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[Groff-commit] groff/contrib/chem ChangeLog Makefile.sub chem....
|
From: |
Bernd Warken |
|
Subject: |
[Groff-commit] groff/contrib/chem ChangeLog Makefile.sub chem.... |
|
Date: |
Thu, 09 Nov 2006 23:56:49 +0000 |
CVSROOT: /cvsroot/groff
Module name: groff
Changes by: Bernd Warken <bwarken> 06/11/09 23:56:49
Modified files:
contrib/chem : ChangeLog Makefile.sub chem.pl
contrib/chem/examples: README.txt
contrib/chem/examples/122: README
Added files:
contrib/chem : chem.man1 chem.pic
Removed files:
contrib/chem : chem.man macros.pic
Log message:
Update chem-0.3.0
CVSWeb URLs:
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/ChangeLog?cvsroot=groff&r1=1.6&r2=1.7
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/Makefile.sub?cvsroot=groff&r1=1.4&r2=1.5
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/chem.pl?cvsroot=groff&r1=1.4&r2=1.5
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/chem.man1?cvsroot=groff&rev=1.1
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/chem.pic?cvsroot=groff&rev=1.1
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/chem.man?cvsroot=groff&r1=1.4&r2=0
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/macros.pic?cvsroot=groff&r1=1.1&r2=0
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/examples/README.txt?cvsroot=groff&r1=1.2&r2=1.3
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/examples/122/README?cvsroot=groff&r1=1.2&r2=1.3
Patches:
Index: ChangeLog
===================================================================
RCS file: /cvsroot/groff/groff/contrib/chem/ChangeLog,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -b -r1.6 -r1.7
--- ChangeLog 9 Nov 2006 08:10:18 -0000 1.6
+++ ChangeLog 9 Nov 2006 23:56:49 -0000 1.7
@@ -1,3 +1,17 @@
+2006-11-10 Bernd Warken
+ ________________________________________________________________
+ * release of chem 0.3.0
+
+ * chem.man1: Rename `chem.man' to translate some address@hidden@'
+ constructs. Some minor corrections. Remove some unused macros.
+
+ * examples/README.txt, examples/122/README: Add information on
+ `roff2*' programs.
+
+ * chem.pic: Rename `macros.pic'.
+
+ * Makefile.sub, chem.pl: Replace `macros.pic' by `chem.pic'.
+
2006-11-09 Werner LEMBERG <address@hidden>
* chem.man: Revised.
Index: Makefile.sub
===================================================================
RCS file: /cvsroot/groff/groff/contrib/chem/Makefile.sub,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -b -r1.4 -r1.5
--- Makefile.sub 7 Nov 2006 23:53:28 -0000 1.4
+++ Makefile.sub 9 Nov 2006 23:56:49 -0000 1.5
@@ -5,7 +5,7 @@
# Copyright (C) 2006 Free Software Foundation, Inc.
# Written by Bernd Warken.
-# Last update: 8 Nov 2006
+# Last update: 9 Nov 2006
# This file is part of `chem' which is part of `groff'.
@@ -27,12 +27,18 @@
########################################################################
MAN1=chem.n
-CLEANADD=chem chem.n README examples/README
+CLEANADD=chem chem.n chem.man README examples/README
# not all make programs have $(RM) predefined.
RM=rm -f
-all: README examples/README chem $(MAN1)
+all: README examples/README chem chem.man
+
+chem.man: $(srcdir)/chem.man1
+ sed \
+ -e "s|@tmacdir@|$(DESTDIR)$(tmacdir)|g" \
+ -e "s|@picdir@|$(DESTDIR)$(datasubdir)/pic|g" \
+ $< >$@
README: $(srcdir)/README.txt
sed -e "s|@g@|$(g)|g" $< >$@
@@ -54,7 +60,7 @@
install_data: chem \
README examples/README \
- $(srcdir)/macros.pic \
+ $(srcdir)/chem.pic \
$(srcdir)/examples/*.chem $(srcdir)/examples/122/*
-test -d $(DESTDIR)$(bindir) || $(mkinstalldirs) $(DESTDIR)$(bindir)
$(RM) $(DESTDIR)$(bindir)/$(g)chem
@@ -62,7 +68,7 @@
-test -d $(DESTDIR)$(datasubdir)/pic \
|| $(mkinstalldirs) $(DESTDIR)$(datasubdir)/pic
$(RM) $(DESTDIR)$(datasubdir)/pic/chem.pic
- $(INSTALL_DATA) $(srcdir)/macros.pic \
+ $(INSTALL_DATA) $(srcdir)/chem.pic \
$(DESTDIR)$(datasubdir)/pic/chem.pic
-test -d $(DESTDIR)$(exampledir)/chem \
|| $(mkinstalldirs) $(DESTDIR)$(exampledir)/chem/122
Index: chem.pl
===================================================================
RCS file: /cvsroot/groff/groff/contrib/chem/chem.pl,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -b -r1.4 -r1.5
--- chem.pl 7 Nov 2006 23:53:28 -0000 1.4
+++ chem.pl 9 Nov 2006 23:56:49 -0000 1.5
@@ -30,8 +30,8 @@
# settings
########################################################################
-my $Program_Version = '0.2.0';
-my $Last_Update = '8 Nov 2006';
+my $Program_Version = '0.3.0';
+my $Last_Update = '10 Nov 2006';
# this setting of the groff version is only used before make is run,
# otherwise @VERSION@ will set it.
@@ -57,7 +57,7 @@
my $Chem_Name;
my $Groff_Version;
-my $File_macros_pic;
+my $File_chem_pic;
my $File_pic_tmac;
BEGIN {
@@ -74,7 +74,7 @@
my $chem_dir = $FindBin::Bin;
$at_at{'BINDIR'} = $chem_dir;
$at_at{'G'} = '';
- $File_macros_pic = File::Spec->catfile($chem_dir, 'macros.pic');
+ $File_chem_pic = File::Spec->catfile($chem_dir, 'chem.pic');
$File_pic_tmac = File::Spec->catfile($chem_dir, '..', 'pic.tmac');
$Groff_Version = '';
$Chem_Name = 'chem';
@@ -84,7 +84,7 @@
$at_at{'G'} = '@g@';
$at_at{'PICDIR'} = '@picdir@';
$at_at{'TMACDIR'} = '@tmacdir@';
- $File_macros_pic =
+ $File_chem_pic =
File::Spec->catfile($at_at{'PICDIR'}, 'chem.pic');
$File_pic_tmac = File::Spec->catfile($at_at{'TMACDIR'}, 'pic.tmac');
$Chem_Name = $at_at{'G'} . 'chem';
@@ -820,7 +820,7 @@
#
sub init {
if ($First_Time) {
- printf "copy \"%s\"\n", $File_macros_pic;
+ printf "copy \"%s\"\n", $File_chem_pic;
printf "\ttextht = %g; textwid = .1; cwid = %g\n",
$Params{'textht'}, $Params{'cwid'};
printf "\tlineht = %g; linewid = %g\n",
Index: examples/README.txt
===================================================================
RCS file: /cvsroot/groff/groff/contrib/chem/examples/README.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -b -r1.2 -r1.3
--- examples/README.txt 6 Nov 2006 23:17:25 -0000 1.2
+++ examples/README.txt 9 Nov 2006 23:56:49 -0000 1.3
@@ -4,8 +4,20 @@
groffer <file>
-`groffer' calls `chem' automatically. Or get a suitable `groff'
-output by running
+`groffer' calls `chem' automatically.
+
+If you want to transform example files to a different format use the
+`roff2*' programs:
+
+`roff2dvi' prints dvi format to standard output,
+`roff2html' generates html output,
+`roff2pdf' outputs pdf mode,
+`roff2ps' produces PostScript output,
+`roff2text' generates text output in the groff device `latin1',
+`roff2x' prints the output in the groff device X that is
+ suitable for programs like `gxditview' or `xditview'.
+
+To get a suitable `groff' output run
@address@hidden <file> | groff -p ...
@@ -25,7 +37,7 @@
####### License
-Last update: 6 Nov 2006
+Last update: 9 Nov 2006
Copyright (C) 2006 Free Software Foundation, Inc.
Written by Bernd Warken.
Index: examples/122/README
===================================================================
RCS file: /cvsroot/groff/groff/contrib/chem/examples/122/README,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -b -r1.2 -r1.3
--- examples/122/README 6 Nov 2006 23:17:25 -0000 1.2
+++ examples/122/README 9 Nov 2006 23:56:49 -0000 1.3
@@ -26,15 +26,27 @@
groffer <file>
-`groffer' calls `chem' automatically. Or get a suitable `groff'
-output by running
+`groffer' calls `chem' automatically.
+
+If you want to transform example files to a different format use the
+`roff2*' programs:
+
+`roff2dvi' prints dvi format to standard output,
+`roff2html' generates html output,
+`roff2pdf' outputs pdf mode,
+`roff2ps' produces PostScript output,
+`roff2text' generates text output in the groff device `latin1',
+`roff2x' prints the output in the groff device X that is
+ suitable for programs like `gxditview' or `xditview'.
+
+To get a suitable `groff' output run
@address@hidden <file> | groff -p ...
####### License
-Last update: 6 Nov 2006
+Last update: 9 Nov 2006
Copyright (C) 2006 Free Software Foundation, Inc.
Written by Bernd Warken.
Index: chem.man1
===================================================================
RCS file: chem.man1
diff -N chem.man1
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ chem.man1 9 Nov 2006 23:56:49 -0000 1.1
@@ -0,0 +1,1078 @@
+.TH @address@hidden @MAN1EXT@ "@MDATE@" "Groff Version @VERSION@"
+.SH NAME
address@hidden@chem \- groff preprocessor for producing chemical structure
diagrams
+.
+.
+.SH "SYNOPSIS"
+.\" The .SH was moved to this place in order to appease `apropos'.
+.
+.mso www.tmac
+.
+.\" --------------------------------------------------------------------
+.\" Legalize
+.\" --------------------------------------------------------------------
+.
+.ig
address@hidden@chem.1 - man page for @address@hidden (section 1).
+
+Source file position: <groff_source_top>/contrib/chem/chem.man
+Installed position: $prefix/share/man/man1/@address@hidden
+
+Last update: 9 Nov 2006
+..
+.
+.
+.de author
+This file was written by
+.MTO "" "Bernd Warken" .
+It is based on the documentation of
+.URL http://cm.bell-labs.com/cm/cs/who/bwk/index.html "Brian
Kernighan\f[R]'s\f[]"
+original
+.I awk
+version of
+.IR chem .
+..
+.
+.
+.de copyleft
+Copyright (C) 2006 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[CR]GNU General Public
+License\f[] along with
+.IR groff ,
+see the files \%\f[CB]COPYING\f[] and \%\f[CB]LICENSE\f[] 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" .
+.hy
+..
+.
+.
+.\" --------------------------------------------------------------------
+.\" Setup
+.\" --------------------------------------------------------------------
+.
+.if n \{\
+. mso tty-char.tmac
+. ftr CR R
+. ftr CI I
+. ftr CB B
+.\}
+.
+.if '\*[.T]'dvi' \{\
+. ftr CB CW
+.\}
+.
+.ds Ellipsis "\&.\|.\|.\&\""
+.
+.
+.\" --------------------------------------------------------------------
+.\" Macro definitions
+.
+.\" Ignore all arguments like a comment, even after a .eo call.
+.de c
+..
+.
+.c --------------------------------------------------------------------
+.c .TP+ ()
+.c
+.c Continuation line for .TP header.
+.c
+.de TP+
+. br
+. ns
+. TP \\$1
+..
+.
+.c --------------------------------------------------------------------
+.c .File_name (<path_name>)
+.c
+.c Display a file or directory name in CB font.
+.c
+.de File_name
+. Header_CB \\$@
+..
+.
+.c --------------------------------------------------------------------
+.c .Header_CB (<path_name>)
+.c
+.c Display a line in CB font, for example after .TP
+.c
+.de Header_CB
+. nh
+. Text \f[CB]\\$1\f[]\\$2
+. hy
+..
+.
+.c --------------------------------------------------------------------
+.c Static register for inter-macro communication in `.Synopsis'.
+.c
+.nr chem:Synopsis.level 0
+.
+.c --------------------------------------------------------------------
+.c .Synopsis ()
+.c
+.c Begin a synopsis section, to be ended by a ./Synopsis macro.
+.c
+.de Synopsis
+. if (\\n[chem:Synopsis.level] > 0) \
+. Error .\\$0: previous .Synopsis was not closed by ./Synopsis.
+. nh
+. ds @1 \\$1\"
+. nr @old_indent \\n[.i]
+. ad l
+. in +\w'address@hidden'u
+. ti address@hidden
+. B address@hidden
+. rr @old_indent
+. rm @1
+. nr chem:Synopsis.level +1\" marker for ./Synopsis
+..
+.
+.c --------------------------------------------------------------------
+.c ./Synopsis ()
+.c
+.c Close a synopsis section opened by the previous .Synopsis macro.
+.c
+.de /Synopsis
+. if (\\n[chem:Synopsis.level] <= 0) \
+. Error .\\$0: no previous call of .Synopsis
+. br
+. ad
+. in
+. hy
+. nr chem:Synopsis.level -1
+..
+.
+.c --------------------------------------------------------------------
+.c .Text (<text>...)
+.c
+.c Treat the arguments as text, no matter how they look like.
+.c
+.de Text
+. if (\\n[.$] == 0) \
+. return
+. nh
+. nop \)\\$*\)
+. hy
+..
+.
+.\" End of macro definitions
+.
+.
+.\" --------------------------------------------------------------------
+.\" SH "SYNOPSIS"
+.\" --------------------------------------------------------------------
+.
+.ad l
+.Synopsis @address@hidden
+.RI [ "\%option" \*[Ellipsis]]
+.RB [ \-\- ]
+.RI [ "\%filespec" \*[Ellipsis]]
+./Synopsis
+.
+.Synopsis @address@hidden
+\f[CB]\-h\fP\f[CR]|\fP\f[CB]\-\-help\fP
+./Synopsis
+.
+.Synopsis @address@hidden
+\f[CB]\-v\fP\f[CR]|\fP\f[CB]\-\-version\fP
+./Synopsis
+.
+.
+.P
+There are no other options than \f[CB]\-h\f[], \f[CB]\-\-help\f[],
+\f[CB]\-v\f[] and \%\f[CB]\-\-version\f[]; 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 @address@hidden
+program is a
+.B groff
+preprocessor like
+.BR @address@hidden ,
+.BR @address@hidden ,
+.BR @address@hidden ,
+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 @address@hidden
+originates from the Perl source file
+.File_name chem.pl .
+It tells
+.B @address@hidden
+to include a copy of the macro file
+.File_name chem.pic .
+.
+Moreover the
+.I groff
+source file
+.File_name 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
+\f[I]chem data\f[]
+\&.cend
+.ft
+.fi
+.
+.
+.P
+Lines containing the keywords
+.B .cstart
+and
+.B .cend
+start and end the input for
+.BR @address@hidden ,
+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 @address@hidden
+followed by
+.BR groffer :
+.
+.IP
+.B @address@hidden [file\*[Ellipsis]] | groffer
+.
+.P
+If you want to create just
+.B groff
+output, you must run
+.B @address@hidden
+followed by
+.B groff
+with the option
+.B \-p
+for the activation of
+.BR @address@hidden :
+.IP
+.B @address@hidden [file\*[Ellipsis]] | groff -p \*[Ellipsis]
+.
+.
+.\" --------------------------------------------------------------------
+.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 ,
+\*[Ellipsis]) and strings.
+.
+.
+.\" --------------------------------------------------------------------
+.SS Setting Variables
+.\" --------------------------------------------------------------------
+.
+There are some variables that can be set by commands.
+.
+Such commands have two possible forms, either
+.br
+.RS
+.I "variable value"
+.RE
+.br
+or
+.br
+.RS
+.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
+.\" --------------------------------------------------------------------
+.
+.IP
+.B bond
+.RI [ direction ]
+.RI [ length\~n ]
+.RB [ from
+.IR Name | picstuff ]
+.
+.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
+.TP 10m
+.B CH3
+.TP+
+.B bond
+(this one goes right from the CH3)
+.TP+
+.B C
+(at the right end of the bond)
+.TP+
+.B double bond up
+(from the C)
+.TP+
+.B O
+(at the end of the double bond)
+.TP+
+.B bond right from C
+.TP+
+.B CH3
+.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.
+.
+.IP
+.B ring
+.RB [ \%pointing\ ( up | right | left | down )]
+.RB [ \%aromatic ]
+.RB [ put\ Mol\ at\ \f[I]n\f[] ]
+.RB [ \%double
+.IR i , j
+.IR k , l
+\*[Ellipsis]]
+.RI [ picstuff ]
+.
+.
+.P
+The vertices of a ring are numbered 1, 2, \*[Ellipsis] 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 ,
+\*[Ellipsis],
+.BI .V n\f[R],\f[]
+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\ \f[R]\*[Ellipsis];\f[]
+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\f[R],\f[]
+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
+.BP 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]\*[Ellipsis]\[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 :
+\*[Ellipsis]
+.
+.
+.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
+.TP+
+\&
+.B bond 30 from First
+.RE
+.
+.
+.\" --------------------------------------------------------------------
+.SS Miscellaneous
+.\" --------------------------------------------------------------------
+.
+The specific construction
+.RS
+.TP
+.BR bond\ \*[Ellipsis] " ; 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 @address@hidden
+is a
+.B @address@hidden
+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 $...$
+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
+.File_name @picdir@/chem.pic
+A collection of
+.I pic
+macros needed by
+.BR @address@hidden .
+.
+.TP
+.File_name @tmacdir@/pic.tmac
+A macro file which redefines
+.B .PS
+and
+.BR .PE
+to center
+.I pic
+diagrams.
+.
+.
+.\" --------------------------------------------------------------------
+.SH "BUGS"
+.\" --------------------------------------------------------------------
+.
+Report bugs to the
+.MTO address@hidden "bug-groff mailing list" .
+.
+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 "@address@hidden --version" .
+.
+.
+.P
+You can also use the
+.MTO address@hidden "groff mailing list" ,
+but you must first subscribe to this list.
+.
+You can do that by visiting the
+.URL http://\:lists.gnu.org/\:mailman/\:listinfo/\:groff \
+"groff mailing list web page" .
+.
+.
+.P
+See
+.BR \%groff (@MAN1EXT@)
+for information on availability.
+.
+.
+.\" --------------------------------------------------------------------
+.SH "SEE ALSO"
+.\" --------------------------------------------------------------------
+.
+.BR \%groff (@MAN1EXT@),
+.BR address@hidden@pic (@MAN1EXT@),
+.B \%groffer (@MAN1EXT@).
+.
+.
+.P
+You can still get the original
+.URL http://cm.bell-labs.com/netlib/typesetting/chem.gz \
+"chem awk source" .
+.
+Its
+.File_name README
+file was used for this manual page.
+.
+.
+.P
+The other classical document on
+.I chem
+is
+.URL http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz 122.ps .
+.
+.
+.\" --------------------------------------------------------------------
+.SH "AUTHOR"
+.\" --------------------------------------------------------------------
+.author
+.
+.
+.\" --------------------------------------------------------------------
+.SH "COPYING"
+.\" --------------------------------------------------------------------
+.copyleft
+.
+.
+.\" --------------------------------------------------------------------
+.\" Emacs settings
+.\" --------------------------------------------------------------------
+.
+.\" Local Variables:
+.\" mode: nroff
+.\" End:
Index: chem.pic
===================================================================
RCS file: chem.pic
diff -N chem.pic
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ chem.pic 9 Nov 2006 23:56:49 -0000 1.1
@@ -0,0 +1,97 @@
+# macros for chem
+
+# Source file position: <groff-source>/contrib/chem/chem.pic
+# Installed position: <prefix>/lib/groff/chem
+
+# Copyright (C) 2006 Free Software Foundation, Inc.
+# Written by Brian Kernighan <http://cm.bell-labs.com/cm/cs/who/bwk>,
+# modified by Bernd Warken.
+
+# This file is part of `chem', which is part of `groff'.
+
+# `groff' is free software; 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.
+
+# `groff' is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+
+# 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. If not, write to the Free Software
+# Foundation, 51 Franklin St - Fifth Floor, Boston, MA 02110-1301,
+# USA.
+
+########################################################################
+
+pi = 3.141592654
+deg = 57.29578
+# cr = 0.08 # radius of invis circle at ring vertices (see cr[vh])
+# crh = 0.16; crw = 0.12 # ht & wid of invis ellipse around atoms at ring
vertices
+# dav = 0.015 # vertical shift up for atoms in atom macro
+
+# atom(text, wid, ht, carbon position, crh, crw, dav)
+define atom { [
+ T: $1 wid $2 ht $3-2*$7
+ C: ellipse invis ht $5 wid $6 at T.w + ($4,$7)
+ L: ellipse invis ht $5 wid $6 at T.w + (cwid/2,$7)
+ R: ellipse invis ht $5 wid $6 at T.e + (-cwid/2,$7)
+] }
+
+# bond(length, angle in degrees, whatever)
+define bond {
+ line $3 by ($1) * sin(($2)/deg), ($1) * cos(($2)/deg)
+}
+
+# fancy bonds: r, theta, from/at
+define doublebond {
+ line $3 invis by ($1) * sin(($2)/deg), ($1) * cos(($2)/deg)
+ V1: last line.start; V2: last line.end; dx = V2.x-V1.x; dy = V2.y-V1.y
+ norm = sqrt(dx*dx + dy*dy)
+ ny = dx * .02 / norm
+ nx = -dy * .02 / norm
+ line from V1 + (nx,ny) to V2 + (nx,ny)
+ line from V1 - (nx,ny) to V2 - (nx,ny)
+ move to V2
+}
+define triplebond {
+ line $3 invis by ($1) * sin(($2)/deg), ($1) * cos(($2)/deg)
+ V1: last line.start; V2: last line.end; dx = V2.x-V1.x; dy = V2.y-V1.y
+ norm = sqrt(dx*dx + dy*dy)
+ ny = dx * .025 / norm
+ nx = -dy * .025 / norm
+ line from V1 + (nx,ny) to V2 + (nx,ny)
+ line from V1 - (nx,ny) to V2 - (nx,ny)
+ line from V1 to V2
+ move to V2
+}
+define backbond {
+ line $3 invis by ($1) * sin(($2)/deg), ($1) * cos(($2)/deg)
+ V1: last line.start; V2: last line.end; dx = V2.x-V1.x; dy = V2.y-V1.y
+ norm = sqrt(dx*dx + dy*dy)
+ n = norm / .025
+ ny = dx * .02 / norm
+ nx = -dy * .02 / norm
+ for i = 1 to n-1 do {
+ XZ: i/n <V1,V2>
+ line from XZ + (nx,ny) to XZ - (nx,ny)
+ }
+ move to V2
+}
+define frontbond {
+ line $3 invis by ($1) * sin(($2)/deg), ($1) * cos(($2)/deg)
+ V1: last line.start; V2: last line.end; dx = V2.x-V1.x; dy = V2.y-V1.y
+ ah = arrowht; aw = arrowwid; ahead = arrowhead
+ arrowht = sqrt(dx*dx + dy*dy)
+ arrowwid = 0.05
+ arrowhead = 7
+ line <- from V1 to V2
+ arrowht = ah; arrowwid = aw; arrowhead = ahead
+}
+### Emacs settings
+# Local Variables:
+# mode: Nroff
+# End:
Index: chem.man
===================================================================
RCS file: chem.man
diff -N chem.man
--- chem.man 9 Nov 2006 08:10:18 -0000 1.4
+++ /dev/null 1 Jan 1970 00:00:00 -0000
@@ -1,1111 +0,0 @@
-.TH @address@hidden @MAN1EXT@ "@MDATE@" "Groff Version @VERSION@"
-.SH NAME
address@hidden@chem \- groff preprocessor for producing chemical structure
diagrams
-.
-.
-.SH "SYNOPSIS"
-.\" The .SH was moved to this place in order to appease `apropos'.
-.
-.mso www.tmac
-.
-.\" --------------------------------------------------------------------
-.\" Legalize
-.\" --------------------------------------------------------------------
-.
-.ig
address@hidden@chem.1 - man page for @address@hidden (section 1).
-
-Source file position: <groff_source_top>/contrib/chem/chem.man
-Installed position: $prefix/share/man/man1/@address@hidden
-
-Last update: 9 Nov 2006
-..
-.
-.
-.de author
-This file was written by
-.MTO "" "Bernd Warken" .
-It is based on the documentation of
-.URL http://cm.bell-labs.com/cm/cs/who/bwk/index.html "Brian
Kernighan\f[R]'s\f[]"
-original
-.I awk
-version of
-.IR chem .
-..
-.
-.
-.de copyleft
-Copyright (C) 2006 Free Software Foundation, Inc.
-.
-.
-.P
-This file is part of
-.IR chem ,
-which is part of
-.IR groff ,
-a free software project.
-.
-You can redistribute it and/or modify it under the terms of the
-.nh
-.B GNU General Public License
-.hy
-as published by the
-.nh
-.BR "Free Software Foundation" ,
-.hy
-either version\~2, or (at your option) any later version.
-.
-.
-.P
-You should have received a copy of the \f[CR]GNU General Public
-License\f[] along with
-.IR groff ,
-see the files \%\f[CB]COPYING\f[] and \%\f[CB]LICENSE\f[] in the top
-directory of the
-.I groff
-source package.
-.
-Or read the
-.I man page
-.BR gpl (1).
-You can also write to the
-.nh
-.B Free Software Foundation, 51 Franklin St - Fifth Floor, Boston,
-.BR "MA 02110-1301, USA" .
-.hy
-..
-.
-.
-.\" --------------------------------------------------------------------
-.\" Setup
-.\" --------------------------------------------------------------------
-.
-.if n \{\
-. mso tty-char.tmac
-. ftr CR R
-. ftr CI I
-. ftr CB B
-.\}
-.
-.if '\*[.T]'dvi' \{\
-. ftr CB CW
-.\}
-.
-.ds Ellipsis "\&.\|.\|.\&\""
-.
-.
-.\" --------------------------------------------------------------------
-.\" Macro definitions
-.
-.\" Ignore all arguments like a comment, even after a .eo call.
-.de c
-..
-.
-.c --------------------------------------------------------------------
-.c .CB (<text>...)
-.c
-.c Print in constant-width bold font.
-.c
-.de CB
-. ft CB
-. Text \\$*
-. ft
-..
-.
-.c --------------------------------------------------------------------
-.c .CI (<text>...)
-.c
-.c Print in constant-width italic font.
-.c
-.de CI
-. ft CI
-. Text \\$*
-. ft
-..
-.
-.c --------------------------------------------------------------------
-.c .CR (<text>...)
-.c
-.c Print in constant-width roman font.
-.c
-.de CR
-. ft CR
-. Text \\$*
-. ft
-..
-.
-.c --------------------------------------------------------------------
-.c .TP+ ()
-.c
-.c Continuation line for .TP header.
-.c
-.de TP+
-. br
-. ns
-. TP \\$1
-..
-.
-.c --------------------------------------------------------------------
-.c .File_name (<path_name>)
-.c
-.c Display a file or directory name in CB font.
-.c
-.de File_name
-. Header_CB \\$@
-..
-.
-.c --------------------------------------------------------------------
-.c .Header_CB (<path_name>)
-.c
-.c Display a line in CB font, for example after .TP
-.c
-.de Header_CB
-. nh
-. Text \f[CB]\\$1\f[]\\$2
-. hy
-..
-.
-.c --------------------------------------------------------------------
-.c Static register for inter-macro communication in `.Synopsis'.
-.c
-.nr chem:Synopsis.level 0
-.
-.c --------------------------------------------------------------------
-.c .Synopsis ()
-.c
-.c Begin a synopsis section, to be ended by a ./Synopsis macro.
-.c
-.de Synopsis
-. if (\\n[chem:Synopsis.level] > 0) \
-. Error .\\$0: previous .Synopsis was not closed by ./Synopsis.
-. nh
-. ds @1 \\$1\"
-. nr @old_indent \\n[.i]
-. ad l
-. in +\w'address@hidden'u
-. ti address@hidden
-. B address@hidden
-. rr @old_indent
-. rm @1
-. nr chem:Synopsis.level +1\" marker for ./Synopsis
-..
-.
-.c --------------------------------------------------------------------
-.c ./Synopsis ()
-.c
-.c Close a synopsis section opened by the previous .Synopsis macro.
-.c
-.de /Synopsis
-. if (\\n[chem:Synopsis.level] <= 0) \
-. Error .\\$0: no previous call of .Synopsis
-. br
-. ad
-. in
-. hy
-. nr chem:Synopsis.level -1
-..
-.
-.c --------------------------------------------------------------------
-.c .Text (<text>...)
-.c
-.c Treat the arguments as text, no matter how they look like.
-.c
-.de Text
-. if (\\n[.$] == 0) \
-. return
-. nh
-. nop \)\\$*\)
-. hy
-..
-.
-.\" End of macro definitions
-.
-.
-.\" --------------------------------------------------------------------
-.\" SH "SYNOPSIS"
-.\" --------------------------------------------------------------------
-.
-.ad l
-.Synopsis @address@hidden
-.RI [ "\%option" \*[Ellipsis]]
-.RB [ \-\- ]
-.RI [ "\%filespec" \*[Ellipsis]]
-./Synopsis
-.
-.Synopsis @address@hidden
-\f[CB]\-h\fP\f[CR]|\fP\f[CB]\-\-help\fP
-./Synopsis
-.
-.Synopsis @address@hidden
-\f[CB]\-v\fP\f[CR]|\fP\f[CB]\-\-version\fP
-./Synopsis
-.
-.
-.P
-There are no other options than \f[CB]\-\-help\f[] and
-\%\f[CB]\-\-version\f[]; 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 @address@hidden
-program is a
-.B groff
-preprocessor like
-.BR @address@hidden ,
-.BR @address@hidden ,
-.BR @address@hidden ,
-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 @address@hidden
-originates from the Perl source file
-.File_name chem.pl .
-It tells
-.B @address@hidden
-to include a copy of
-.File_name macros.pic .
-.
-Moreover the
-.I groff
-source file
-.File_name 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
-\f[I]chem data\f[]
-\&.cend
-.ft
-.fi
-.
-.
-.P
-Lines containing the keywords
-.B .cstart
-and
-.B .cend
-start and end the input for
-.BR @address@hidden ,
-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 @address@hidden
-followed by
-.BR groffer :
-.
-.IP
-.B @address@hidden [file\*[Ellipsis]] | groffer
-.
-.P
-If you want to create just
-.B groff
-output, you must run
-.B @address@hidden
-followed by
-.B groff
-with the option
-.B \-p
-for the activation of
-.BR @address@hidden :
-.IP
-.B @address@hidden [file\*[Ellipsis]] | groff -p \*[Ellipsis]
-.
-.
-.\" --------------------------------------------------------------------
-.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 ,
-\*[Ellipsis]) and strings.
-.
-.
-.\" --------------------------------------------------------------------
-.SS Setting Variables
-.\" --------------------------------------------------------------------
-.
-There are some variables that can be set by commands.
-.
-Such commands have two possible forms, either
-.br
-.RS
-.I "variable value"
-.RE
-.br
-or
-.br
-.RS
-.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
-.\" --------------------------------------------------------------------
-.
-.IP
-.B bond
-.RI [ direction ]
-.RI [ length\~n ]
-.RB [ from
-.IR Name | picstuff ]
-.
-.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
-.TP 10m
-.B CH3
-.TP+
-.B bond
-(this one goes right from the CH3)
-.TP+
-.B C
-(at the right end of the bond)
-.TP+
-.B double bond up
-(from the C)
-.TP+
-.B O
-(at the end of the double bond)
-.TP+
-.B bond right from C
-.TP+
-.B CH3
-.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.
-.
-.IP
-.B ring
-.RB [ \%pointing\ ( up | right | left | down )]
-.RB [ \%aromatic ]
-.RB [ put\ Mol\ at\ \f[I]n\f[] ]
-.RB [ \%double
-.IR i , j
-.IR k , l
-\*[Ellipsis]]
-.RI [ picstuff ]
-.
-.
-.P
-The vertices of a ring are numbered 1, 2, \*[Ellipsis] 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 ,
-\*[Ellipsis],
-.BI .V n\f[R],\f[]
-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\ \f[R]\*[Ellipsis];\f[]
-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\f[R],\f[]
-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
-.BP 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]\*[Ellipsis]\[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 :
-\*[Ellipsis]
-.
-.
-.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
-.TP+
-\&
-.B bond 30 from First
-.RE
-.
-.
-.\" --------------------------------------------------------------------
-.SS Miscellaneous
-.\" --------------------------------------------------------------------
-.
-The specific construction
-.RS
-.TP
-.BR bond\ \*[Ellipsis] "; 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 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 @address@hidden
-is a
-.B @address@hidden
-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 $...$
-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
-.File_name @libdir@/groff/chem/macros.pic
-A collection of
-.B @address@hidden
-macros needed by
-.BR @address@hidden .
-.
-.TP
-.File_name @tmacdir@/pic.tmac
-A macro file which redefines
-.B .PS
-and
-.BR .PE
-to center
-.I pic
-diagrams.
-.
-.
-.\" --------------------------------------------------------------------
-.SH "BUGS"
-.\" --------------------------------------------------------------------
-.
-Report bugs to the
-.MTO address@hidden "bug-groff mailing list" .
-.
-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 "@address@hidden --version" .
-.
-.
-.P
-You can also use the
-.MTO address@hidden "groff mailing list" ,
-but you must first subscribe to this list.
-.
-You can do that by visiting the
-.URL http://\:lists.gnu.org/\:mailman/\:listinfo/\:groff \
-"groff mailing list web page" .
-.
-.
-.P
-See
-.BR \%groff (@MAN1EXT@)
-for information on availability.
-.
-.
-.\" --------------------------------------------------------------------
-.SH "SEE ALSO"
-.\" --------------------------------------------------------------------
-.
-.BR \%groff (@MAN1EXT@),
-.BR address@hidden@pic (@MAN1EXT@),
-.B \%groffer (@MAN1EXT@)
-.
-.
-.P
-You can still get the original
-.URL http://cm.bell-labs.com/netlib/typesetting/chem.gz \
-"chem awk source" .
-.
-Its
-.File_name README
-file was used for this manual page.
-.
-.
-.P
-The other classical document on
-.I chem
-is
-.URL http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz 122.ps .
-.
-.
-.\" --------------------------------------------------------------------
-.SH "AUTHOR"
-.\" --------------------------------------------------------------------
-.author
-.
-.
-.\" --------------------------------------------------------------------
-.SH "COPYING"
-.\" --------------------------------------------------------------------
-.copyleft
-.
-.
-.\" --------------------------------------------------------------------
-.\" Emacs settings
-.\" --------------------------------------------------------------------
-.
-.\" Local Variables:
-.\" mode: nroff
-.\" End:
Index: macros.pic
===================================================================
RCS file: macros.pic
diff -N macros.pic
--- macros.pic 26 Oct 2006 22:13:49 -0000 1.1
+++ /dev/null 1 Jan 1970 00:00:00 -0000
@@ -1,97 +0,0 @@
-# macros for chem
-
-# Source file position: <groff-source>/contrib/chem/macros.pic
-# Installed position: <prefix>/lib/groff/chem
-
-# Copyright (C) 2006 Free Software Foundation, Inc.
-# Written by Brian Kernighan <http://cm.bell-labs.com/cm/cs/who/bwk>,
-# modified by Bernd Warken.
-
-# This file is part of `chem', which is part of `groff'.
-
-# `groff' is free software; 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.
-
-# `groff' is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# General Public License for more details.
-
-# 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. If not, write to the Free Software
-# Foundation, 51 Franklin St - Fifth Floor, Boston, MA 02110-1301,
-# USA.
-
-########################################################################
-
-pi = 3.141592654
-deg = 57.29578
-# cr = 0.08 # radius of invis circle at ring vertices (see cr[vh])
-# crh = 0.16; crw = 0.12 # ht & wid of invis ellipse around atoms at ring
vertices
-# dav = 0.015 # vertical shift up for atoms in atom macro
-
-# atom(text, wid, ht, carbon position, crh, crw, dav)
-define atom { [
- T: $1 wid $2 ht $3-2*$7
- C: ellipse invis ht $5 wid $6 at T.w + ($4,$7)
- L: ellipse invis ht $5 wid $6 at T.w + (cwid/2,$7)
- R: ellipse invis ht $5 wid $6 at T.e + (-cwid/2,$7)
-] }
-
-# bond(length, angle in degrees, whatever)
-define bond {
- line $3 by ($1) * sin(($2)/deg), ($1) * cos(($2)/deg)
-}
-
-# fancy bonds: r, theta, from/at
-define doublebond {
- line $3 invis by ($1) * sin(($2)/deg), ($1) * cos(($2)/deg)
- V1: last line.start; V2: last line.end; dx = V2.x-V1.x; dy = V2.y-V1.y
- norm = sqrt(dx*dx + dy*dy)
- ny = dx * .02 / norm
- nx = -dy * .02 / norm
- line from V1 + (nx,ny) to V2 + (nx,ny)
- line from V1 - (nx,ny) to V2 - (nx,ny)
- move to V2
-}
-define triplebond {
- line $3 invis by ($1) * sin(($2)/deg), ($1) * cos(($2)/deg)
- V1: last line.start; V2: last line.end; dx = V2.x-V1.x; dy = V2.y-V1.y
- norm = sqrt(dx*dx + dy*dy)
- ny = dx * .025 / norm
- nx = -dy * .025 / norm
- line from V1 + (nx,ny) to V2 + (nx,ny)
- line from V1 - (nx,ny) to V2 - (nx,ny)
- line from V1 to V2
- move to V2
-}
-define backbond {
- line $3 invis by ($1) * sin(($2)/deg), ($1) * cos(($2)/deg)
- V1: last line.start; V2: last line.end; dx = V2.x-V1.x; dy = V2.y-V1.y
- norm = sqrt(dx*dx + dy*dy)
- n = norm / .025
- ny = dx * .02 / norm
- nx = -dy * .02 / norm
- for i = 1 to n-1 do {
- XZ: i/n <V1,V2>
- line from XZ + (nx,ny) to XZ - (nx,ny)
- }
- move to V2
-}
-define frontbond {
- line $3 invis by ($1) * sin(($2)/deg), ($1) * cos(($2)/deg)
- V1: last line.start; V2: last line.end; dx = V2.x-V1.x; dy = V2.y-V1.y
- ah = arrowht; aw = arrowwid; ahead = arrowhead
- arrowht = sqrt(dx*dx + dy*dy)
- arrowwid = 0.05
- arrowhead = 7
- line <- from V1 to V2
- arrowht = ah; arrowwid = aw; arrowhead = ahead
-}
-### Emacs settings
-# Local Variables:
-# mode: Nroff
-# End: