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Updated: Thursday, June 13, 2019
 
 

chem (1)

Name

chem - groff preprocessor for producing chemical structure diagrams

Synopsis

chem [option ....]  [--] [filespec ....]

chem -h | --help

chem -v | --version

Description

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
       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 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
       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 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/share/groff/1.22.3/pic/chem.pic
              A collection of pic macros needed by chem.

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

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

       /usr/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.


ATTRIBUTES
       See attributes(7) for descriptions of the following attributes:


       +---------------+------------------+
       |ATTRIBUTE TYPE | ATTRIBUTE VALUE  |
       +---------------+------------------+
       |Availability   | text/groff       |
       +---------------+------------------+
       |Stability      | Uncommitted      |
       +---------------+------------------+
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>.



NOTES
       This     software     was    built    from    source    available    at
       https://github.com/oracle/solaris-userland.   The  original   community
       source                was                downloaded                from
       https://ftp.gnu.org/gnu/groff/groff-1.22.3.tar.gz

       Further information about this software can be found on the open source
       community website at https://www.gnu.org/software/groff.



Groff Version 1.22.3            4 November 2014                        CHEM(1)