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CHEM(1) 										  CHEM(1)

NAME
       chem - groff preprocessor for producing chemical structure diagrams

SYNOPSIS
       chem [option...] [--] [filespec...]
       chem -h | --help
       chem -v | --version

OPTION USAGE
       There  are  no other options than -h, --help, -v, and --version; these options provoke the
       printing of a version or usage information, respectively, and all filespec  arguments  are
       ignored.  A filespec argument is either a file name of an existing file or a minus charac-
       ter -, meaning standard input.  If no argument is specified then standard input	is  taken
       automatically.

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.

       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 lan-
       guage.

       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.

       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 op-
       tion -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/1.22.2/pic/chem.pic
	      A collection of pic macros needed by chem.

       /usr/share/groff/1.22.2/tmac/pic.tmac
	      A macro file which redefines .PS and .PE to center pic diagrams.

       /usr/share/doc/groff-1.22.2/examples/chem/*.chem
	      Example files for chem.

       /usr/share/doc/groff-1.22.2/examples/chem/122/*.chem
	      Example files from the classical chem book 122.ps.

BUGS
       Report bugs to the bug-groff mailing list <bug-groff@gnu.org>.  Include a complete,  self-
       contained example that will allow the bug to be reproduced, and say which version of groff
       and chem you are using.	You can get both version numbers by calling chem --version.

       You can also use the groff mailing list <groff@gnu.org>, but you must first  subscribe  to
       this  list.   You  can  do  that  by  visiting  the  groff  mailing list web page <http://
       lists.gnu.org/mailman/listinfo/groff>.

       See groff(1) for information on availability.

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  122.ps <http://cm.bell-labs.com/cm/cs/cstr/
       122.ps.gz>.

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

COPYING
       Copyright (C) 2006, 2007, 2008, 2009 Free Software Foundation, Inc.

       This file is part of chem, which is part of groff,  a  free  software  project.	 You  can
       redistribute it and/or modify it under the terms of the GNU General Public License as pub-
       lished by the Free Software Foundation, either version 2, or (at your  option)  any  later
       version.

       You  should  have  received a copy of the GNU General Public License along with groff, see
       the files COPYING and LICENSE in the top directory of the groff source package.	 Or  read
       the man page gpl(1).  You can also write to the Free Software Foundation, 51 Franklin St -
       Fifth Floor, Boston, MA 02110-1301, USA.

Groff Version 1.22.2			 7 February 2013				  CHEM(1)
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