Chemtool(10 Jan 2001)

NAME
Chemtool Version 1.3.0

SYNOPSIS
chemtool [<filename>]

DESCRIPTION
Chemtool is a program for drawing organic molecules easily and export them as a X bitmap, Xfig, or EPS 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.

USAGE
This program is very simple to use. You can 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. octagon). All bonds are initially drawn as single lines that can be converted to other types later.

Setting bond style:

In bond style mode, clicking on any bond in the diagram cycles its representation through the sequence
 - single bond
 - 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. 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 special character '|' switches to italics

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).

When you want to use symbols as sub- or superscripts, place the sub- or superscripting character before the '@' character, e.g. K_@a .

Spaces in the text must be entered as backslash characters (e.g. '-\ H_2O').

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. To include the PicTeX-file in your LaTeX document, you will need the pictex macro package. 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 appearh ighlighted 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:
    clicking on this button will immediately delete the marked portion of the structure.

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) 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. Drawing functions not available within Chemtool: For features not currently supported by chemtool, like curved arrows, colors 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 curved arrows in chemtool sometime, but duplicating the more general-purpose features of xfig seems rather pointless.)

INSTALLATION:
To build Chemtool type:

 xmkmf
 make
 make install

DEPENDENCIES:
All versions later than 1.1.8 require the GTK widget library and its companion Glib, both available from www.gtk.org. All output functions except xbm depend on the transfig package version 3.2.0 or later, available from www-epb.lbl.gov/xfig. Brian Smith's XFig drawing package is highly recommended - it supports all the things that are missing in Chemtool like curved arrows, general drawing functions and image import.

COPYRIGHT:
Copyright 1998-1999 Thomas Volk Copyright 2000-2001 Martin Kroeker Parts Copyright 2000-2001 Radek Liboska You may use and distribute this software under the terms of the GNU General Public License. This software comes with ABSOLUTELY NO WARRANTY.

BUGS:
Send report to:

AUTHORS:
Thomas Volk (program creator, maintainer up to 1.1.1)
 E-Mail:    Thomas.Volk@student.uni-ulm.de

Dr. Martin Kroeker (primary developer since 1.1.2)
 E-Mail:    martin@ruby.chemie.uni-freiburg.de or mk@daveg.com

Webpage: http://www.uni-ulm.de/~s_tvolk
 Alternative site and Development versions: http://tutor.oc.chemie.tu-darmstadt.de/~martin/chemtool.html