Provided by: chemtool_1.6.13-1_amd64 bug

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

       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.

SEE ALSO

       babel(1), cht(1), fig2dev(1), fig2sxd(1), transfig(1), xfig(1)

       Homepage:
       http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html