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Chemtool Version 1.4
- this document is in serious need of updating, now that chemtool is at 1.6 -
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Chemtool is a program for drawing organic molecules easily and store them as
a X bitmap file. It runs under the X Window System using the GTK widget set.
An older version (1.1.8) that requires only the standard Athena Widget Set
(Xlib) is still available for situations where GTK cannot be installed for
some reason. In principle, all features added since 1.1.8 could be
back-ported to the Xlib-based version if necessary.
A screenshot of version 1.3 is available here.
Here is one of a more recent version, showing the new menubar and more of its abilities.
Chemtool has been translated to several languages - you can currently choose between Brazilian Portuguese,
Czech, French, German, Polish and Russian in addition to English.
And finally, this screenshot shows chemtool running on an
SGI workstation. As far as i know, it also works well on SUN Solaris.
----------------------> Usage:
This program is intended to be very simple to use. You should be able to
find out most things by yourself. :-)
Drawing of bonds:
Bonds can be drawn in 4 different angle settings (hexagon with 30deg. intervals,
two pentagons with 72deg. intervals (different orientation), and a 45deg. i
octagon). (Intermediate angles are possible in all of these modes as well -
just ignore the marker points in this case). Pressing the mouse button 1
sets the starting point of a bond and also displays a set of markers at the
appropriate angular positions. Dragging the mouse while holding down the
button draws a line in the desired direction.
All bonds are initially drawn as single lines (or the linetype that is
preselected from the menubar) that can be converted to other types later.
Pressing the middle mousebutton on a bond increments its type code (see below),
while pressing the third (usually the right) button deletes the bond next
to the cursor position.
Semiaumomatic drawing of rings:
Rings of 3 to 12 members can be drawn easily by holding down the Ctrl key
while drawing a line. This line will then become the first segment of a ring
that is automatically drawn in clockwise direction. The size of the ring
defaults to that appropriate for the selected drawing mode (i.e. 5, 6 or 8
sides), but it can be set on a per-ring basis by pressing Ctlr-
before drawing the ring, where numbers 3-9 correspond to 3 to 9-membered
rings, while 0 to 2 select 10, 11 and 12-membered rings, respectively.
Newly drawn rings can be deleted by pressing Ctrl and mouse button 3 together.
Drawing of curved lines:
Curved lines for objects like arrows or orbital lobes can be drawn in spline
curve mode by specifing four control points that form a bounding polygon
(startpoint, two points on either side of the peak, endpoint). Of the regular
bondtypes available in the Style menu, the 'single line', 'semiarrow', arrow
and 'dashed line' retain their usual function, while the 'wide line' type
is used to denote a filled polygon. The control points are only visible in
'Move' mode, where they can be dragged around to change the form of a curve
after it is drawn.
Setting bond style:
In bond style mode, clicking on any bond in the diagram cycles its representation
through the sequence
- double bond
- double bond (shorter line on the other side)
- centered double bond
- triple bond
- wedge-shaped bond
- dashed wedge-shaped bond
- wavy line
- half arrow
- arrow
- wide bond
- circle
- dotted line
- single bond that 'cuts out' a segment from any bond it crosses
The additional bond type available in the pulldown menu,
- curved arrow
is only available for drawing. It is actually a shortcut for one of
the curve drawing functions described above, with the second and third
control points automatically generated. As such, it can not be converted
to or from any of the conventional bond types.
(One can, however, convert it to any of the other curve types, e.g. to change
the type of arrowhead). The shape of the arrow will usually need to be
adjusted by shifting the control point that appears alongside it in 'Move'
mode.
Pressing the middle mousebutton on a bond when in 'Bondtype' mode reverses
the direction of that bond.
Inserting text:
Text written into the text box can be positioned with the cursor and may
appear left, middle or right-aligned in the drawing.
There are two special characters to be used for sub- and superscripting
the following character:
'^' to shift up (e.g. N^+)
'_' to shift down (e.g. CH_3)
The control character '|' is used to itializise the following character,
as in |t-Bu.
The special character '@' switches to symbol mode, which uses the standard
X11 symbol font. All alphabetic keys produce the corresponding greek
characters in this mode, and several other symbols are available if their
standard latin1 equivalents are already mapped onto the keyboard:
yen -> infinity
hyphen -> uparrow
macron -> downarrow
The symbols 'plusminus' and 'registered' (trademark) are already in the
standard font, although they are not normally available on the keyboard.
Use the following commands (or add the declarations to your .xmodmaprc )
to make them available via + (+):
xmodmap -e 'keysym r = r R registered' \
-e 'keysym o = o O yen' \
-e 'keysym p = p P plusminus' \
-e 'keysym u = u U hyphen' \
-e 'keysym d = d D macron'
(this leads to AltGr-P = plusminus, AltGr-R = registered in normal mode and
AltGr-O = infinity, AltGr-U = uparrow, AltGr-D = downarrow in symbol font).
For 'dots-and-crosses' diagrams, the following mappings to the symbol
font might be useful:
acute -> cross (e.g. keysym x = x X acute)
middle dot -> filled dot (e.g. keysym d = d D periodcentered)
(using the degree sign for the open dot).
When you want to use symbols as sub- or superscripts, place the sub- or
superscripting character before the '@' character, e.g. K_@a .
The right mousebutton can be used to delete text anchored at the cursor
position.
Centering:
If there is not enough space for your molecule you can
put it in the middle of the sheet with the center button.
Exporting to foreign formats:
You can export your molecules as an X bitmap, an encapsulated postscript file,
an input file for Brian Smith' XFig program or in the PicTeX format.
The PicTeX and Postscript output functions rely on the fig2dev program from the
transfig package.
You can create the outputs in different sizes according to the current zoom
scale. The PicTeX and Postscript modes additionally allow scaling to an
arbitrary percentage selectable on the export menu .
To include the PicTeX-file in your LaTeX document, you will need the pictex
macro package. Depending on the versions you use, you might also have to load
the 'color' package in the preamble of your LaTeX file.
If you experience 'TeX capacity exceeded' error messages, increase the
extra_mem_bot parameter in your texmf.cnf file (usually located in
/usr/share/texmf/web2c, /usr/local/texmf or /etc/texmf).
Pictex is known for its unusual (by tex standards) memory requirements, and
the standard settings often do not account for this (although you may find a
comment a la 'change this if you use pictex' in the texmf.cnf file).
Something like extra_mem_bot=400000 should not hurt on any moderately modern
system.
Selecting all or parts of a drawing for transformations:
Using the 'Mark' button, you can easily select parts of the current drawing
by enclosing them with a 'rubberband' rectangle. The selected parts will appear
highlighted in blue and are immediately available for
- moving: simply drag the fragment to the desired position with the mouse
while holding down the left mouse button
- rotating: horizontal movement of the mouse translates to smooth rotation
around the pivot point selected when pressing the mouse button
- flipping (mirroring) the fragment about a horizontal or vertical mirror
plane through its center: this is performed by clicking on the appropraite
the menu button
- copying : clicking on the 'Copy' menu button creates an exact copy of the
selected fragment slightly offset to the original. The mark is
automatically transfered to the new copy.
- rescaling: horizontal mouse movement is translated into a smooth
increase or decrease of size of the marked fragment
- deleting : to delete the marked fragment, simply click the third
(usually the right) mouse button after it is highlighted.
- optimizing: clicking on the 'bucket and broom' symbol invokes a function
that removes overlapping (duplicate) bonds and labels from
the drawing.
Adding previously saved figures:
To add another molecule from a previously saved chemtool drawing, specify its
filename in the dialog box that comes up when you press the 'Add' button.
The newly added molecule is automatically made active so that it can be
repositioned as desired.
Adding one of the predefined templates:
Pressing the 'Templates' button opens a second window with a small collection
of predefined structures. Simply click on the preview of the desired molecule
to add it to your drawing. The Template window can be kept open throughout a
chemtool session - if it is hidden by another window, you can move it to the
front by clicking the 'Template' button in chemtool again.
The data in the template system differ from normal chemtool drawings only by
the fact that they are stored within the program, and in a slightly awkward
format (x and y coordinates listed separately in the source file templates.h).
These are meant to provide a convenient basis set available to all users, but
not individually extendable (you can use the 'Add' function for your own
structures). Please let us know if you want specific molecules added to the
templates - their name or ideally a regular chemtool drawing file is all we
need. (send email to martin@ruby.chemie.uni-freiburg.de)
Determining sum formula and molecular weight:
Since development version 1.3a7, the distribution contains a helper program,
cht, by Radek Liboska (Prague) to calculate sum formula and (exact) molecular
weight from a chemtool drawing file. It is also available from within chemtool
to calculate these data for the current structure or a marked fragment of
it. Cht can be misled by duplicate bonds ( chemtool does not remove overlapping
bonds, such as they might result from fusing ring systems, automatically) and
by the 'aromatic ring' symbol, so you should avoid these and check the
plausibility of the generated sum formula where possible.
Drawing functions not available within Chemtool:
For features not currently supported by chemtool, like color or
general line-drawing functions, getting Brian Smith's XFig
drawing package from www-epb.lbl.gov/xfig is highly recommended.
About the only thing it does not offer is support for 'chemical' linetypes
and drawing angles - which is why chemtool was written as a sort of
companion program. (There will probably be more of the most sorely needed
drawing options added to chemtool over time, but duplicating the more
general-purpose features of xfig seems rather pointless.)
----------------------> Licensing :
For license information see the file 'COPYING' in this package, i.e. the
GNU General Public License. This software comes with ABSOLUTELY NO WARRANTY.