Libris Britannia 4/science library(b).zip/science library(b)/SCIENTIF/CHEMISTR/4098.ZIP/MOLEC230.ZIP/MOLECULE.DOC

Text File | 1989-06-11 | 9.7 KB | 204 lines

Program:  Molecule v2.30 by P. Fraundorf (c) 1982,1989

  This is a program for examination and editing of molecular
models, crystal interfaces, and wire frame objects in 2 and
3 dimensions, on MS-DOS computers.  It provides an ability
to view object wireframe images interactively and while
rotating (optionally in red/green stereo), ability to view
textured objects with hidden surface removal in stationary,
wobbling, and red/green stereo form, and facility to
reorient the object in crystallographic (lattice and
reciprocal lattice) projection.  Simple text, and stereo-3D,
object point editors are provided, along with facility for
storing and retrieving ASCII format model files from disk.

Requirements:  MS-DOS computer, CGA graphics adapter (or
better), one 360K disk drive (or better), and adequate
memory (up to 640KB depending on graphics resolution
desired).  An Intel math coprocessor is supported if
available.

Distribution:  This program is available in shareware and
registered packages.  The shareware package, which can be
downloaded from bulletin boards like Compuserve's IBMAPP
forum and the GENIE IBM forum, includes the executable
MOLECULE.EXE, a small ASCII font file 3x5.FON, and this
documentation file (MOLECULE.DOC).  The shareware program is
fully functional, and free distribution is encouraged,
although as usual the shareware package is formally intended
for evaluation only.  The registered package includes
executables MAKEMOL.EXE which constructs molecule (.MOL)
files describing faceted crystals of arbitrary size and
shape for use with MOLECULE.EXE, and MAKEXTL.EXE for making
".XTL" files which hold information on the c-axis basis
triplet and the position of atoms in a crystal, for use with
MAKEMOL.EXE.  The registered package is available, in return
for a $54.25 registration fee, from:

                    Orion Codeworks
                    PO Box 737
                    Maryville IL 62062 USA.

These programs are part of a growing set of programs that
have been developed in the context of various electron, X-
ray, and scanning tip crystallographic studies.  They
include routines for analysis of periodicity in electron
phase contrast images, for analysis of powder diffraction
data, and for analysis of electron single crystal data as
well.  Some of these routines are already available in
shareware form as well, and that number is expected to
increase.  Since the programs have been put together to aid
in the solution of our technical problems, of course, what
you apply them for is your own affair.  Hopefully, however,
BECAUSE they have been developed as tools rather than as
products, user's with specific applications may be by that
same token pleasantly suprised at their depth.

Operation:
     This program is designed to be self-explanatory, once
you understand what it can and cannot do.  This note is
simply to remind you what the program does.  It is
especially targeted for those who are learning about the
program for the first time.

     In short, the program is designed to work with three-
dimensional "objects" whose structure can be described by 4-
column lists of numbers, in which each 4-column "record"
contains respectively the x, y, and z coordinates of an atom
(or line segment endpoint), followed by a number which
denotes the size of that atom.  This last number, in
addition to determining the size of atoms drawn at the point
with coordinates x, y and z, is also used to determine the
color of the atom at that point.  In particular, it can be
given a negative value, indicating that the contrast for
that particular atom should be somehow reversed.  These
lists can be written to, or read from, files with the ".MOL"
extension on the disk.  Here, the letters MOL are a
shorthand mnemonic for the word MOLecule, the type of object
that this program was primarily designed to model.  The
program's line-drawing modes make it possible also to encode
and view wire-frame objects, like the room layout
exemplified by the ROOM.MOL model file in the distribution
archive.

     The program is started by typing its name (Molecule)
from the MS-DOS prompt.  Initial questions cover:  (1) the
graphics mode you would like to use (CGA will be fastest,
while the other modes may give higher resolution if your
monitor and adapter will support them),  (2) whether you
want a white background (the w/b default is usually
preferable unless you have a screen dump program which
cannot invert contrast before dumping an image to a
printer), and  (3) whether you want to disable the algorithm
for z-axis (out of the screen) blurring of red/green stereo
images.  This latter algorithm has been put in place to tone
down some novel pattern recognition effects which assert
themselves because of the effectiveness of 3D texturing
algorithms used in this program.

     Once the opening questions are answered, the user is
confronted with a spreadsheet-like menu structure.  Menu
items are accessed with arrow keys followed by <Enter>, or
by pressing the first letter of the menu choice.  Generally
the <Esc> key will extricate you from what you are involved
in, although in some cases time may pass before your
pressing of <Esc> has noticable effect.

     The main (opening) menu covers the major sections of
the program:  files, setup, interact, draw, edit, print and
quit.  The FILES menu facilitates loading and writing
of".MOL" files, and also allows one to dump screen images to
disk in one or more standard forms.  SETUP facilitates
reorientation of the object by keyboard input of angles,
cartesian direction cosines, and zone or Miller indices.  It
also facilitates modifications of the image itself (e.g.
width, perspective angles, etc.).   INTERACT invokes an
interactive point/line viewing mode, in which key pad keys
allow one to manually reorient the object image.  In
addition to facility for auto rotation about the object's z-
axis, this facility provides access to a 3D point editor
designed to be used with a color monitor and red/green (red
on left) 3D glasses.  <Esc> exits both this editor, and the
INTERACT mode itself.  DRAW facilitates the more elaborate
display formats.  These include a fast draw "circle" mode, a
line draw mode for wire frame objects, a 3D brush mode for
textured spheres, and the 3D stereo and wobbling 3D image
modes as well.  Because these formats take time on most any
computer, it is assumed that your have already selected the
desired object orientation (via SETUP or INTERACT) prior to
beginning with DRAW.  EDIT invokes a crude text editor for
modification of the presently loaded object list, PRINT
toggles the PrtSc interrupt in case you have a memory
resident screen dump program presently loaded, and QUIT of
course charts the way back to DOS.

     That's it in a nutshell.  Try working with the example
MOLecule files provided with the program, and then try
putting together some MOLecule files of your own.  As
indicated above, some helpful utilities for putting atoms
into crystallographic MOLeclule files are provided on
registration.  I would also like to hear about it if you
manage to put together programs for making other MOLecule
file types, e.g. for 3D room or building layouts, for the
position of atoms in amorphous or quasicrystalline
structures, etc.  Ideas (sent to Orion Codeworks) for
improving the program would be welcome as well.

Upgrade History:

06/10/89 v2.30 Support for EGA and VGA 320x200 modes
               Update of PrtScreen Routine for non-CGA
               Add On-Screen Indexing to Draw Routines
               Add Ability to Read "XTL" Info from Files

06/06/89 v2.21 Standardize Aspect Ratio Defaults
               Formalize VGA Support
               Decrease Dynamic Memory Usage of Wobble

06/04/89 v2.20 First Shareware Release
               Add Crystal Indexing and 3D Wobble Options
               Add Scale Bar to Images
               Add Hercules Graphics (QBherc.com) Support

09/20/89 v2.00 Translation to IBM QuickBASIC
               Add EGA Support

10/15/82 v1.00 First CGA Version in IBM BASICA

                              P. Fraundorf  06/06/89

         ----------------end-of-author's-documentation---------------

                        Software Library Information:

                   This disk copy provided as a service of

                        The Public (Software) Library

         We are not the authors of this program, nor are we associated
         with the author in any way other than as a distributor of the
         program in accordance with the author's terms of distribution.

         Please direct shareware payments and specific questions about
         this program to the author of the program, whose name appears
         elsewhere in  this documentation. If you have trouble getting
         in touch with the author,  we will do whatever we can to help
         you with your questions. All programs have been tested and do
         run.  To report problems,  please use the form that is in the
         file PROBLEM.DOC on many of our disks or in other written for-
         mat with screen printouts, if possible.  The P(s)L cannot de-
         bug programs over the telephone.

         Disks in the P(s)L are updated monthly, so if you did not get
         this disk  directly from the P(s)L,  you should be aware that
         the files in this set may no  longer be the current versions.

         For a copy of the latest monthly software library newsletter
         and a list of the 1,800+ disks in the library, call or write

                        The Public (Software) Library
                              P.O.Box 35705 - F
                           Houston, TX 77235-5705
                               [phone]