man > CHEM

chem(1)                                General Commands Manual                               chem(1)

Name
       chem - embed chemical structure diagrams in groff documents

Synopsis
       chem [--] [file ...]

       chem -h
       chem --help

       chem -v
       chem --version

Description
       chem  produces chemical structure diagrams.  Today's version is best suited for organic chem‐
       istry (bonds, rings).  The chem program is a groff preprocessor like eqn, pic, tbl, etc.   It
       generates  pic  output  such that all chem parts are translated into diagrams of the pic lan‐
       guage.

       If no operands are given, or if file is “-”, chem reads the standard input  stream.   -h  and
       --help  display  a  usage  message, whereas -v and --version display version information; all
       exit.

       The program chem originates from the Perl source file chem.pl.  It tells  pic  to  include  a
       copy of the macro file chem.pic.  Moreover the groff source file pic.tmac is loaded.

       In a style reminiscent of eqn and pic, the chem diagrams are written in a special language.

       A set of chem lines looks like this

              .cstart
              chem data
              .cend

       Lines  containing  the  keywords  .cstart and .cend start and end the input for chem, respec‐
       tively.  In pic context, i.e., after the call of .PS, chem input can optionally be started by
       the line begin chem and ended by the line with the single word end instead.

       Anything outside these initialization lines is copied through without modification; all  data
       between the initialization lines is converted into pic commands to draw the diagram.

       As an example,

              .cstart
              CH3
              bond
              CH3
              .cend

       prints two CH3 groups with a bond between them.

       If  you want to create just groff output, you must run chem followed by groff with the option
       -p for the activation of pic:

              chem [file ...] | groff -p ...

Language
       The chem input language is rather small.  It provides rings of several styles and  a  way  to
       glue  them  together  as  desired,  bonds of several styles, moieties (e.g., C, NH3, ..., and
       strings.

   Setting variables
       There are some variables that can be set by commands.  Such commands have two possible forms,
       either

              variable value

       or

              variable = value

       This sets the given variable to the argument value.  If more arguments  are  given  only  the
       last argument is taken, all other arguments are ignored.

       There are only a few variables to be set by these commands:

       textht arg
              Set the height of the text to arg; default is 0.16.

       cwid arg
              Set the character width to arg; default is 0.12.

       db arg Set the bond length to arg; default is 0.2.

       size arg
              Scale the diagram to make it look plausible at point size arg; default is 10 point.

   Bonds
       This

              bond [direction] [length n] [from Name|picstuff]

       draws  a single bond in direction from nearest corner of Name.  bond can also be double bond,
       front bond, back bond, etc.  (We will get back to Name soon.)

       direction is the angle in degrees (0 up, positive clockwise) or a  direction  word  like  up,
       down,  sw (= southwest), etc.  If no direction is specified, the bond goes in the current di‐
       rection (usually that of the last bond).

       Normally the bond begins at the last object placed;  this can be changed  by  naming  a  from
       place.  For instance, to make a simple alkyl chain:
              CH3
              bond                (this one goes right from the CH3)
              C                   (at the right end of the bond)
              double bond up      (from the C)
              O                   (at the end of the double bond)
              bond right from C
              CH3

       A  length  in inches may be specified to override the default length.  Other pic commands can
       be tacked on to the end of a bond command, to created dotted or dashed bonds or to specify  a
       to place.

   Rings
       There are lots of rings, but only five- and six-sided rings get much support.  ring by itself
       is  a six-sided ring; benzene is the benzene ring with a circle inside.  aromatic puts a cir‐
       cle into any kind of ring.

              ring [pointing (up|right|left|down)] [aromatic] [put Mol at n] [double i,j k,l ...
                   [picstuff]

       The vertices of a ring are numbered 1, 2, ... from the vertex that points in the natural com‐
       pass direction.  So for a hexagonal ring with the point at the top,  the  top  vertex  is  1,
       while if the ring has a point at the east side, that is vertex 1.  This is expressed as

              R1: ring pointing up
              R2: ring pointing right

       The  ring  vertices are named .V1, ..., .Vn, with .V1 in the pointing direction.  So the cor‐
       ners of R1 are R1.V1 (the top), R1.V2, R1.V3, R1.V4 (the bottom), etc., whereas for R2, R2.V1
       is the rightmost vertex and R2.V4 the leftmost.  These vertex names are used  for  connecting
       bonds or other rings.  For example,

              R1: benzene pointing right
              R2: benzene pointing right with .V6 at R1.V2

       creates two benzene rings connected along a side.

       Interior double bonds are specified as double n1,n2 n3,n4 ...; each number pair adds an inte‐
       rior bond.  So the alternate form of a benzene ring is

              ring double 1,2 3,4 5,6

       Heterocycles  (rings with something other than carbon at a vertex) are written as put X at V,
       as in

              R: ring put N at 1 put O at 2

       In this heterocycle, R.N and R.O become synonyms for R.V1 and R.V2.

       There are two five-sided rings.  ring5 is pentagonal with a side that matches  the  six-sided
       ring;  it  has  four natural directions.  A flatring is a five-sided ring created by chopping
       one corner of a six-sided ring so that it exactly matches the six-sided rings.

       The description of a ring has to fit on a single line.

   Moieties and strings
       A moiety is a string of characters beginning with a capital letter, such as  N(C2H5)2.   Num‐
       bers  are  converted to subscripts (unless they appear to be fractional values, as in N2.5H).
       The name of a moiety is determined  from  the  moiety  after  special  characters  have  been
       stripped out: e.g., N(C2H5)2) has the name NC2H52.

       Moieties  can  be  specified  in two kinds.  Normally a moiety is placed right after the last
       thing mentioned, separated by a semicolon surrounded by spaces, e.g.,

              B1: bond ; OH

       Here the moiety is OH; it is set after a bond.

       As the second kind a moiety can be positioned as the first word in a pic-like command, e.g.,

              CH3 at C + (0.5,0.5)

       Here the moiety is CH3.  It is placed at a position relative to C, a moiety used  earlier  in
       the chemical structure.

       So  moiety  names  can  be  specified as chem positions everywhere in the chem code.  Beneath
       their printing moieties are names for places.

       The moiety BP is special.  It is not printed but just serves as a mark to be referred  to  in
       later chem commands.  For example,

              bond ; BP

       sets  a mark at the end of the bond.  This can be used then for specifying a place.  The name
       BP is derived from branch point (i.e., line crossing).

       A string within double quotes " is interpreted as a part of a chem command.  It represents  a
       string that should be printed (without the quotes).  Text within quotes "..." is treated more
       or less like a moiety except that no changes are made to the quoted part.

   Names
       In  the  alkyl chain above, notice that the carbon atom C was used both to draw something and
       as the name for a place.  A moiety always defines a name for a place;  you can use  your  own
       names for places instead, and indeed, for rings you will have to.  A name is just

              Name: ...

       Name  is  often  the  name of a moiety like CH3, but it need not to be.  Any name that begins
       with a capital letter and which contains only letters and numbers is valid:

              First: bond
                     bond 30 from First

   Miscellaneous
       The specific construction

              bond ... ; moiety

       is equivalent to

              bond
              moiety

       Otherwise, each item has to be on a separate line (and only one line).  Note that there  must
       be whitespace after the semicolon which separates the commands.

       A  period  character . or a single quote ' in the first column of a line signals a troff com‐
       mand, which is copied through as-is.

       A line whose first non-blank character is a hash character (#) is treated as  a  comment  and
       thus ignored.  However, hash characters within a word are kept.

       A line whose first word is pic is copied through as-is after the word pic has been removed.

       The command

              size n

       scales the diagram to make it look plausible at point size n (default is 10 point).

       Anything else is assumed to be pic code, which is copied through with a label.

       Since chem is a pic preprocessor, it is possible to include pic statements in the middle of a
       diagram  to  draw  things not provided for by chem itself.  Such pic statements should be in‐
       cluded in chem code by adding pic as the first word of this line for clarity.

       The following pic commands are accepted as chem commands, so no pic command word is needed:

              define Start the definition of pic macro within chem.

              [      Start a block composite.

              ]      End a block composite.

              {      Start a macro definition block.

              }      End a macro definition block.

       The macro names from define statements are stored and their call is accepted as a  chem  com‐
       mand as well.

   Wish list
       This TODO list was collected by Brian Kernighan.

       Error  checking is minimal; errors are usually detected and reported in an oblique fashion by
       pic.

       There is no library or file inclusion mechanism, and there is  no  shorthand  for  repetitive
       structures.

       The  extension mechanism is to create pic macros, but these are tricky to get right and don't
       have all the properties of built-in objects.

       There is no in-line chemistry yet (e.g., analogous to the $...$ construct of eqn).

       There is no way to control entry point for bonds on groups.  Normally a bond connects to  the
       carbon atom if entering from the top or bottom and otherwise to the nearest corner.

       Bonds from substituted atoms on heterocycles do not join at the proper place without adding a
       bit of pic.

       There is no decent primitive for brackets.

       Text (quoted strings) doesn't work very well.

       A squiggle bond is needed.

Files
       /usr/share/groff/1.23.0/pic/chem.pic
              A collection of pic macros needed by chem.

       /usr/share/groff/1.23.0/tmac/pic.tmac
              A macro file which redefines .PS, .PE, and .PF to center pic diagrams.

       /usr/share/doc/groff-base/examples/chem/*.chem
              Example files for chem.

       /usr/share/doc/groff-base/examples/chem/122/*.chem
              Example  files  from  the chem article by its authors, “CHEM—A Program for Typesetting
              Chemical Structure Diagrams: User Manual” (CSTR #122).

Authors
       The GNU version of chem was written by Bernd Warken.  It is based  on  the  documentation  of
       Brian Kernighan's original awk version of chem.

See also
       “CHEM—A  Program  for  Typesetting Chemical Diagrams: User Manual” by Jon L. Bentley, Lynn W.
       Jelinski, and Brian W. Kernighan, 1992, AT&T Bell Laboratories  Computing  Science  Technical
       Report No. 122

       groff(1), pic(1)

groff 1.23.0                                31 March 2024                                    chem(1)