1CHEMTOOL(1)                      User commands                     CHEMTOOL(1)
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NAME

6       chemtool - chemical structures editor
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SYNOPSIS

10       chemtool [filename]
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DESCRIPTION

14       chemtool  is a program for drawing organic molecules and exporting them
15       as a X bitmap, PNG, PicTeX,  Xfig, SVG, SXD, MDL or EPS file.  It  runs
16       under the X Window System using the GTK widget set.
17
18       The program offers essentially unlimited undo/redo, two text fonts plus
19       symbols, seven colors, drawing at several zoom scales, and  square  and
20       hexagonal backdrop grids for easier alignment.
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22

EXAMPLES

24       In  all  drawing  and editing modes, mouse button one (usually the left
25       button) is used to mark or draw objects, while button three (the  right
26       button)  can  be used to delete objects of the current type. The middle
27       button is mainly used in the bond drawing modes where  it  allows  fast
28       changing  of bondtypes.  Starting with version 1.5, the default storage
29       directory for datafiles, and the filename  extension  to  use,  can  be
30       saved via a configuration dialog.
31
32   Drawing of bonds:
33       Bonds  can  be  drawn  in  4 different angle settings (hexagon with 30°
34       intervals, two pentagons with 72°  intervals  (different  orientation),
35       and a 45° i octagon). (Intermediate angles are possible in all of these
36       modes as well - just ignore the marker points in this case).
37
38       The bond style chooser in the center of the button bar  determines  the
39       type  of  bond that is drawn - initially, this is a single bond. If you
40       want to change the type of a bond later, either click on  it  with  the
41       middle  button  of your mouse to advance to the next type(s), or select
42       the appropriate type in the chooser and then switch  to  bondtype  mode
43       and  pick  all bonds that you want to change over to the new type. (The
44       color used for the bond is updated at  the  same  time  if  necessary.)
45       Pressing  the  middle  mousebutton  on  a  bond when in 'Bondtype' mode
46       reverses the direction of that bond.
47
48       Using the third (usually the right) mouse button deletes the bond  next
49       to the cursor position.
50
51       The available bond types are:
52
53               · single bond
54
55               · double bond
56
57               · double bond (shorter line on the other side)
58
59               · centered double bond
60
61               · triple bond (flanking lines shorter than central)
62
63               · triple bond (with equal line lengths)
64
65               · quadruple bond
66
67               · wedge-shaped bond
68
69               · dashed wedge-shaped bond
70
71               · wavy line
72
73               · half arrow
74
75               · regular arrow
76
77               · wide bond
78
79               · circle
80
81               · dotted line
82
83               · overlapping  single  bond  (which cuts out a segment from any
84                 bond it crosses)
85
86               · light pi orbital lobe
87
88               · dark pi orbital lobe
89
90
91   Semiautomatic drawing of rings:
92       Rings of 3 to 12 members can be drawn easily by holding down  the  Ctrl
93       key  while drawing a line. This line will then become the first segment
94       of a ring that is automatically drawn in clockwise direction. The  size
95       of  the ring defaults to that appropriate for the selected drawing mode
96       (i.e. 5, 6 or 8 sides), but it can be set on a per-ring basis by press‐
97       ing Ctlr-<number> before drawing the ring, where numbers 3-9 correspond
98       to 3 to 9-membered rings, while 0 to 2 select 10,  11  and  12-membered
99       rings, respectively.
100
101       Newly  drawn  rings  can be deleted by pressing Ctrl and mouse button 3
102       together.
103
104
105   Drawing of curved lines:
106       Curved lines for objects like arrows or orbital lobes can be  drawn  in
107       spline  curve mode by specifying four control points that form a bound‐
108       ing polygon (startpoint, two points on either side of  the  peak,  end‐
109       point). Of the regular bondtypes available in the Style menu, the 'sin‐
110       gle line', 'semiarrow', arrow and  'dashed  line'  retain  their  usual
111       function,  while  the 'wide line' type is used to denote a filled poly‐
112       gon. The control points are only visible in Move mode, where  they  can
113       be dragged around to change the form of a curve after it is drawn.
114
115
116   Setting bond style
117       In  bond  style  mode,  clicking on any bond in the diagram changes its
118       representation to the type selected in the pull-down menu next  to  the
119       Type button.
120
121       The additional bond type available in the pulldown menu,
122
123              curved arrow
124
125       is only available for drawing. It is actually a shortcut for one of the
126       curve drawing functions described above, with the second and third con‐
127       trol  points  automatically generated. As such, it can not be converted
128       to or from any of the conventional bond types.
129
130       (One can, however, convert it to any of the other curve types, e.g.  to
131       change the type of arrowhead). The shape of the arrow will usually need
132       to be adjusted by shifting the control point that appears alongside  it
133       in 'Move' mode.
134
135
136   Inserting text
137       Text  written  into  the text box can be positioned with the cursor and
138       may appear left, middle or right-aligned in the drawing. Text size  and
139       color  is  selectable from a fixed list of choices.  There are two spe‐
140       cial characters to be used for sub- and  superscripting  the  following
141       character:
142
143               '^' to shift up     (e.g. N^+)
144
145               '_' to shift down   (e.g. CH_3)
146
147
148       The control character '|' is used to italicise the following character,
149       as in |t-Bu.
150
151       A bold  fonttype,  typically  used  for  numbering  compounds,  can  be
152       selected by preceding the character with a '#'.
153
154       The special character '@' switches to symbol mode, which uses the stan‐
155       dard X11 symbol font. All alphabetic  keys  produce  the  corresponding
156       Greek  characters in this mode, and several other symbols are available
157       if their standard Latin1 equivalents are already mapped onto  the  key‐
158       board:
159
160               yen -> infinity
161
162               hyphen -> uparrow
163
164               macron -> downarrow
165
166
167       The symbols 'plusminus' and 'registered' (trademark) are already in the
168       standard font, although they are not normally  available  on  the  key‐
169       board.   Use  the  following  commands (or add the declarations to your
170       .xmodmaprc  )  to  make  them  available  via   <AltGr>+<Key>   (<Righ‐
171       tAlt>+<Key>):
172
173               xmodmap -e 'keysym r = r R registered'  \
174                       -e 'keysym o = o O yen' \
175                       -e 'keysym p = p P plusminus' \
176                       -e 'keysym u = u U hyphen' \
177                       -e 'keysym d = d D macron'
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179       (this leads to AltGr-P = plusminus, AltGr-R = registered in normal mode
180       and AltGr-O = infinity, AltGr-U = uparrow, AltGr-D = downarrow in  sym‐
181       bol font).
182
183
184       For  'dots-and-crosses'  diagrams, the following mappings to the symbol
185       font might be useful: acute -> cross  (e.g. keysym x = x X acute)  mid‐
186       dle  dot  -> filled dot (e.g. keysym d = d D periodcentered) (using the
187       degree sign for the open dot).
188
189
190       Circled versions of the plus and minus signs for denoting ionic  charge
191       are available as @+ and @- .
192
193
194       When you want to use symbols as sub- or superscripts, place the sub- or
195       superscripting character before the '@' character, e.g. K_@a .
196
197       In text mode, the right mouse button deletes the label  at  the  cursor
198       position.   Changing  the size, font or color of a label can be done by
199       left-clicking on it after choosing the desired combination of settings.
200       When  the text entry box above the drawing area is empty, only the set‐
201       tings are updated without changing the contents of the label, otherwise
202       the  label text is replaced as well. If you want to copy the text of an
203       existing label to the text entry box, click on it with the middle mouse
204       button.
205
206
207   Labeling shortcuts
208       In  all bond drawing modes, several keyboard shortcuts are available to
209       add atom symbols without having to leave drawing  mode.  The  label  is
210       placed  at  the current drawing position (the endpoint of the last line
211       drawn, or the spot last clicked on).
212
213       The keys 'c','h','n','o','s','p' and 'r' insert the corresponding capi‐
214       tal  letter, 'l' (lowercase L) inserts 'Cl', while '1', '2', '3' insert
215       CH,CH_2 and CH_3, respectively. The asterisk key (*) inserts  a  filled
216       circle.
217
218       Pressing the space bar once allows you to enter arbitrary labels, which
219       will be placed at the current position when you press the Return key.
220
221
222   Drawing electron pairs
223       The keys of the numeric keypad can be  used  to  draw  short  'electron
224       pair'  lines  next  to  an element symbol - if one imagines the element
225       symbol to be sitting on the central '5' key, each key draws the  appro‐
226       priate  electron  pair  for  its  position. When used together with the
227       Shift key, two dots are drawn instead of a line - simply delete one  of
228       the dots again if you need an odd number of electrons.
229
230
231   Numbering atoms
232       For  quick  numbering  of the atoms in a molecule, switch to one of the
233       text modes, hold down the Control key and pick each atom in  succession
234       with the left mouse button. Numbering starts at 1, and the sequence can
235       be reset at any time by clicking the right mouse button. If you need to
236       use  your own numbering scheme, clicking the middle button (while still
237       holding down the Control key) makes it pick up whatever  number  is  in
238       the text entry field.
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240
241   Centering
242       If  there  is  not enough space for your molecule you can put it in the
243       middle of the sheet with the center button.
244
245
246   Exporting to foreign formats:
247       You can export your molecules as an X bitmap, a PNG or  EMF  image,  an
248       encapsulated  postscript  file,  an input file for Brian Smith' xfig(1)
249       program, an MDL ver. 2000 molfile for  data  exchange  with  commercial
250       packages,  an SVG file for XHTML web pages, or in the PicTeX format for
251       direct inclusion in LaTeX documents.  The PicTeX, PNG,  EMF  and  Post‐
252       script  output functions rely on the fig2dev81) program from the trans‐
253       fig(1) package and are only available when this program was detected on
254       startup.  If  the fig2sxd(1) program is installed, an additional export
255       option is  available  for  OpenOffice  SXD  format.  Likewise,  if  the
256       (open)babel  program  is installed, an additional Export menu providing
257       access to all filetypes supported by this tool becomes available.
258
259       You can create the outputs in different sizes according to the  current
260       zoom  scale.  Postscript  and PicTeX files can also be created at arbi‐
261       trary scales selectable on the export file menu.
262
263       An option in the configuration menu can  be  set  to  call  fig2dev  in
264       international  language  mode, which will automatically render any text
265       written in the alternate (Times) font using the postscript font  appro‐
266       priate  for  the  current  locale (currently Croatian, Cyrillic, Czech,
267       Hungarian, Japanese, Korean, Polish).  See  the  fig2dev  documentation
268       for details.
269
270       To  include  the  PicTeX-file in your LaTeX document, you will need the
271       pictex macro package. Depending on the versions you use, you might also
272       have  to  load  the 'color' package in the preamble of your LaTeX file.
273       If you experience 'TeX capacity exceeded' error messages, increase  the
274       extra_mem_bot   parameter   in   your   texmf.cnf   file   (usually  in
275       /usr/share/texmf/web2c, /usr/local/texmf  or  /etc/texmf).   Pictex  is
276       known  for  its unusual (by tex standards) memory requirements, and the
277       standard settings do not account for this (although you may find a com‐
278       ment  a  la  'change  this  if  you use pictex' in the texmf.cnf file).
279       Something like extra_mem_bot=400000 should not hurt on  any  moderately
280       modern system.
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282
283   Printing drawings
284       Since  version 1.5, direct printing of diagrams to a Postscript-capable
285       printing device (or more typically a print queue  running  ghostscript)
286       is  possible. The paper size, magnification, printer name and the print
287       command to use (currently either lp(1), lpr(1) or kprinter(1))  can  be
288       stored in the Configuration Dialog.
289
290
291   Selecting all or parts of a drawing for transformations:
292       Using  the  'Mark'  button,  you can easily select parts of the current
293       drawing by enclosing them with a 'rubberband' rectangle.
294
295       If you need to add atoms outside of the rectangular area to your selec‐
296       tion, simply draw another rubberband around them while holding down the
297       Ctrl key.
298
299       The selected parts will appear highlighted in blue and are  immediately
300       available for
301
302
303       moving      simply  drag  the fragment to the desired position with the
304                   mouse while holding down the left  mouse  button.  (If  you
305                   only need to move individual atoms or bonds, you can simply
306                   pick and drag them in 'Move' mode without  having  to  mark
307                   them first).
308
309       rotating    horizontal movement of the mouse translates to smooth rota‐
310                   tion around the pivot  point  selected  when  pressing  the
311                   mouse button
312
313       flipping    (mirroring)  the  fragment  about  a horizontal or vertical
314                   mirror plane through  its  center:  this  is  performed  by
315                   clicking on the appropriate menu button
316
317       copying     clicking on the 'Copy' menu button creates an exact copy of
318                   the selected fragment slightly offset to the original.  The
319                   mark is automatically transferred to the new copy.
320
321       rescaling   horizontal  mouse  movement  is  translated  into  a smooth
322                   increase or decrease of size of the marked fragment
323
324       deleting    to delete the marked fragment, simply click the third (usu‐
325                   ally the right) mouse button after it is highlighted.
326
327       framing     choosing  one of the icons from the drop-down list of frame
328                   and bracket styles draws the corresponding object,  e.g.  a
329                   pair of round parentheses, around the highlighted fragment.
330
331       optimizing  clicking  on  the 'bucket and broom' symbol invokes a func‐
332                   tion that removes overlapping (duplicate) bonds and  labels
333                   from the drawing and straightens lines that are almost hor‐
334                   izontal or vertical.
335
336
337   Adding previously saved figures:
338       To add another molecule  from  a  previously  saved  chemtool  drawing,
339       select it in the file selection window that comes up when you press the
340       'Add' button.  Single clicking on any filename in the list  displays  a
341       small  preview  of  the  molecule to aid in selection.  The newly added
342       molecule is automatically made active so that it can be repositioned as
343       desired.
344
345       If you want to add it to a predefined position on another molecule, you
346       can mark that attachment site by left-clicking on it instead  of  drag‐
347       ging the marker rectangle. A small green dot will appear at what is now
348       the reference position for the new part. If  you  save  molecules  with
349       such  a  marker  set, it will in turn define their attachment site when
350       they are added to another drawing.
351
352
353   Adding one of the predefined templates:
354       Selecting 'Templates' from the 'Tools' menu opens a second window  with
355       a  small collection of predefined structures. Simply click on the image
356       of the desired molecule to add it to your drawing. The Template  window
357       can  be  kept  open  throughout a chemtool session - if it is hidden by
358       another window, you can move it to the front  by  selecting  the  'Tem‐
359       plate' menu in chemtool again.
360
361       The  data  in  the template system differ from normal chemtool drawings
362       only by the fact that they are stored within  the  program,  and  in  a
363       slightly  awkward  format (x and y coordinates listed separately in the
364       source file templates.h).  These are  meant  to  provide  a  convenient
365       basis  set available to all users, but not individually extendable (you
366       can use the 'Add' function for your own structures). Please let us know
367       if  you  want specific molecules added to the templates - their name or
368       ideally a regular chemtool drawing file is all we need. (send email  to
369       martin@ruby.chemie.uni-freiburg.de)
370
371
372   Importing foreign file formats:
373       Chemtool  provides functions for importing files in both the PDB format
374       used by the Protein Database (and by most molecular modeling  packages)
375       and  the proprietary MDL molfile format used by ISISdraw and understood
376       by other structure drawing packages and database frontends.
377
378       As both are 3D file formats, while chemtool  only  handles  2D  projec‐
379       tions,  imported  molecules  are read into a temporary storage at first
380       and displayed in blue on the canvas. This 3D representation can then be
381       rotated using the mouse. Only after pressing the Return key on the key‐
382       board is it converted into the final 2D projection that can be  edited.
383       While  such  a 3d import is in progress, all normal drawing and editing
384       functions are disabled.
385
386       With MDL molfile import, the carbon atom labels are automatically  dis‐
387       carded.  For  PDB  import,  the amount of labeling can be chosen in the
388       file selection dialog, which offers retention  of  either  all  labels,
389       only  those  of non-hydrogen atoms, or only the non-numeric part of the
390       labels.
391
392       If the program babel is installed - either the original version written
393       by  Pat  Walters  or  the more recent OpenBabel effort -  chemtool will
394       automatically offer a menu option for importing from any  of  the  file
395       formats this supports.
396
397
398   Determining sum formula and molecular weight:
399       The  distribution  contains  a helper program, cht(1), by Radek Liboska
400       (Prague) to calculate sum formula and (exact) molecular weight  from  a
401       chemtool  drawing  file.  It  is also available from within chemtool to
402       calculate these data for the current structure or a marked fragment  of
403       it.  cht  can  be  misled by duplicate bonds ( chemtool does not remove
404       overlapping bonds, such as they might result from fusing ring  systems,
405       automatically)  and  by the 'aromatic ring' symbol, so you should avoid
406       these and check the plausibility of the  generated  sum  formula  where
407       possible.
408
409
410   Drawing functions not available within Chemtool:
411       For  features  not  currently supported by chemtool, like general line-
412       drawing functions, getting Brian Smith's XFig drawing package  xfig  is
413       highly  recommended.  About the only thing it does not offer is support
414       for 'chemical' linetypes and drawing angles - which is why chemtool was
415       written as a sort of companion program. (There will probably be more of
416       the most sorely needed drawing options added to chemtool over time, but
417       duplicating  the  more  general-purpose  features  of xfig seems rather
418       pointless.)
419
420

LICENSE

422       chemtool and its companion program cht are available under the terms of
423       the GNU General Public License (see the file 'COPYING' in the package).
424       This software comes with ABSOLUTELY NO WARRANTY.
425
426

AUTHORS

428       Thomas Volk
429              Original author and maintainer up to 1.1.1.
430
431       Dr. Martin Kroeker <martin@ruby.chemie.uni-freiburg.de>
432              Maintainer and primary author since 1.1.2.
433
434       Radek Liboska, PhD <liboska@uochb.cas.cz>
435
436       Michael Banck <mbanck@gmx.net>
437
438       and many others.
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440

SEE ALSO

442       babel(1), cht(1), fig2dev(1), fig2sxd(1), transfig(1), xfig(1)
443
444       Homepage:
445       http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html
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4501.6.13                            23 Dec 2011                      CHEMTOOL(1)
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