Tribblix: manual page: chemtool.1

CHEMTOOL(1) User commands CHEMTOOL(1)

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<degree> intervals, two pentagons with 72<degree> intervals
(different orientation), and a 45<degree> 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:

+o single bond

+o double bond

+o double bond (shorter line on the other side)

+o centered double bond

+o triple bond (flanking lines shorter than central)

+o triple bond (with equal line lengths)

+o quadruple bond

+o wedge-shaped bond

+o dashed wedge-shaped bond

+o wavy line

+o half arrow

+o regular arrow

+o wide bond

+o circle

+o dotted line

+o overlapping single bond (which cuts out a segment from any
bond it crosses)

+o light pi orbital lobe

+o 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

Thomas Volk
Original author and maintainer up to 1.1.1.

Dr. Martin Kroeker <martin@ruby.chemie.uni-freiburg.de>
Maintainer and primary author since 1.1.2.

Radek Liboska, PhD <liboska@uochb.cas.cz>

Michael Banck <mbanck@gmx.net>

and many others.