1CHEM(1)                     General Commands Manual                    CHEM(1)
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NAME

6       chem - groff preprocessor for producing chemical structure diagrams
7

SYNOPSIS

9       chem [--] [filespec ...]
10
11       chem -h
12       chem --help
13
14       chem -v
15       chem --version
16

DESCRIPTION

18       chem  produces  chemical  structure  diagrams.  Today's version is best
19       suited for organic chemistry (bonds, rings).  The  chem  program  is  a
20       groff  preprocessor  like  eqn, pic, tbl, etc.  It generates pic output
21       such that all chem parts are translated into diagrams of the  pic  lan‐
22       guage.
23
24       A  filespec argument is either a file name of an existing file or a mi‐
25       nus character -, meaning standard input.  If no argument  is  specified
26       then  standard  input  is taken automatically.  -h and --help display a
27       usage message, whereas -v and --version  display  version  information;
28       all exit.
29
30       The  program  chem  originates  from  the Perl source file chem.pl.  It
31       tells pic to include a copy of the macro file chem.pic.   Moreover  the
32       groff source file pic.tmac is loaded.
33
34       In a style reminiscent of eqn and pic, the chem diagrams are written in
35       a special language.
36
37       A set of chem lines looks like this
38
39              .cstart
40              chem data
41              .cend
42
43       Lines containing the keywords .cstart and .cend start and end the input
44       for  chem,  respectively.  In pic context, i.e., after the call of .PS,
45       chem input can optionally be started by the line begin chem  and  ended
46       by the line with the single word end instead.
47
48       Anything  outside  these initialization lines is copied through without
49       modification; all data between the initialization  lines  is  converted
50       into pic commands to draw the diagram.
51
52       As an example,
53
54              .cstart
55              CH3
56              bond
57              CH3
58              .cend
59
60       prints two CH3 groups with a bond between them.
61
62       To actually view this, you must run chem followed by groffer:
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64              chem [file ...] | groffer
65
66       If  you want to create just groff output, you must run chem followed by
67       groff with the option -p for the activation of pic:
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69              chem [file ...] | groff -p ...
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THE LANGUAGE

72       The chem input language is rather small.  It provides rings of  several
73       styles  and  a  way  to glue them together as desired, bonds of several
74       styles, moieties (e.g., C, NH3, ..., and strings.
75
76   Setting Variables
77       There are some variables that can be set by  commands.   Such  commands
78       have two possible forms, either
79
80              variable value
81
82       or
83
84              variable = value
85
86       This  sets the given variable to the argument value.  If more arguments
87       are given only the last argument is taken, all other arguments are  ig‐
88       nored.
89
90       There are only a few variables to be set by these commands:
91
92       textht arg
93              Set the height of the text to arg; default is 0.16.
94
95       cwid arg
96              Set the character width to arg; default is 0.12.
97
98       db arg Set the bond length to arg; default is 0.2.
99
100       size arg
101              Scale  the  diagram to make it look plausible at point size arg;
102              default is 10 point.
103
104   Bonds
105       This
106
107              bond [direction] [length n] [from Name|picstuff]
108
109       draws a single bond in direction from nearest corner of Name.  bond can
110       also  be double bond, front bond, back bond, etc.  (We will get back to
111       Name soon.)
112
113       direction is the angle in degrees (0 up, positive clockwise) or  a  di‐
114       rection  word like up, down, sw (= southwest), etc.  If no direction is
115       specified, the bond goes in the current direction (usually that of  the
116       last bond).
117
118       Normally  the  bond  begins  at  the  last  object placed;  this can be
119       changed by naming a from place.  For instance, to make a  simple  alkyl
120       chain:
121
122              CH3
123              bond                (this one goes right from the CH3)
124              C                   (at the right end of the bond)
125              double bond up      (from the C)
126              O                   (at the end of the double bond)
127              bond right from C
128              CH3
129
130       A  length  in  inches  may be specified to override the default length.
131       Other pic commands can be tacked on to the end of a  bond  command,  to
132       created dotted or dashed bonds or to specify a to place.
133
134   Rings
135       There are lots of rings, but only 5 and 6-sided rings get much support.
136       ring by itself is a 6-sided ring; benzene is the benzene  ring  with  a
137       circle inside.  aromatic puts a circle into any kind of ring.
138
139              ring [pointing (up|right|left|down)] [aromatic] [put Mol at n]
140                   [double i,j k,l ... [picstuff]
141
142       The vertices of a ring are numbered 1, 2,  ...  from  the  vertex  that
143       points  in the natural compass direction.  So for a hexagonal ring with
144       the point at the top, the top vertex is 1, while  if  the  ring  has  a
145       point at the east side, that is vertex 1.  This is expressed as
146
147              R1: ring pointing up
148              R2: ring pointing right
149
150       The ring vertices are named .V1, ..., .Vn, with .V1 in the pointing di‐
151       rection.  So the corners of R1 are R1.V1 (the top), R1.V2, R1.V3, R1.V4
152       (the  bottom),  etc., whereas for R2, R2.V1 is the rightmost vertex and
153       R2.V4 the leftmost.  These vertex names are used for  connecting  bonds
154       or other rings.  For example,
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156              R1: benzene pointing right
157              R2: benzene pointing right with .V6 at R1.V2
158
159       creates two benzene rings connected along a side.
160
161       Interior  double  bonds  are  specified as double n1,n2 n3,n4 ...; each
162       number pair adds an interior bond.  So the alternate form of a  benzene
163       ring is
164
165              ring double 1,2 3,4 5,6
166
167       Heterocycles  (rings  with something other than carbon at a vertex) are
168       written as put X at V, as in
169
170              R: ring put N at 1 put O at 2
171
172       In this heterocycle, R.N and R.O become synonyms for R.V1 and R.V2.
173
174       There are two 5-sided rings.  ring5 is  pentagonal  with  a  side  that
175       matches  the  6-sided ring; it has four natural directions.  A flatring
176       is a 5-sided ring created by chopping one corner of a 6-sided  ring  so
177       that it exactly matches the 6-sided rings.
178
179       The description of a ring has to fit on a single line.
180
181   Moieties and Strings
182       A  moiety  is  a  string of characters beginning with a capital letter,
183       such as N(C2H5)2.  Numbers are converted to subscripts (unless they ap‐
184       pear  to  be  fractional values, as in N2.5H).  The name of a moiety is
185       determined from the moiety after special characters have been  stripped
186       out: e.g., N(C2H5)2) has the name NC2H52.
187
188       Moieties  can  be  specified in two kinds.  Normally a moiety is placed
189       right after the last thing mentioned, separated  by  a  semicolon  sur‐
190       rounded by spaces, e.g.,
191
192              B1: bond ; OH
193
194       Here the moiety is OH; it is set after a bond.
195
196       As  the  second  kind a moiety can be positioned as the first word in a
197       pic-like command, e.g.,
198
199              CH3 at C + (0.5,0.5)
200
201       Here the moiety is CH3.  It is placed at a position relative  to  C,  a
202       moiety used earlier in the chemical structure.
203
204       So  moiety  names  can be specified as chem positions everywhere in the
205       chem code.  Beneath their printing moieties are names for places.
206
207       The moiety BP is special.  It is not printed but just serves as a  mark
208       to be referred to in later chem commands.  For example,
209
210              bond ; BP
211
212       sets a mark at the end of the bond.  This can be used then for specify‐
213       ing a place.  The name BP is derived  from  branch  point  (i.e.,  line
214       crossing).
215
216       A string within double quotes " is interpreted as a part of a chem com‐
217       mand.  It represents a string  that  should  be  printed  (without  the
218       quotes).   Text within quotes "..." is treated more or less like a moi‐
219       ety except that no changes are made to the quoted part.
220
221   Names
222       In the alkyl chain above, notice that the carbon atom C was  used  both
223       to draw something and as the name for a place.  A moiety always defines
224       a name for a place;  you can use your own names for places instead, and
225       indeed, for rings you will have to.  A name is just
226
227              Name: ...
228
229       Name  is  often  the  name of a moiety like CH3, but it need not to be.
230       Any name that begins with a capital letter and which contains only let‐
231       ters and numbers is valid:
232
233              First: bond
234                     bond 30 from First
235
236   Miscellaneous
237       The specific construction
238
239              bond ... ; moiety
240
241       is equivalent to
242
243              bond
244              moiety
245
246       Otherwise,  each item has to be on a separate line (and only one line).
247       Note that there must be whitespace after the semicolon which  separates
248       the commands.
249
250       A  period character . or a single quote ' in the first column of a line
251       signals a troff command, which is copied through as-is.
252
253       A line whose first non-blank character  is  a  hash  character  (#)  is
254       treated as a comment and thus ignored.  However, hash characters within
255       a word are kept.
256
257       A line whose first word is pic is copied through as-is after  the  word
258       pic has been removed.
259
260       The command
261
262              size n
263
264       scales  the  diagram to make it look plausible at point size n (default
265       is 10 point).
266
267       Anything else is assumed to be pic code, which is copied through with a
268       label.
269
270       Since  chem is a pic preprocessor, it is possible to include pic state‐
271       ments in the middle of a diagram to draw things  not  provided  for  by
272       chem  itself.   Such  pic statements should be included in chem code by
273       adding pic as the first word of this line for clarity.
274
275       The following pic commands are accepted as chem  commands,  so  no  pic
276       command word is needed:
277
278              define Start the definition of pic macro within chem.
279
280              [      Start a block composite.
281
282              ]      End a block composite.
283
284              {      Start a macro definition block.
285
286              }      End a macro definition block.
287
288       The macro names from define statements are stored and their call is ac‐
289       cepted as a chem command as well.
290
291   WISH LIST
292       This TODO list was collected by Brian Kernighan.
293
294       Error checking is minimal; errors are usually detected and reported  in
295       an oblique fashion by pic.
296
297       There is no library or file inclusion mechanism, and there is no short‐
298       hand for repetitive structures.
299
300       The extension mechanism is to create pic macros, but these  are  tricky
301       to get right and don't have all the properties of built-in objects.
302
303       There  is  no  in-line chemistry yet (e.g., analogous to the $...$ con‐
304       struct of eqn).
305
306       There is no way to control entry point for bonds on groups.  Normally a
307       bond connects to the carbon atom if entering from the top or bottom and
308       otherwise to the nearest corner.
309
310       Bonds from substituted atoms on heterocycles do not join at the  proper
311       place without adding a bit of pic.
312
313       There is no decent primitive for brackets.
314
315       Text (quoted strings) doesn't work very well.
316
317       A squiggle bond is needed.
318

FILES

320       /usr/share/groff/1.22.4/pic/chem.pic
321              A collection of pic macros needed by chem.
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323       /usr/share/groff/1.22.4/tmac/pic.tmac
324              A macro file which redefines .PS and .PE to center pic diagrams.
325
326       /usr/share/doc/groff/examples/chem/*.chem
327              Example files for chem.
328
329       /usr/share/doc/groff/examples/chem/122/*.chem
330              Example  files  from the classical chem article CHEM  A Program
331              for Typesetting Chemical Structure Diagrams [CSTR #122].
332

AUTHORS

334       The   GNU   version   of   chem   was   written   by    Bernd    Warken
335       ⟨groff-bernd.warken-72@web.de⟩.   It  is  based on the documentation of
336       Brian  Kernighan's  original  awk   version   of   chem   at   ⟨http://
337       cm.bell-labs.com/cm/cs/who/bwk/index.html⟩.
338

SEE ALSO

340       groff(1), pic(1), groffer(1).
341
342       You   can   still   get   the   original   chem   awk  source  ⟨http://
343       cm.bell-labs.com/netlib/typesetting/chem.gz⟩.  Its README file was used
344       for this manual page.
345
346       The  other  classical  document  on  chem  is  CHEM    A  Program  for
347       Typesetting  Chemical   Structure   Diagrams   [CSTR   #122]   ⟨http://
348       cm.bell-labs.com/cm/cs/cstr/122.ps.gz⟩.
349
350
351
352groff 1.22.4                     17 March 2021                         CHEM(1)
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