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CHEM(1)			    General Commands Manual		       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, respec-
       tively, and all filespec	arguments are ignored.	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.

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 lan-
       guage.

       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 ig-
       nored.

       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 di-
       rection 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 ap-
       pear 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 sur-
       rounded 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 specify-
       ing  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 com-
       mand.   It  represents  a  string  that	should be printed (without the
       quotes).	 Text within quotes "...." is treated more or less like	a moi-
       ety 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 let-
       ters 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	state-
       ments  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 ac-
       cepted 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	short-
       hand 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  $....$  con-
       struct 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/local/share/groff/1.22.3/pic/chem.pic
	      A	collection of pic macros needed	by chem.

       /usr/local/share/groff/1.22.3/tmac/pic.tmac
	      A	macro file which redefines .PS and .PE to center pic diagrams.

       /usr/local/share/doc/groff-1.22.3/examples/chem/*.chem
	      Example files for	chem.

       /usr/local/share/doc/groff-1.22.3/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	repro-
       duced, 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>.

COPYING
       Copyright (C) 2006-2014 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 version 2	(GPL2) as published by the Free	 Soft-
       ware Foundation.

       The   license   text   for   GPL2  is  available	 in  the  internet  at
       <http://www.gnu.org/licenses/gpl-2.0.html>.

AUTHORS
       This file was written by	Bernd Warken <groff-bernd.warken-72@web.de>.

       It is based on the documentation	of Brian Kernighan's original awk ver-
       sion of chem at <http://cm.bell-labs.com/cm/cs/who/bwk/index.html>.

Groff Version 1.22.3		4 November 2014			       CHEM(1)

NAME | SYNOPSIS | OPTION USAGE | DESCRIPTION | THE LANGUAGE | FILES | BUGS | SEE ALSO | COPYING | AUTHORS

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