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gchem.1 - man page for gchem (section 1).

Source file position:  <groff_source_top>/contrib/chem/chem.man
Installed position:    $prefix/share/man/man1/gchem.1

Last update: 05 Jan 2009
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This file was written by Bernd Warken <groff-bernd.warken-72@web.de>.
It is based on the documentation of
.UR http://\:cm.bell-labs.com/\:cm/\:cs/\:who/\:bwk/\:index.html
Brian Kernighan
.UE 's
original
.I awk
version of
.IR chem .
..
.
.
.de co
Copyright (C) 2006, 2007, 2008, 2009 Free Software Foundation, Inc.
.
.
.P
This file is part of
.IR chem ,
which is part of
.IR groff ,
a free software project.
.
You can redistribute it and/or modify it under the terms of the
.nh
.B "GNU General Public License"
.hy
as published by the
.nh
.BR "Free Software Foundation" ,
.hy
either version\~2, or (at your option) any later version.
.
.
.P
You should have received a copy of the \f(CRGNU General Public
License\fP along with
.IR groff ,
see the files \%\f(CBCOPYING\fP and \%\f(CBLICENSE\fP in the top
directory of the
.I groff
source package.
.
Or read the
.I man page
.BR gpl (1).
You can also write to the
.nh
.B "Free Software Foundation, 51 Franklin St - Fifth Floor, Boston,"
.BR "MA 02110-1301, USA" .
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.\" --------------------------------------------------------------------
.\" Local macro definitions
.
.ds El \&.\|.\|.\&
.
.\" .File_name  (<path_name>)
.\"
.\" Display a file or directory name in CB font.
.\"
.de FN
.  CB \\$@
..
.
.\" .CB  (<path_name>)
.\"
.\" Display a line in CB font, for example after .TP
.\"
.de CB
.nh
\\&\\f(CB\\$1\\fP\\$2
.hy
..
.
.\" End of macro definitions
.
.
.TH GCHEM 1 "7 February 2013" "Groff Version 1.22.2"
.SH NAME
gchem \- groff preprocessor for producing chemical structure diagrams
.
.
.SH "SYNOPSIS"
.\" --------------------------------------------------------------------
.\" SH "SYNOPSIS"
.\" --------------------------------------------------------------------
.
.SY gchem
.RI [ "\%option" \*(El]
.OP \-\-
.RI [ "\%filespec" \*(El]
.
.SY gchem
.B \-h
|
.B \-\-help
.
.SY gchem
.B \-v
|
.B \-\-version
.YS
.
.
.\" --------------------------------------------------------------------
.SH OPTION USAGE
.\" --------------------------------------------------------------------
.
.P
There are no other options than
.BR \-h ,
.BR \-\-help ,
.BR \-v ,
and
.BR \%\-\-version ;
these options provoke the printing of a version or usage information,
respectively, and all
.I filespec
arguments are ignored.
.
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.
.
.
.\" --------------------------------------------------------------------
.SH DESCRIPTION
.\" --------------------------------------------------------------------
.
.I chem
produces chemical structure diagrams.
.
Today's version is best suited for organic chemistry (bonds, rings).
.
The
.B gchem
program is a
.B groff
preprocessor like
.BR geqn ,
.BR gpic ,
.BR gtbl ,
etc.
.
It generates
.I pic
output such that all
.I chem
parts are translated into diagrams of the
.I pic
language.
.
.
.P
The program
.B gchem
originates from the Perl source file
.FN chem.pl .
It tells
.B gpic
to include a copy of the macro file
.FN chem.pic .
.
Moreover the
.I groff
source file
.FN 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 gchem ,
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 gchem
followed by
.BR groffer :
.
.IP
.B "gchem [file\*(El] | groffer"
.
.P
If you want to create just
.B groff
output, you must run
.B gchem
followed by
.B groff
with the option
.B \-p
for the activation of
.BR gpic :
.IP
.B "gchem [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 gchem
is a
.B gpic
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
.FN /usr/share/groff/1.22.2/pic/chem.pic
A collection of
.I pic
macros needed by
.BR gchem .
.
.TP
.FN /usr/share/groff/1.22.2/tmac/pic.tmac
A macro file which redefines
.B .PS
and
.BR .PE
to center
.I pic
diagrams.
.
.TP
.FN /usr/share/doc/groff-1.22.2/examples/chem/*.chem
Example files for
.IR chem .
.
.TP
.FN /usr/share/doc/groff-1.22.2/examples/chem/122/*.chem
Example files from the classical
.I chem
book
.BR 122.ps .
.
.
.\" --------------------------------------------------------------------
.SH "BUGS"
.\" --------------------------------------------------------------------
.
Report bugs to the
.MT bug-groff@\:gnu.org
bug-groff mailing list
.ME .
.
Include a complete, self-contained example that will allow the bug to
be reproduced, and say which version of
.I groff
and
.I chem
you are using.
.
You can get both version numbers by calling
.BR "gchem --version" .
.
.
.P
You can also use the
.MT groff@\:gnu.org
groff mailing list
.ME ,
but you must first subscribe to this list.
.
You can do that by visiting the
.UR http://\:lists.gnu.org/\:mailman/\:listinfo/\:groff
groff mailing list web page
.UE .
.
.
.P
See
.BR \%groff (1)
for information on availability.
.
.
.\" --------------------------------------------------------------------

.\" Oracle has added the ARC stability level to this manual page
.SH ATTRIBUTES
See
.BR attributes (5)
for descriptions of the following attributes:
.sp
.TS
box;
cbp-1 | cbp-1
l | l .
ATTRIBUTE TYPE	ATTRIBUTE VALUE 
=
Availability	text/groff
=
Stability	Uncommitted
.TE 
.PP
.SH "SEE ALSO"
.\" --------------------------------------------------------------------
.
.BR \%groff (1),
.BR \%gpic (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
.FN 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
122.ps
.UE .
.
.
.\" --------------------------------------------------------------------
.SH "AUTHOR"
.\" --------------------------------------------------------------------
.au
.
.
.\" --------------------------------------------------------------------
.SH "COPYING"
.\" --------------------------------------------------------------------
.co
.
.
.\" --------------------------------------------------------------------
.\" Emacs settings
.\" --------------------------------------------------------------------
.
.\" Local Variables:
.\" mode: nroff
.\" End:


.SH NOTES

.\" Oracle has added source availability information to this manual page
This software was built from source available at https://java.net/projects/solaris-userland.  The original community source was downloaded from  http://ftp.gnu.org/gnu/groff/groff-1.22.2.tar.gz

Further information about this software can be found on the open source community website at http://www.gnu.org/software/groff/.