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[Groff-commit] groff/contrib/chem ChangeLog Makefile.sub chem....
|
From: |
Werner LEMBERG |
|
Subject: |
[Groff-commit] groff/contrib/chem ChangeLog Makefile.sub chem.... |
|
Date: |
Fri, 10 Nov 2006 10:04:43 +0000 |
CVSROOT: /cvsroot/groff
Module name: groff
Changes by: Werner LEMBERG <wl> 06/11/10 10:04:43
Modified files:
contrib/chem : ChangeLog Makefile.sub chem.pl
Added files:
contrib/chem : chem.man
Removed files:
contrib/chem : chem.man1
Log message:
* chem.man1: Rename back to...
* chem.man: This.
Use @G@, @MACRODIR@, and @address@hidden
* Makefile.sub (CLEANADD, all): Don't handle chem.man.
(chem.man): Remove rule.
(chem): s/tmacdir/MACRODIR/, s/picdir/PICDIR/.
* chem.pl: s/tmacdir/MACRODIR/, s/picdir/PICDIR/.
CVSWeb URLs:
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/ChangeLog?cvsroot=groff&r1=1.7&r2=1.8
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/Makefile.sub?cvsroot=groff&r1=1.5&r2=1.6
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/chem.pl?cvsroot=groff&r1=1.5&r2=1.6
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/chem.man?cvsroot=groff&rev=1.6
http://cvs.savannah.gnu.org/viewcvs/groff/contrib/chem/chem.man1?cvsroot=groff&r1=1.1&r2=0
Patches:
Index: ChangeLog
===================================================================
RCS file: /cvsroot/groff/groff/contrib/chem/ChangeLog,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -b -r1.7 -r1.8
--- ChangeLog 9 Nov 2006 23:56:49 -0000 1.7
+++ ChangeLog 10 Nov 2006 10:04:43 -0000 1.8
@@ -1,3 +1,15 @@
+2006-11-10 Werner LEMBERG <address@hidden>
+
+ * chem.man1: Rename back to...
+ * chem.man: This.
+ Use @G@, @MACRODIR@, and @address@hidden
+
+ * Makefile.sub (CLEANADD, all): Don't handle chem.man.
+ (chem.man): Remove rule.
+ (chem): s/tmacdir/MACRODIR/, s/picdir/PICDIR/.
+
+ * chem.pl: s/tmacdir/MACRODIR/, s/picdir/PICDIR/.
+
2006-11-10 Bernd Warken
________________________________________________________________
* release of chem 0.3.0
Index: Makefile.sub
===================================================================
RCS file: /cvsroot/groff/groff/contrib/chem/Makefile.sub,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -b -r1.5 -r1.6
--- Makefile.sub 9 Nov 2006 23:56:49 -0000 1.5
+++ Makefile.sub 10 Nov 2006 10:04:43 -0000 1.6
@@ -27,18 +27,12 @@
########################################################################
MAN1=chem.n
-CLEANADD=chem chem.n chem.man README examples/README
+CLEANADD=chem chem.n README examples/README
# not all make programs have $(RM) predefined.
RM=rm -f
-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" \
- $< >$@
+all: README examples/README chem $(MAN1)
README: $(srcdir)/README.txt
sed -e "s|@g@|$(g)|g" $< >$@
@@ -51,8 +45,8 @@
sed -f "$(SH_DEPS_SED_SCRIPT)" \
-e "s|@g@|$(g)|g" \
-e "s|@BINDIR@|$(DESTDIR)$(bindir)|g" \
- -e "s|@tmacdir@|$(DESTDIR)$(tmacdir)|g" \
- -e "s|@picdir@|$(DESTDIR)$(datasubdir)/pic|g" \
+ -e "s|@MACRODIR@|$(DESTDIR)$(tmacdir)|g" \
+ -e "s|@PICDIR@|$(DESTDIR)$(datasubdir)/pic|g" \
-e "s|@VERSION@|$(version)$(revision)|g" \
-e "$(SH_SCRIPT_SED_CMD)" \
$(srcdir)/chem.pl >$@
Index: chem.pl
===================================================================
RCS file: /cvsroot/groff/groff/contrib/chem/chem.pl,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -b -r1.5 -r1.6
--- chem.pl 9 Nov 2006 23:56:49 -0000 1.5
+++ chem.pl 10 Nov 2006 10:04:43 -0000 1.6
@@ -82,8 +82,8 @@
$Groff_Version = '@VERSION@';
$at_at{'BINDIR'} = '@BINDIR@';
$at_at{'G'} = '@g@';
- $at_at{'PICDIR'} = '@picdir@';
- $at_at{'TMACDIR'} = '@tmacdir@';
+ $at_at{'PICDIR'} = '@PICDIR@';
+ $at_at{'TMACDIR'} = '@MACRODIR@';
$File_chem_pic =
File::Spec->catfile($at_at{'PICDIR'}, 'chem.pic');
$File_pic_tmac = File::Spec->catfile($at_at{'TMACDIR'}, 'pic.tmac');
Index: chem.man
===================================================================
RCS file: chem.man
diff -N chem.man
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ chem.man 10 Nov 2006 10:04:43 -0000 1.6
@@ -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 @DATASUBDIR@/pic/chem.pic
+A collection of
+.I pic
+macros needed by
+.BR @address@hidden .
+.
+.TP
+.File_name @MACRODIR@/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.man1
===================================================================
RCS file: chem.man1
diff -N chem.man1
--- chem.man1 9 Nov 2006 23:56:49 -0000 1.1
+++ /dev/null 1 Jan 1970 00:00:00 -0000
@@ -1,1078 +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 --------------------------------------------------------------------
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-.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>)
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-.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.
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-. 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.
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-.de Text
-. if (\\n[.$] == 0) \
-. return
-. nh
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-..
-.
-.\" End of macro definitions
-.
-.
-.\" --------------------------------------------------------------------
-.\" SH "SYNOPSIS"
-.\" --------------------------------------------------------------------
-.
-.ad l
-.Synopsis @address@hidden
-.RI [ "\%option" \*[Ellipsis]]
-.RB [ \-\- ]
-.RI [ "\%filespec" \*[Ellipsis]]
-./Synopsis
-.
-.Synopsis @address@hidden
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-./Synopsis
-.
-.Synopsis @address@hidden
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-./Synopsis
-.
-.
-.P
-There are no other options than \f[CB]\-h\f[], \f[CB]\-\-help\f[],
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-A
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-.
-If no argument is specified then standard input is taken
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-.
-.
-.\" --------------------------------------------------------------------
-.SH DESCRIPTION
-.\" --------------------------------------------------------------------
-.
-.I chem
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-.
-Today's version is best suited for organic chemistry (bonds, rings).
-.
-The
-.B @address@hidden
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-.B groff
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-.BR @address@hidden ,
-.BR @address@hidden ,
-.BR @address@hidden ,
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-It generates
-.I pic
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-.I pic
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-.
-.
-.P
-The program
-.B @address@hidden
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-It tells
-.B @address@hidden
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-.
-Moreover the
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-.
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-In a style reminiscent of
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-.
-.
-.P
-A set of
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-.
-.IP
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-.ft B
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-.ft
-.fi
-.
-.
-.P
-Lines containing the keywords
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-.BR @address@hidden ,
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-In
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-.
-.
-.P
-Anything outside these initialization lines is copied through
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-.
-.P
-As an example,
-.
-.IP
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-.ft B
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-.ft
-.fi
-.
-.
-.P
-prints two
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-.
-.
-.P
-To actually view this, you must run
-.B @address@hidden
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-.BR groffer :
-.
-.IP
-.B @address@hidden [file\*[Ellipsis]] | groffer
-.
-.P
-If you want to create just
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-.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
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-.br
-.RS
-.IB "variable " = " value"
-.RE
-.
-.
-.P
-This sets the given
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-.
-.
-.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
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-.B bond
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-.BR "double bond" ,
-.BR "front bond" ,
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-(We will get back to
-.I Name
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-.
-.
-.P
-.I direction
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-or a direction word like
-.BR up ,
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-.
-If no direction is specified, the bond goes in the current direction
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-.
-.
-.P
-Normally the bond begins at the last object placed; this
-can be changed by naming a
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-place.
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-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
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-.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 ,
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-.B .V1
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-So the corners of
-.B R1
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-.B R1.V1
-(the
-.IR top ),
-.BR R1.V2 ,
-.BR R1.V3 ,
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-(the
-.IR bottom ),
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-.B R2.V1
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-.B R2.V4
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-These vertex names are used for connecting bonds or other rings. For
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-.
-.IP
-.ft B
-.nf
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-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.
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-Normally a moiety is placed right after the last thing mentioned,
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-.
-.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
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-.IP
-.B CH3 at C + (0.5,0.5)
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-.P
-Here the moiety is
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-It is placed at a position relative to
-.BR C ,
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-.
-.
-.P
-So moiety names can be specified as
-.I chem
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-.
-Beneath their printing moieties are names for places.
-.
-.
-.P
-The moiety
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-.
-It is not printed but just serves as a mark to be referred to in later
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-.
-For example,
-.
-.IP
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-.
-.P
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-This can be used then for specifying a place.
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-The name
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-.I branch point
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-.
-.
-.P
-A string within double quotes
-.B \[dq]
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-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
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-.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
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-.RE
-.P
-is equivalent to
-.IP
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-.nf
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-.fi
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-.
-.
-.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
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-.
-.
-.P
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-.
-However, hash characters within a word are kept.
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-.
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-A line whose first word is
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-.B pic
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-.
-.
-.P
-The command
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-.B size
-.I n
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-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
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-.
-.
-.P
-Since
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-.I pic
-statements in the middle of a diagram to draw things not provided for
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-.I chem
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-.
-Such
-.I pic
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-.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
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-.B pic
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-.
-.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
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-.
-.
-.\" --------------------------------------------------------------------
-.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
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-.
-.
-.P
-There is no in-line chemistry yet (e.g., analogous to the $...$
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-.
-.
-.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: