.TH CHEM 1 "7 February 2022" "groff 1.22.4"
.SH NAME
chem \- groff preprocessor for producing chemical structure diagrams
.
.\" chem.1 - man page for chem (section 1).
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.\" Copyright (C) 2006-2018 Free Software Foundation, Inc.
.\"
.\" 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 version 2 (GPL2) as published by the Free
.\" Software Foundation.
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.\" ====================================================================
.\" Setup
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.\" Save and disable compatibility mode (for, e.g., Solaris 10/11).
.do nr chem_C \n[.C]
.cp 0
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.\" Characters
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.\" Ellipsis ...
.ie t .ds EL \fS\N'188'\fP\"
.el .ds EL \&.\|.\|.\&\"
.\" called with \*(EL
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.\" ====================================================================
.SH "SYNOPSIS"
.\" ====================================================================
.
.SY chem
.OP \-\-
.RI [ filespec
\*(EL]
.YS
.
.SY chem
.B \-h
.SY chem
.B \-\-help
.YS
.
.SY chem
.B \-v
.SY chem
.B \-\-version
.YS
.
.
.\" ====================================================================
.SH DESCRIPTION
.\" ====================================================================
.
.I chem
produces chemical structure diagrams.
.
Today's version is best suited for organic chemistry (bonds, rings).
.
The
.B chem
program is a
.B groff
preprocessor like
.BR eqn ,
.BR pic ,
.BR tbl ,
etc.
.
It generates
.I pic
output such that all
.I chem
parts are translated into diagrams of the
.I pic
language.
.
.
.P
A
.I filespec
argument is either a file name of an existing file or a minus
character
.BR \- ,
meaning standard input.
.
If no argument is specified then standard input is taken
automatically.
.
.B \-h
and
.B \-\-help
display a usage message,
whereas
.B \-v
and
.B \-\-version
display version information;
all exit.
.
.
.P
The program
.B chem
originates from the Perl source file
.IR chem.pl .
.
It tells
.B pic
to include a copy of the macro file
.IR chem.pic .
.
Moreover the
.I groff
source file
.I pic.tmac
is loaded.
.
.
.P
In a style reminiscent of
.I eqn
and
.IR pic ,
the
.I chem
diagrams are written in a special language.
.
.
.P
A set of
.I chem
lines looks like this
.
.
.IP
.nf
.ft B
\&.cstart
\fIchem data\fP
\&.cend
.ft
.fi
.
.
.P
Lines containing the keywords
.B .cstart
and
.B .cend
start and end the input for
.BR chem ,
respectively.
.
In
.I pic
context, i.e., after the call of
.BR .PS ,
.I chem
input can optionally be started by the line
.B \%begin\~chem
and ended by the line with the single word
.B end
instead.
.
.
.P
Anything outside these initialization lines is copied through
without modification;
all data between the initialization lines is converted into
.I pic
commands to draw the diagram.
.
.
.P
As an example,
.
.IP
.nf
.ft B
\&.cstart
CH3
bond
CH3
\&.cend
.ft
.fi
.
.
.P
prints two
.B CH3
groups with a bond between them.
.
.
.P
To actually view this, you must run
.B chem
followed by
.BR groffer :
.
.IP
.B chem [file \*(EL] | groffer
.
.P
If you want to create just
.B groff
output, you must run
.B chem
followed by
.B groff
with the option
.B \-p
for the activation of
.BR pic :
.IP
.B chem [file \*(EL] | groff \-p \*(EL
.
.
.\" ====================================================================
.SH THE LANGUAGE
.\" ====================================================================
.
The
.I 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.,
.BR C ,
.BR NH3 ,
\*(EL, and strings.
.
.
.\" ====================================================================
.SS Setting Variables
.\" ====================================================================
.
There are some variables that can be set by commands.
.
Such commands have two possible forms, either
.
.RS
.P
.I "variable value"
.RE
.
.P
or
.
.RS
.P
.IB "variable " = " value"
.RE
.
.P
This sets the given
.I variable
to the argument
.IR value .
If more arguments are given only the last argument is taken, all other
arguments are ignored.
.
.
.P
There are only a few variables to be set by these commands:
.
.TP
.BI textht " arg"
Set the height of the text to
.IR arg ;
default is 0.16.
.
.TP
.BI cwid " arg"
Set the character width to
.IR arg ;
default is 0.12.
.
.TP
.BI db " arg"
Set the bond length to
.IR arg ;
default is 0.2.
.
.TP
.BI size " arg"
Scale the diagram to make it look plausible at point size
.IR arg ;
default is 10 point.
.
.
.\" ====================================================================
.SS Bonds
.\" ====================================================================
.
This
.
.RS
.SY bond
.RI [ direction ]
.RI [ length\ n ]
.RB [ from\ \c
.IR Name | picstuff ]
.YS
.RE
.
.P
draws a single bond in direction from nearest corner of
.IR Name .
.B bond
can also be
.BR "double bond" ,
.BR "front bond" ,
.BR "back bond" ,
etc.
.
(We will get back to
.I Name
soon.)
.
.
.P
.I direction
is the angle in degrees (0\~up, positive clockwise)
or a direction word like
.BR up ,
.BR down ,
.B sw
(=\~southwest), etc.
.
If no direction is specified, the bond goes in the current direction
(usually that of the last bond).
.
.
.P
Normally the bond begins at the last object placed;  this
can be changed by naming a
.B from
place.
.
For instance, to make a simple alkyl chain:
.
.RS
.TS
tab (@);
lb l.
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
.TE
.RE
.
.
.P
A length in inches may be specified to override the default length.
.
Other
.I pic
commands can be tacked on to the end of a bond command, to created
dotted or dashed bonds or to specify a
.B to
place.
.
.
.\" ====================================================================
.SS Rings
.\" ====================================================================
.
There are lots of rings, but only 5 and 6-sided rings get
much support.
.
.B ring
by itself is a 6-sided ring;
.B benzene
is the benzene ring with a circle inside.
.B aromatic
puts a circle into any kind of ring.
.
.RS
.SY ring
.RB [ \%pointing\  ( up | right | left | down )]
.RB [ \%aromatic ]
.RB [ put\ Mol\ at\ \fIn\/\fP ]
.RB [ \%double\ \c
.IR i , j\ \/\c
.IR k , l\ \/\c
\*(EL
.RI [ picstuff ]
.YS
.RE
.
.
.P
The vertices of a ring are numbered 1, 2, \*(EL 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
.
.IP
.ft B
.nf
R1: ring pointing up
R2: ring pointing right
.fi
.ft
.
.
.P
The ring vertices are named
.BR .V1 ,
\*(EL,
.BI .V n\fR,\fP
with
.B .V1
in the pointing direction.
.
So the corners of
.B R1
are
.B R1.V1
(the
.IR top ),
.BR R1.V2 ,
.BR R1.V3 ,
.B R1.V4
(the
.IR bottom ),
etc., whereas for
.BR R2 ,
.B R2.V1
is the rightmost vertex and
.B R2.V4
the leftmost.
.
These vertex names are used for connecting bonds or other rings.  For
example,
.
.IP
.ft B
.nf
R1: benzene pointing right
R2: benzene pointing right with .V6 at R1.V2
.fi
.ft
.P
creates two benzene rings connected along a side.
.
.
.P
Interior double bonds are specified as
.BI \%double\  n1 , n2\ n3 , n4\ \fR\*(EL;\fP
each number pair adds an interior bond.
.
So the alternate form of a benzene ring is
.
.IP
.B "ring double 1,2 3,4 5,6"
.
.
.P
Heterocycles (rings with something other than carbon at a vertex) are
written as
.BI put\  X\  at\  V\fR,\fP
as in
.
.IP
.B "R: ring put N at 1 put O at 2"
.
.
.P
In this heterocycle,
.B R.N
and
.B R.O
become synonyms for
.B R.V1
and
.BR R.V2 .
.
.
.P
There are two 5-sided rings.
.
.B ring5
is pentagonal with a side that matches the 6-sided ring; it has four
natural directions.
.
A
.B \%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.
.
.
.P
The description of a ring has to fit on a single line.
.
.
.\" ====================================================================
.SS 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.
.
.
.P
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.,
.
.IP
.B "B1: bond ; OH"
.
.P
Here the moiety is
.BR OH ;
it is set after a bond.
.
.
.P
As the second kind a moiety can be positioned as the first word in a
.IR pic -like
command, e.g.,
.
.IP
.B "CH3 at C + (0.5,0.5)"
.
.P
Here the moiety is
.BR CH3 .
It is placed at a position relative to
.BR C ,
a moiety used earlier in the chemical structure.
.
.
.P
So moiety names can be specified as
.I chem
positions everywhere in the
.I chem
code.
.
Beneath their printing moieties are names for places.
.
.
.P
The moiety
.B BP
is special.
.
It is not printed but just serves as a mark to be referred to in later
.I chem
commands.
.
For example,
.
.IP
.B "bond ; BP"
.
.P
sets a mark at the end of the bond.
.
This can be used then for specifying a place.
.
The name
.B BP
is derived from
.I branch point
(i.e., line crossing).
.
.
.P
A string within double quotes
.B \(dq
is interpreted as a part of a
.I chem
command.
.
It represents a string that should be printed (without the quotes).
.
Text within quotes \(dq\*(EL\(dq is treated more or less
like a moiety except that no changes are made to the quoted part.
.
.
.\" ====================================================================
.SS Names
.\" ====================================================================
.
In the alkyl chain above, notice that the carbon atom
.B 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
.
.IP
.IB Name :
\*(EL
.
.
.P
.I Name
is often the name of a moiety like
.BR CH3 ,
but it need not to be.
.
Any name that begins with a capital letter and which contains
only letters and numbers is valid:
.
.RS
.TP
.B First:
.B bond
.TQ
\&
.B "bond 30 from First"
.RE
.
.
.\" ====================================================================
.SS Miscellaneous
.\" ====================================================================
.
The specific construction
.RS
.TP
.BR bond\  \*(EL " ; moiety"
.RE
.P
is equivalent to
.IP
.ft B
.nf
bond
moiety
.fi
.ft
.
.
.P
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.
.
.
.P
A period character
.B .\&
or a single quote
.B '
in the first column of a line signals a
.I troff
command, which is copied through as-is.
.
.
.P
A line whose first non-blank character is a hash character
.RB ( # )
is treated as a comment and thus ignored.
.
However, hash characters within a word are kept.
.
.
.P
A line whose first word is
.B pic
is copied through as-is after the word
.B pic
has been removed.
.
.
.P
The command
.IP
.B size
.I n
.P
scales the diagram to make it look plausible at point size\~\c
.I n
(default is 10\~point).
.
.
.P
Anything else is assumed to be
.I pic
code, which is copied through with a label.
.
.
.P
Since
.B chem
is a
.B pic
preprocessor, it is possible to include
.I pic
statements in the middle of a diagram to draw things not provided for
by
.I chem
itself.
.
Such
.I pic
statements should be included in
.I chem
code by adding
.B pic
as the first word of this line for clarity.
.
.
.P
The following
.I pic
commands are accepted as
.I chem
commands, so no
.B pic
command word is needed:
.
.IP
.B define
Start the definition of
.I pic
macro within
.IR chem .
.
.RS
.TP
.B [
Start a block composite.
.
.TP
.B ]
End a block composite.
.
.TP
.B {
Start a macro definition block.
.
.TP
.B }
End a macro definition block.
.RE
.
.P
The macro names from
.B define
statements are stored and their call is accepted as a
.I chem
command as well.
.
.
.\" ====================================================================
.SS WISH LIST
.\" ====================================================================
.
.P
This TODO list was collected by Brian Kernighan.
.
.
.P
Error checking is minimal; errors are usually detected and reported in
an oblique fashion by
.IR pic .
.
.
.P
There is no library or file inclusion mechanism, and there is no
shorthand for repetitive structures.
.
.
.P
The extension mechanism is to create
.I pic
macros, but these are tricky to get right and don't have all the
properties of built-in objects.
.
.
.P
There is no in-line chemistry yet (e.g., analogous to the $\*(EL$
construct of eqn).
.
.
.P
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.
.
.
.P
Bonds from substituted atoms on heterocycles do not join at the proper
place without adding a bit of
.IR pic .
.
.
.P
There is no decent primitive for brackets.
.
.
.P
Text (quoted strings) doesn't work very well.
.
.
.P
A squiggle bond is needed.
.
.
.\" ====================================================================
.SH "FILES"
.\" ====================================================================
.
.TP
.I /usr/\:share/\:groff/\:1.22.4/pic/chem.pic
A collection of
.I pic
macros needed by
.BR chem .
.
.TP
.I /usr/\:share/\:groff/\:1.22.4/\:tmac/pic.tmac
A macro file which redefines
.B .PS
and
.B .PE
to center
.I pic
diagrams.
.
.TP
.IR /usr/\:share/\:doc/\:packages/\:groff/examples/chem/ * .chem
Example files for
.IR chem .
.
.TP
.IR /usr/\:share/\:doc/\:packages/\:groff/examples/chem/122/ * .chem
Example files from the classical
.I chem
article
.I "CHEM \[en] A Program for Typesetting Chemical Structure Diagrams"
[CSTR\~#122].
.
.
.\" ====================================================================
.SH AUTHORS
.\" ====================================================================
.
The GNU version of
.B chem
was written by
.MT groff\-bernd.warken\-72@\:web.de
Bernd Warken
.ME .
.
It is based on the documentation of Brian Kernighan's original
.I awk
version of
.I chem
at
.UR http://\:cm.bell\-labs.com/\:cm/\:cs/\:who/\:bwk/\:index.html
.UE .
.
.
.\" ====================================================================
.SH "SEE ALSO"
.\" ====================================================================
.
.BR \%groff (1),
.BR \%pic (1),
.BR \%groffer (1).
.
.
.P
You can still get the original
.UR http://\:cm.bell\-labs.com/\:netlib/\:typesetting/\:chem.gz
chem awk source
.UE .
.
Its
.B README
file was used for this manual page.
.
.
.P
The other classical document on
.I chem
is
.UR http://\:cm.bell\-labs.com/\:cm/\:cs/\:cstr/\:122.ps.gz
.I "CHEM \[en] A Program for Typesetting Chemical Structure Diagrams"
[CSTR\~#122]
.UE .
.
.
.\" Restore compatibility mode (for, e.g., Solaris 10/11).
.cp \n[chem_C]
.
.
.\" ====================================================================
.\" Emacs settings
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.\" Local Variables:
.\" mode: nroff
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