chemtool - chemical structures editor

NAME

       chemtool - chemical structures editor

SYNOPSIS

       chemtool [filename]

DESCRIPTION

       chemtool  is a program for drawing organic molecules and exporting them
       as a X bitmap, PNG, PicTeX,  Xfig, SVG, SXD, 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.

EXAMPLES

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 30°
intervals, two pentagons with 72° intervals (different orientation),
and a 45° 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)

· light pi orbital lobe

· dark pi orbital lobe

Semiautomatic 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-<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 specifying 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 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
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.

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
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 italicise the following character,
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
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 <AltGr>+<Key>
(<RightAlt>+<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
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).

Circled versions of the plus and minus signs for denoting ionic charge
are available as @+ and @- .

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
settings 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
capital 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
appropriate electron pair for its position. When used together with the
Shift key, two dots are drawn instead of a line - simply delete one of
the dots again if you need an odd number of electrons.

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, a PNG or EMF image, an
encapsulated postscript file, an input file for Brian Smith’ xfig(1)
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, PNG, EMF and
Postscript output functions rely on the fig2dev81) program from the
transfig(1) package and are only available when this program was
detected on startup. If the fig2sxd(1) program is installed, an
additional export option is available for OpenOffice SXD format.
Likewise, if the (open)babel program is installed, an additional Export
menu providing access to all filetypes supported by this tool becomes
available.

You can create the outputs in different sizes according to the current
zoom scale. Postscript and PicTeX files can also be created at
arbitrary scales selectable on the export file menu.

An option in the configuration menu can be set to call fig2dev in
international language mode, which will automatically render any text
written in the alternate (Times) font using the postscript font
appropriate for the current locale (currently Croatian, Cyrillic,
Czech, Hungarian, Japanese, Korean, Polish). See the fig2dev
documentation for details.

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
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.

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(1), lpr(1) or kprinter(1)) can be
stored in the Configuration 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
selection, 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 transferred 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.

framing choosing one of the icons from the drop-down list of frame
and bracket styles draws the corresponding object, e.g. a
pair of round parentheses, around the highlighted fragment.

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 vertical.

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
dragging 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
’Template’ 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
projections, 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 keyboard 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
discarded. 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(1), 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 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