CHEM(1)                    OpenBSD Reference 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,
       respectively, 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
       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 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/local/share/groff/1.21/pic/chem.pic
              A collection of pic macros needed by chem.

       /usr/local/share/groff/1.21/tmac/pic.tmac
              A macro file which redefines .PS and .PE to center pic diagrams.

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

       /usr/local/share/doc/groff/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.  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 published 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 1.21             31 December 2010                        CHEM(1)
