Chemtool(1)Chemtool(1)NAME
Chemtool Version 1.6.5
SYNOPSISchemtool [<filename>]
DESCRIPTION
Chemtool is a program for drawing organic molecules and exporting them
as a X bitmap, PicTeX, Xfig, SVG, MDL or EPS file. It runs under the X
Window System using the GTK widget set.
The program offers essentially unlimited undo/redo, two text fonts plus
symbols, seven colors, drawing at several zoom scales, and square and
hexagonal backdrop grids for easier alignment.
USAGE
In all drawing and editing modes, mouse button one (usually the left
button) is used to mark or draw objects, while button three (the right
button) can be used to delete objects of the current type. The middle
button is mainly used in the bond drawing modes where it allows fast
changing of bondtypes. Starting with version 1.5, the default storage
directory for datafiles, and the filename extension to use, can be
saved via a configuration dialog.
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).
The bond style chooser in the center of the button bar determines the
type of bond that is drawn - initially, this is a single bond. If you
want to change the type of a bond later, either click on it with the
middle button of your mouse to advance to the next type(s), or select
the appropriate type in the chooser and then switch to bondtype mode
and pick all bonds that you want to change over to the new type. (The
color used for the bond is updated at the same time if necessary.)
Pressing the middle mousebutton on a bond when in 'Bondtype' mode
reverses the direction of that bond.
Using the third (usually the right) mouse button deletes the bond next
to the cursor position.
The available bond types are :
single bond
double bond
double bond (shorter line on the other side)
centered double bond
triple bond (flanking lines shorter than central)
triple bond (with equal line lengths)
quadruple bond
wedge-shaped bond
dashed wedge-shaped bond
wavy line
half arrow
regular arrow
wide bond
circle
dotted line
overlapping single bond (which cuts out a segment from any bond it
crosses)
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 press‐
ing Ctlr-<number> 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 func‐
tion, 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 changes its
representation to the type selected in the pull-down menu next to the
Type button.
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 con‐
trol 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.
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. Text size and
color is selectable from a fixed list of choices. There are two spe‐
cial 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 charac‐
ter, as in |t-Bu.
A bold fonttype, typically used for numbering compounds, can be
selected by preceding the character with a '#'.
The special character '@' switches to symbol mode, which uses the stan‐
dard 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 key‐
board:
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 key‐
board. Use the following commands (or add the declarations to your
.xmodmaprc ) to make them available via <AltGr>+<Key> (<Righ‐
tAlt>+<Key>):
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 sym‐
bol 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) mid‐
dle 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 .
In text mode, the right mouse button deletes the label at the cursor
position. Changing the size, font or color of a label can be done by
left-clicking on it after choosing the desired combination of settings.
When the text entry box above the drawing area is empty, only the set‐
tings are updated without changing the contents of the label, otherwise
the label text is replaced as well. If you want to copy the text of an
existing label to the text entry box, click on it with the middle mouse
button.
Labeling shortcuts:
In all bond drawing modes, several keyboard shortcuts are available to
add atom symbols without having to leave drawing mode. The label is
placed at the current drawing position (the endpoint of the last line
drawn, or the spot last clicked on).
The keys 'c','h','n','o','s','p' and 'r' insert the corresponding capi‐
tal letter, 'l' (lowercase L) inserts 'Cl', while '1', '2', '3' insert
CH,CH_2 and CH_3, respectively. The asterisk key (*) inserts a filled
circle.
Pressing the space bar once allows you to enter arbitrary labels, which
will be placed at the current position when you press the Return key.
Drawing electron pairs
The keys of the numeric keypad can be used to draw short 'electron
pair' lines next to an element symbol - if one imagines the element
symbol to be sitting on the central '5' key, each key draws the appro‐
priate electron pair for its position.
Numbering atoms
For quick numbering of the atoms in a molecule, switch to one of the
text modes, hold down the Control key and pick each atom in succession
with the left mouse button. Numbering starts at 1, and the sequence can
be reset at any time by clicking the right mouse button. If you need to
use your own numbering scheme, clicking the middle button (while still
holding down the Control key) makes it pick up whatever number is in
the text entry field.
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 post‐
script file, an input file for Brian Smith' XFig program, an MDL ver.
2000 molfile for data exchange with commercial packages, an SVG file
for XHTML web pages, or in the PicTeX format for direct inclusion in
LaTeX documents. 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. Postscript and PicTeX files can also be created at arbi‐
trary scales selectable on the export file 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 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 do not account for this (although you may find a com‐
ment 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.
Printing drawings:
Since version 1.5, direct printing of diagrams to a Postscript-capable
printing device (or more typically a print queue running ghostscript)
is possible. The paper size, magnification, printer name and the print
command to use (currently either lp or lpr) can be stored in the Con‐
figuration Dialog.
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.
If you need to add atoms outside of the rectangular area to your selec‐
tion, simply draw another rubberband around them while holding down the
Ctrl key.
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. (If you only need to
move individual atoms or bonds, you can simply pick and drag
them in 'Move' mode without having to mark them first).
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
appropriate 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 and straightens lines that are almost horizontal or ver‐
tical.
Adding previously saved figures:
To add another molecule from a previously saved chemtool drawing,
select it in the file selection window that comes up when you press the
'Add' button. Single clicking on any filename in the list displays a
small preview of the molecule to aid in selection. The newly added
molecule is automatically made active so that it can be repositioned as
desired.
If you want to add it to a predefined position on another molecule, you
can mark that attachment site by left-clicking on it instead of drag‐
ging the marker rectangle. A small green dot will appear at what is now
the reference position for the new part. If you save molecules with
such a marker set, it will in turn define their attachment site when
they are added to another drawing.
Adding one of the predefined templates:
Selecting 'Templates' from the 'Tools' menu opens a second window with
a small collection of predefined structures. Simply click on the image
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 selecting the 'Tem‐
plate' menu 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)
Importing foreign file formats:
Chemtool provides functions for importing files in both the PDB format
used by the Protein Database (and by most molecular modeling packages)
and the proprietary MDL molfile format used by ISISdraw and understood
by other structure drawing packages and database frontends.
As both are 3D file formats, while chemtool only handles 2D projec‐
tions, imported molecules are read into a temporary storage at first
and displayed in blue on the canvas. This 3D representation can then be
rotated using the mouse. Only after pressing the Return key on the key‐
board is it converted into the final 2D projection that can be edited.
While such a 3d import is in progress, all normal drawing and editing
functions are disabled.
With MDL molfile import, the carbon atom labels are automatically dis‐
carded. For PDB import, the amount of labeling can be chosen in the
file selection dialog, which offers retention of either all labels,
only those of non-hydrogen atoms, or only the non-numeric part of the
labels.
If the program babel is installed - either the original version written
by Pat Walters or the more recent OpenBabel effort - chemtool will
automatically offer a menu option for importing from any of the file
formats this supports.
Determining sum formula and molecular weight:
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 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.)
LICENSE
Chemtool and its companion program Cht are available under the terms of
the GNU General Public License (see the file 'COPYING' in the package).
This software comes with ABSOLUTELY NO WARRANTY.
AUTHORS
Thomas Volk (original author and maintainer up to 1.1.1)
Dr. Martin Kroeker (maintainer and primary author since 1.1.2) mar‐
tin@ruby.chemie.uni-freiburg.de
Radek Liboska, PhD liboska@uochb.cas.cz
Michael Banck mbanck@gmx.net
Webpage:
http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html
SEE ALSOcht(1), xfig(1), transfig(1)
30 Jan 2005 Chemtool(1)
