Provided by: groff_1.22.4-3_amd64 bug

NAME

       chem - groff preprocessor for producing chemical structure diagrams

SYNOPSIS

       chem [--] [filespec ...]

       chem -h
       chem --help

       chem -v
       chem --version

DESCRIPTION

       chem  produces  chemical  structure  diagrams.  Today's version is best suited for organic
       chemistry (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 language.

       A filespec argument is either a file name of an existing file  or  a  minus  character  -,
       meaning  standard  input.   If  no  argument  is  specified  then  standard input is taken
       automatically.  -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,
       respectively.  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.

       To actually view this, you must run chem followed by groffer:

              chem [file ...] | groffer

       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 ...

THE 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
       direction (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 5 and 6-sided rings get much support.  ring by itself is
       a 6-sided ring; benzene is the benzene ring with a circle inside.  aromatic puts a  circle
       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
       compass  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
       corners 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
       interior 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 5-sided rings.  ring5 is pentagonal with a side  that  matches  the  6-sided
       ring;  it  has  four natural directions.  A flatring is a 5-sided ring created by chopping
       one corner of a 6-sided ring so that it exactly matches the 6-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.
       Numbers  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
       command, 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 included 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
       command 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/1.22.4/pic/chem.pic
              A collection of pic macros needed by chem.

       /usr/share/groff/1.22.4/tmac/pic.tmac
              A macro file which redefines .PS and .PE 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  classical  chem article CHEM  A Program for Typesetting
              Chemical Structure Diagrams [CSTR #122].

AUTHORS

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

SEE ALSO

       groff(1), pic(1), groffer(1).

       You  can  still  get  the  original  chem  awk   source   ⟨http://cm.bell-labs.com/netlib/
       typesetting/chem.gz⟩.  Its README file was used for this manual page.

       The  other  classical  document  on  chem  is  CHEM    A Program for Typesetting Chemical
       Structure Diagrams [CSTR #122] ⟨http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz⟩.