm).
5.2.3 Save as IFF
Saves the screen as an IFF file. This file may be read by any of
the current graphic programs (like DPaint or Butcher).
ATTENTION: Saving is not possible if the IFF-library is not
(properly) installed. In this case an error message will be
displayed.
The IFF file may be compressed (default). See "Preferences...IFF
compression".
5.2.4 End (Amiga-Q)
Terminates the program.
5.3 Input
Data input and color changing
5.3.1 Molecule data (Amiga-M)
The input window will be opened and, if present, the current
molecule data will be displayed in a list. You can scroll the list
with the arrows or the proportional gadget. The atom's data may be
changed if you click on an atom and the mode gadget is switched to
"EDIT". You can add new atoms to the molecule if you switch the
mode gadget to "ADD".
5.3.2 Palette (Amiga-P)
Here you can change all of the 16 colors of Chemesthetics. Please
note that most of the colors are used by Chemesthetics to draw the
atoms. The color distribution vastly corresponds with Antropow's
color distribution for atoms.
5.4 Paint
Selection of the paint mode.
5.4.1 Outlines (Amiga-O)
Draws only the outlines of each atom. It serves as a quick survey
wether the entered data is right or wrong. Reflection, shadowing
etc. are not considered.
5.4.2 Calottes (Amiga-K)
Draws a calotte model considering ALL entered data. Because of the
mass of data it can take up to one hour or more to draw a large
molecule.
5.5 Preferences
Preferences of Chemesthetics
5.5.1 IFF compression
Here you can decide wether the IFF file will be compressed
(default) or not. For compression the CmpByteRun1-algorithm is
used. Compression may reduce size of the output file dramatically,
so it is highly recommended you take advantage of this feature. As
far as I know, all standard graphic tools can read this format.
However you could switch compression off if you want to. (See also
the docs for the IFF-library.)
6 Hints for data selection
Most of the needed data may be extracted from simple chemistry
books. Calotte models are shown there very often. If they are not
too complex they may be taken over easily. Also the size
relationships between atoms are shown in tables or outlines, so
there is no need to guess.
To get a feeling for the data you could also have a look into the
example data files that (should) come with this program. You could
compare those data easily with the corresponding data in a
chemistry book. The water molecule for example can be found almost
every chemistry book.
May be I will release some more data files later on public domain
disks.
7 Miscalleanous
I would be very pleased to receive suggestions of any kind
(improvements, error reports etc.). If someone modifies the source
code I would like to receive a copy. Besides I am interested in
modifications concerning the new 5.0 Version of the Aztec C Compiler
or the Lattice C Compiler.
Chemesthetics automatically recognises if it runs on a NTSC- or
PAL-machine. On NTSC-machines circles will appear as ellipses in the
current version. This will be fixed in the next version.
This program has been written in C and has been compiled with the
Aztec C 3.6 compiler. It uses routines of the Arp-Library
(FileRequest(), CloseWindowSafely()) and the IFF-Library
(SaveBitMap()).
The program was tested under the following environment:
Amiga500
512 KByte RAM Extension
Kickstart 1.2
Arp-Library Version 39.1
IFF-Library Version 16.1
Chemesthetics V2.00 (C) 1990 Metalwox, state: 23. December 1990