chem(1) — Linux manual page

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chem(1)                  General Commands Manual                 chem(1)

Name         top

       chem - embed chemical structure diagrams in groff documents

Synopsis         top

       chem [--] [file ...]

       chem -h
       chem --help

       chem -v
       chem --version

Description         top

       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.

       If no operands are given, or if file is “-”, chem reads the
       standard input stream.  -h and --help display a usage message,
       whereas -v and --version display version information; all exit.

       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.

       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 ...

Language         top

       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         top

       /usr/local/share/groff/1.23.0/pic/chem.pic
              A collection of pic macros needed by chem.

       /usr/local/share/groff/1.23.0/tmac/pic.tmac
              A macro file which redefines .PS and .PE to center pic
              diagrams.

       /usr/local/share/doc/groff-1.23.0/examples/chem/*.chem
              Example files for chem.

       /usr/local/share/doc/groff-1.23.0/examples/chem/122/*.chem
              Example files from the chem article by its authors, “CHEM—
              A Program for Typesetting Chemical Structure Diagrams:
              User Manual” (CSTR #122).

Authors         top

       The GNU version of chem was written by Bernd Warken ⟨groff-bernd
       .warken-72@web.de⟩.  It is based on the documentation of Brian
       Kernighan's original awk version of chem.

See also         top

       “CHEM—A Program for Typesetting Chemical Diagrams: User Manual”
       by Jon L. Bentley, Lynn W. Jelinski, and Brian W. Kernighan,
       1992, AT&T Bell Laboratories Computing Science Techical Report
       No. 122

       groff(1), pic(1)

COLOPHON         top

       This page is part of the groff (GNU troff) project.  Information
       about the project can be found at 
       ⟨http://www.gnu.org/software/groff/⟩.  If you have a bug report
       for this manual page, see ⟨http://www.gnu.org/software/groff/⟩.
       This page was obtained from the project's upstream Git repository
       ⟨https://git.savannah.gnu.org/git/groff.git⟩ on 2021-06-20.  (At
       that time, the date of the most recent commit that was found in
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groff 1.23.0.rc1.654-4e1db-dirt1y6 June 2021                       chem(1)