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%chem

Section: User Commands (1)
Updated: 2 July 2023
Index Return to Main Contents

Name

chem - embed chemical structure diagrams in groff documents
.nr d-fallback 1
.nr d-fallback 1

Synopsis

[--] [file~...] -h --help -v --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 [lq]-[rq], 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

: [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 fiv- and si-sided rings get much support. ring by itself is a si-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 fiv-sided rings. ring5 is pentagonal with a side that matches the si-sided ring; it has four natural directions. A flatring is a fiv-sided ring created by chopping one corner of a si-sided ring so that it exactly matches the si-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 dq is interpreted as a part of a chem command. It represents a string that should be printed (without the quotes). Text within quotes dq...dq 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 [aq] in the first column of a line signals a troff command, which is copied through a-is. A line whose first no-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 a-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 buil-in objects. There is no i-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-1.23.0/:examples/:chem/:*.chem: Example files for chem.
/usr/:share/:doc/:groff-1.23.0/:examples/:chem/:122/:*.chem: Example files from the chem article by its authors, [lq]CHEM[em]A Program for Typesetting Chemical Structure Diagrams: User Manual[rq] (CSTR~#122).