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    Command:

    chem

    
    
    

    SYNOPSIS

           [option...] [filespec...] -h | --help -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:
    
           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
                  [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.
    
                  R1: ring pointing up
                  R2: ring pointing right
    
           The ring vertices are named .V1, ..., .Vn, with .V1 in the pointing di-
           rection.  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.,
           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
    
                  [      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/share/groff/1.21/pic/chem.pic
                  A collection of pic macros needed by chem.
    
           /usr/share/groff/1.21/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 book 122.ps.
    
           You can still get the original chem awk source Its README file was used
           for this manual page.
    
           The other classical document on chem is 122.ps
    
    
    

    AUTHOR

           This  file  was written by Bernd Warken.  It is based on the documenta-
           tion of Brian Kernighan 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)

    
    
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