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526. ARKMOD: Arkansas Molecular Display Program
by William B. Melchior, Jr., National Center for
Toxicological Research, Jefferson, Arkansas 72079,
after Yoshitaka Beppu, Department of Physics, Nagoya
University, Chikusa-ku, Nagoya, Japan
ARKMOD is a modification of Beppu's NAMOD (QCPE 370), a
program for making ball-and-stick drawings of
molecules. Most of the algorithms, e.g., hidden line
elimination, are from the original NAMOD. ARKMOD has
some changes in the details of the way molecules are
drawn, but the biggest change is in the way the program
is used. The documentation will describe how to set up
the program for a particular computer/plotter
combination and how to use it.
Several new features have been added. Two of these
have been adopted from Molecular Mechanics programs by
N. L. Allinger which are also available from QCPE.
ARKMOD produces ball-and-stick drawings of a molecule
from a list of the atomic coordinates. There are
numerous options that can be used to (1) manage the
input of information, (2) obtain information about the
molecule, (3) control the appearance of the drawing,
and (4) change the orientation of the molecule in the
drawing.
Coordinates can be either Cartesian coordinates or
reduced crystal coordinates; any units may be used.
Plots may be labelled. The program automatically finds
bonds, but the calculated bonds can be adjusted if
unusual bond lengths produce errors.
Information which can be obtained includes bond
lengths, bond angles, and atomic coordinates. The
latter can be used, for instance, after rotating a
molecule or after inputting crystal coordinates.
The molecule can be reoriented in several ways: It can
be rotated about any Cartesian coordinate or about a
vector between any two atoms, or it can be moved so
that given atoms lie in given planes and along given
axes.
The drawing can be altered in many ways, some of which
are listed here. The scale can be adjusted as desired,
including an option which automatically shrinks a
molecule until it just fits in the allotted space.
Individual atoms can be adjusted in size or removed
totally from the plot. The thickness of the bonds can
be controlled. Perspective can be introduced. The
plot can be centered on any atom.
One of the most important changes from NAMOD is the
ability to easily produce multiple drawings, e.g., of
different orientations or in different styles, in a
single job, without having to reenter the atomic
coordinates each time. This is especially convenient
when combined with the program's ability to be used in
an interactive mode with a graphics terminal.
Finally, most of the program is used as provided. Only
a few subroutines need to be adjusted to prepare the
program for any computer/plotter combination, and all
the options can be used without any further
reprogramming.
FORTRAN 77 (VAX)
Lines of Code: 3600
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