chem (1)

NAME

SYNOPSIS

OPTION USAGE

DESCRIPTION

THE LANGUAGE

Setting Variables
Bonds
Rings
Moieties and Strings
Names
Miscellaneous
WISH LIST

NAME

chem - groff preprocessor for producing chemical structure diagrams

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, 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

: 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

: [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.

: [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/share/groff/1.22.2/pic/chem.pic": A collection of pic macros needed by chem.
"/usr/share/groff/1.22.2/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.

BUGS

Report bugs to the bug-groff mailing list 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 but you must first subscribe to this list. You can do that by visiting the groff mailing list web page

See groff(1) for information on availability.

AUTHOR

This file was written by Bernd Warken <groff-bernd.warken-72@web.de>. It is based on the documentation of Brian Kernighan original awk version of chem.

COPYING

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.