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HTML rendering created 2024-06-26 by Michael Kerrisk, author of The Linux Programming Interface. For details of in-depth Linux/UNIX system programming training courses that I teach, look here. Hosting by jambit GmbH. |
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Name | Synopsis | Description | Language | Files | Authors | See also | COLOPHON |
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chem(1) General Commands Manual chem(1)
chem - embed chemical structure diagrams in groff documents
chem [--] [file ...]
chem -h
chem --help
chem -v
chem --version
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 ...
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
bond [direction] [length n] [from Name|picstuff]
The bond command 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.
/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, .PE, and .PF 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).
The GNU version of chem was written by Bernd Warken ⟨groff-bernd
[email protected]⟩. It is based on the documentation of Brian
Kernighan's original awk version of chem.
“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 Technical Report
No. 122
groff(1), pic(1)
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 2024-06-14. (At
that time, the date of the most recent commit that was found in
the repository was 2024-06-10.) If you discover any rendering
problems in this HTML version of the page, or you believe there
is a better or more up-to-date source for the page, or you have
corrections or improvements to the information in this COLOPHON
(which is not part of the original manual page), send a mail to
[email protected]
groff 1.23.0.1273-9d53-dirty 6 June 2024 chem(1)
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HTML rendering created 2024-06-26 by Michael Kerrisk, author of The Linux Programming Interface. For details of in-depth Linux/UNIX system programming training courses that I teach, look here. Hosting by jambit GmbH. |
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