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Chemesthetics V2.10 Manual (C) 1990, 1991 by Joerg Fenin Chemesthetics V2.10 ---------------------------------------------------------------------- Table of contents What is Chemesthetics . . . . . . . . . . . . . . . . . . . 3 Copyright, Distribution etc. . . . . . . . . . . . . . . . 3 Installation . . . . . . . . . . . . . . . . . . . . . . . 4 Files . . . . . . . . . . . . . . . . . . . . . . . . . 5 How to use Chemesthetics . . . . . . . . . . . . . . . . . 6 The entering of data . . . . . . . . . . . . . . . . . . 6 Display a molecule . . . . . . . . . . . . . . . . . . . 8 Save a molecule . . . . . . . . . . . . . . . . . . . . 8 Short menu overview . . . . . . . . . . . . . . . . . . . . 9 Copyright . . . . . . . . . . . . . . . . . . . . . . . 9 Credits . . . . . . . . . . . . . . . . . . . . . . 9 Project . . . . . . . . . . . . . . . . . . . . . . . . 9 Load Mol (Amiga-L) . . . . . . . . . . . . . . . . 9 Save Mol (Amiga-S) . . . . . . . . . . . . . . . . 9 new Mol (Amiga-N) . . . . . . . . . . . . . . . . . 9 Save as IFF . . . . . . . . . . . . . . . . . . . . 10 End (Amiga-Q) . . . . . . . . . . . . . . . . . . . 10 Edit . . . . . . . . . . . . . . . . . . . . . . . . . . 10 Molecule data (Amiga-M) . . . . . . . . . . . . . . 10 Palette (Amiga-P) . . . . . . . . . . . . . . . . . 10 Paint . . . . . . . . . . . . . . . . . . . . . . . . . 11 Outlines (Amiga-O) . . . . . . . . . . . . . . . . 11 Calottes (Amiga-K) . . . . . . . . . . . . . . . . 11 Preferences . . . . . . . . . . . . . . . . . . . . . . 11 Y/X relation . . . . . . . . . . . . . . . . . . . 11 Icon for .CDM-files . . . . . . . . . . . . . . . . 11 Icon for IFF . . . . . . . . . . . . . . . . . . . 11 Title line . . . . . . . . . . . . . . . . . . . . 12 Hints for data selection . . . . . . . . . . . . . . . . . 12 Miscalleanous . . . . . . . . . . . . . . . . . . . . . . . 13 Revision History . . . . . . . . . . . . . . . . . . . . . 14 ---------------------------------------------------------------------- Manual - 10/20 1991 2 Chemesthetics V2.10 ---------------------------------------------------------------------- 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 this called CDCHEM was published in the c't computer magazine. It was written by Robert Kaufmann in TurboPascal for an MS-DOS compatible. Unfortunately it had two great disadvantages: the input of new data was extremly uncomfortable, and of course, it was written for a PC (gualp!). 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 V2.10 is copyrighted (C) 1991 Joerg Fenin / Metalworx The arp.library is (C) copyright AmigaDos Resource Project. The palette requester is (C) copyright 1989 Jonathan Potter. The req.library is (C) copyright 1989 Bruce Dawson & Colin Fox. A lot of the example files have been taken from 'Molec3D' from S. Albrecht and have been converted into Chemesthetics data files. Chemesthetics is Freeware, that means it may be copied or distributed freely as long as the following rules are obeyed: - The copyright-information remains unchanged - The following files are distributed *TOGETHER*: Chemesthetics (English version) Chem_E.dat Chemesthetics.doc or Chemesthetics (German version) Chem_G.dat ---------------------------------------------------------------------- Manual - 10/20 1991 3 Chemesthetics V2.10 ---------------------------------------------------------------------- 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 (exeception: Fred Fish, he may charge more). - 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 and all other PD-distributors that charge more than DM 5,- / $ 5,- for one disk. After a call from Mr Schweitzer from the Karstadt AG Essen I removed the restrictions for the Karstadt AG after he assured me that, despite of the high copying fee, they are not making any profit with the pd-disks. However, I recommend to compare prices carefully. 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 15,- / US$ 15 you can become a registered user. After sending me the money you will recieve the latest version (including serial number). Unfortunately I could not send a printed manual anymore, 'cause I don't have access to a laser printer anymore and I would not allow anyone to put up with a printout by my last century nine needler. On the other hand I reduced the registration fee down by DM 5,- / US $ 5,-. (Since banks charge a high amount for foreign cheques the registration fee is US$ 15, although it is (still) more than DM 15,-. Actually not much more than DM 15,- will be left from a US$ 15,- cheque.) The program may be ordered at: Joerg Fenin Zum Jaegerfeld 19 2100 Hamburg 90 Germany 3 Installation Copy the Arp- and the req.library into your LIBS: drawer. That's it! (I know it's quite annoying to fill up your boot disk with two libs but for the sake of a good user interface I decided to use the file requester of the req.library. Even though it would have ---------------------------------------------------------------------- Manual - 10/20 1991 4 Chemesthetics V2.10 ---------------------------------------------------------------------- been possible to skip the arp.library in this release because just two routines are used of it (ArpAlloc, CloseWindowSafely), I decided to leave in the program because it has so many interesting routines, some of them I will certainly use in future releases. From Version 2.06 onward I use the official ILBM-writing-routine (ilbmw.c) from Commodore's IFF disk (AmigaLibDisk #185), so that I could kick out iff.library (sorry Christian, it really wasn't bad, it was faster than ilbmw.c, but it was too much copying mess just for the one feature I used of it.). I hope most of the PD distributors will publish my package as a whole. In that case you just have to click on the 'InstallLibs'-icons. All needed libraries will be copied to libs: automatically. 3.1 Files The following files are supplied (if not changed by some pd- distributor) (.info files left out!): Chemesthetics/ c/ IconX - used by the script files LhArc - Version 1.30 of the file compressor (needed to extract Source.LZH) MuchMore - Text displayer Contents - small entry for the AmigaLibDisk-contents file English/ Chemesthetics - main executable (English) Chemesthetics.doc - english documentation Chems_g.dat - data file (includes atoms and its colors), needed! Examples/ - some example files German/ Chemesthetics - main executable (German) Chemesthetics.doc - German documentation Chems_e.dat - data file (includes atoms and its colors), needed! Examples/ - some example files Hints_for_Distributors - a few hints for those who would like to include Chemesthetics in a PD series InstallLibs - small script that installs arp- and req.library in the LIBS: drawer libs/ ---------------------------------------------------------------------- Manual - 10/20 1991 5 Chemesthetics V2.10 ---------------------------------------------------------------------- arp.library - nothing left to say req.library - for the requesters Pictures/ - Pictures made of the examples Source/ SrcReadMe! - Some facts for programmers Source.LZH - all needed source files compressed into one archive (use lharc to extract) lmkfile - type lmk (Lattice users only) for automatic compile and link, copy it to the source root directory pdomain/ *.h - include files for the use of the arp.library, req.library and ilbm.w, you have to change the -i directive in the lmkfile to this directory for successful compilation *.c - C source files *.h - includes for the above convm3d/ *.c - source files for ConvM3D lmkfile - type lmk (Lattice users only) for automatic compile and link 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. ---------------------------------------------------------------------- Manual - 10/20 1991 6 Chemesthetics V2.10 ---------------------------------------------------------------------- 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. You can delete an atom by clicking on the 'DELETE' gadget in the upper right corner. Therefore you have to select it first (remember to set the mode-gadget to 'EDIT'). 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 reasonable value is for example X=20000, Y=-100000, Z=20000. All inputs are made in picometers (1 pm = 10-12 meters). 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 (i.e. the atom will appear white). ---------------------------------------------------------------------- Manual - 10/20 1991 7 Chemesthetics V2.10 ---------------------------------------------------------------------- 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 atom. 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. In order to get some information on how long you can spend some time with your girl friend I provided the time-info window. It will display the time taken so far for drawing and will calculate an excepted end time for the drawing process after each molecule. To keep calculation effort as low as possible it will not be the exact result but it will become more exact after each finished atom. See also ->Preferences... time-info window. 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. As default an icon will be saved along with the data file. You can turn this off in the preferences. With 'Save IFF' the screen will be saved as an IFF graphics file. If 'Icon for IFF' was selected in the preferences menu an icon will be saved along with the file. ---------------------------------------------------------------------- Manual - 10/20 1991 8 Chemesthetics V2.10 ---------------------------------------------------------------------- 5 Short menu overview 5.1 Copyright Copyright-Information 5.1.1 Credits Information about who supported the completion of this programm. 5.2 Project Input and output functions 5.2.1 Load Mol (Amiga-L) Opens the (great) file requester of the req.library (thanks to Bruce & Colin) 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). As default a Project icon will be saved along with the data file (with /Chemesthetics as it's tool). However Chemesthetics does not (yet) recognize if it is launched via one of this icons. So you still have to load a molecule manually. You can switch off the icon creation in the preferencs. 5.2.3 new Mol (Amiga-N) If you have a molecule in memory and you would like to load or enter a new one, I recommend to delete the values for the old molecule first. After a security verification, the values for magnification and the light source will be set to their defaults, all other values will be set to zero. (Hint for the technical user: Due to using ArpAlloc() of the arp.library for memory allocation, the used memory for the old memory will not be released until the program terminates (the arp.library will be closed). If you enter or load a new molecule new memory will be allocated.) ---------------------------------------------------------------------- Manual - 10/20 1991 9 Chemesthetics V2.10 ---------------------------------------------------------------------- 5.2.4 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). By default an icon will be saved along with the file. It will be a PROJECT icon with 'C:IView' as the project's tool. See 'Preferences...Icon for IFF' to prevent icon creation. Any IFF file will be compressed, using the official compression algorithm provided by ilbmw.c from Commodore's official IFF disk (AmigaLibDisk #185). I personally don't know any tool that does not work with this compression mode. However there are tools to convert compressed files into uncompressed ones. 5.2.5 End (Amiga-Q) Terminates the program. 5.3 Edit 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". You can delete an atom after first selecting it (i.e. clicking on it) and then click on the 'DELETE' gadget in the upper right corner. ATTENTION: No security verfication will be made before the deletion. 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. You can restore Chemesthetics' defaults by clicking on the "DEFAULT" gadget. At this point I would like to thank Jonathan Potter for his paletterequester. ---------------------------------------------------------------------- Manual - 10/20 1991 10 Chemesthetics V2.10 ---------------------------------------------------------------------- 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 whether 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. By default a time-info window will be displayed during the drawing process. It will show the time taken so far by the drawing and the time still needed (approximately). 5.5 Preferences Preferences of Chemesthetics 5.5.1 Y/X relation Because of different screen resolutions in x- and y-direction, circles usually appear as ellipses. The y/x relation value corrects this. Chemesthetics automatically assumes a value of 1.5 for PAL screens (256 pixels in y-direction) and 2.0 for NTSC screens (200 pixels in y-direction). However you could manually overwrite this value. 5.5.2 Icon for .CDM-files By default a PROJECT icon will be saved along with the data file. It will have '/Chemesthetics' as it's default tool. However, Chemesthetics currently does not recognise if it is launched via one of theses icons or normally. So you still have to load a datafile by hand. You can switch off icon creation for data files if you want to. 5.5.3 Icon for IFF Here you can decide whether an icon will be saved along with the IFF graphics file (default) or not. The icon will be of type PROJECT with 'C:IView' as its tool. If you copy IView (provided for example on this disk, if this is an AmigaLibDisk) to the C: ---------------------------------------------------------------------- Manual - 10/20 1991 11 Chemesthetics V2.10 ---------------------------------------------------------------------- drawer of your boot(hard)disk, you can easily view all the drawn pictures by simply double-clicking on the icons. 5.5.4 Title line In order to get more space for the drawing (especially important on NTSC screens I guess), I switched off the menu line since version 2.05. That means that you have to press the menu button of your mouse (right mouse button) to get the program's menus. However if you would like to have it there permanently you can switch this gadget (and the menu line) on. Another click on this gadget switches off the title line again. 5.5.5 Time-info window To get an idea about how long a drawing will take, I provided this info window during calotte painting. It will show the following information: Atom Ss: uuu/xxx time: yyy.yy min. exepected time: zzz.zz min. Ss: short sign of the atom (e.g. O for Oxygen) uuu: current atom just drawn xxx: total number of atoms in molecule yyy.yy: time in minutes and seconds taken so far for drawing zzz.zz: expected total time for drawing process If you don't want this window to show up switch off this gadget. 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. Another good source for atom data is the shareware program Elements by Paul Miller located for example on AmigaLibDisk 384. 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. ---------------------------------------------------------------------- Manual - 10/20 1991 12 Chemesthetics V2.10 ---------------------------------------------------------------------- 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. Chemesthetics automatically recognises if it runs on a NTSC- or PAL-machine. This program has been written in C and has been compiled and optimized under the SAS/Lattice C compiler V5.10a. It uses routines of the arp.library (ArpAlloc(), CloseWindowSafely()) and the req.library (FileRequester(), SimpleRequest(), TwoGadRequest(), SetLocation(), ReadLocation, SetSize()). The program was tested under the following environment: Amiga500 Kickstart 1.2 512 KByte RAM Extension arp.library Version 39.1 req.library Version 2.5 ---------------------------------------------------------------------- Manual - 10/20 1991 13 Chemesthetics V2.10 ---------------------------------------------------------------------- 8 Revision History (sorted descending, the most recent version is at the top of the list) V2.10 - Oct 20 91 - removed terrible bug in memory management in the main input routine - added time-info window for time statistics during the drawing process - icons will now by default created for data (.CDM) files - added preferences items for 'icons for .CDM-files' and 'time-info window' - expanded the magnification gadget in the input routine for two decimal places V2.07 - 16.10.91 - third published version (becauese of a bug, see below!) - Memory for atoms is now requested dynamically and not by a static array. You can now have up to 500 atoms in one molecule. - During I/O operations the mousepointer is changed into a waitpointer. - Library calls are now made direct and not with the amiga.lib gluecode (now using #pragmas). This should make those calls faster and more compact. - For startup the catch.o code is used. This means that certain software errors may be trapped and caught, producing a snapshot of the situation that leads to the error. This snapshot file may be used by the SAS/Lattice traceback utility tb to get information about the exception. - Due to a bug in the optimization process, global optimzing has been switched off for eingabe.c and palettereq.c. This caused V2.06 to meditate when calling the main input function or the palette requster. V2.06 - 13.06.91 - second published version - Now using ilbmw.c from the official Commodore IFF disk (AmigaLibDisk #185) to do the IFF saving, as a result I kicked out the iff.library (sorry Christian). - Possibility to let an icon be created automatically when an iff file is written (default) V2.05 - 29.04.91 - Switched off the menu line to get more ---------------------------------------------------------------------- Manual - 10/20 1991 14 Chemesthetics V2.10 ---------------------------------------------------------------------- space for the drawings, i.e. you have to use the menu button of your mouse to get the menus. (could be turned on again in the preferences menu) - Changed the main window's type to BACKDROP, that means that requesters could not be put in the background anymore, also it does not contain a title line anymore to get a bit more room for the drawings. V2.04 - 21.04.91 - Implemented use of the req.library of Bruce Dawson & Colin Fox. Now its file requester is used instead of the one of the arp.library. Also removed my own MessageRequest() and exchanged it by the related routines of the req.library - Small window with the serial number will be displayed on startup, detaches itself after a few seconds if not closed by the user V2.03 - 13.04.91 - preferences window to set up y/x relation and iff saving mode (actually because there was a bug with the checkmark in the preferences menu) - fixed bug in SaveIFF (Chemesthetics didn't take over the entered file name) - changed colors to get a slight OS2.0 feeling - drawing statistics (time and number of atoms) - removed some minor bugs (This version became possible because the first (!, not bad ?) registered user wrote in and asked for the latest version. Actually the was no runnig version at this time, so I had to sit down and did some work to get it run again. Thanks Jim!) V2.02 - 10.03.91 - recompiled under SAS/Lattice C 5.10a, therefore some minor changes and adaptions had to be done - optimized run-time performance, drawings are now ca. 30% faster V2.01 - 17.02.91 - data is not linked into chip-mem automatically anymore, instead TypeOfMem() is used for graphics data to decide wheter to transfer it into chip- mem or if it is already there by coincidence. ---------------------------------------------------------------------- Manual - 10/20 1991 15 Chemesthetics V2.10 ---------------------------------------------------------------------- - editing of non existing atoms is not longer possible - editing is not longer possible when you are in ADD-mode - several minor changes V2.00 - 27.12.90 - first published version V1.00 - Spring 1990 - first running version Chemesthetics V2.10 (C) 1990,1991 Metalwox, Manual update: 10/20 1991 ---------------------------------------------------------------------- Manual - 10/20 1991 16