Ubuntu Manpage: chem - embed chemical structure diagrams in groff documents

Name

       chem - embed chemical structure diagrams in groff documents

Synopsis

       chem [--] [file ...]

       chem -h
       chem --help

       chem -v
       chem --version

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.

       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

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

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 five- and six-sided rings get much support. ring by
itself is a six-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 five-sided rings. ring5 is pentagonal with a side that matches the six-
sided ring; it has four natural directions. A flatring is a five-sided ring created by
chopping one corner of a six-sided ring so that it exactly matches the six-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/share/groff/1.23.0/pic/chem.pic
              A collection of pic macros needed by chem.

       /usr/share/groff/1.23.0/tmac/pic.tmac
              A macro file which redefines .PS, .PE, and .PF 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 chem article by its authors, “CHEM—A Program for Typesetting
              Chemical Structure Diagrams: User Manual” (CSTR #122).

Authors