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diff --git a/contrib/chem/ChangeLog b/contrib/chem/ChangeLog new file mode 100644 index 0000000..ad40944 --- /dev/null +++ b/contrib/chem/ChangeLog @@ -0,0 +1,373 @@ +2022-08-18 G. Branden Robinson <g.branden.robinson@gmail.com> + + * chem.pl: Refactor. + - Rename scalars. + Copyright -> copyright + Program_Version -> chem_version + Groff_Version -> groff_version + Chem_Name -> chem + before_make -> is_in_source_tree + - Rename hash. + at_at -> makevar + - Drop unused hash member `$makevar{'BINDIR'}`. + - Drop scalar `Groff_Version_Preset`, which apparently hadn't + been updated since groff 1.20. Instead, follow grog(1) and + set the `groff_version` scalar to "DEVELOPMENT" if this is + the version from the groff source tree. Overwrite its value + with that determined by make(1) if available. + - Tighten usage and version messages; make the latter more + conformant with the format recommended in the GNU Coding + Standards. Explicitly identify license as GNU GPLv2. + (usage): Refer to "pic" with its command prefix if it is known + to have one. (If running "unbuilt", we have no way to know.) + +2022-08-18 G. Branden Robinson <g.branden.robinson@gmail.com> + + * chem.pl: Stop copying "pic.tmac" (fallback troff macro + definitions) into the output. It might not be necessary and it + is inappropriate to do so if a macro package offers its own + definitions or the user has made other arrangements on the + command line. (The same thing can be achieved with the "-mpic" + argument to the formatter or a front end.) Bump version number. + +2022-06-15 G. Branden Robinson <g.branden.robinson@gmail.com> + + * chem.1.man: Fix markup nits. Use idiomatic input style, + placing newlines after sentences and commas. Also put an empty + request between sentences. + + Fixes <https://savannah.gnu.org/bugs/?51328>. + +2022-04-12 Ingo Schwarze <schwarze@openbsd.org> + + Delete the harmful, ill-designed, buggy, and essentially + unmaintained and untested --with-doc option of the configure + script. See the NEWS file for more details on the rationale. + + * chem.am: Delete three BUILD_EXAMPLES conditionals. + +2020-04-22 G. Branden Robinson <g.branden.robinson@gmail.com> + + * chem.1.man: + * examples/122/README.txt: + * examples/README.txt: Delete references to groffer. + +2018-02-28 Werner LEMBERG <wl@gnu.org> + + * chem.am (chem, README): Use $(AM_V_GEN) to silence file generation. + +2015-08-22 Bernd Warken <bernd.warken@web.de> + + * chem.1.man: Rename `chem.man'. + + * chem.am: Include renaming. + +2015-08-05 Bernd Warken <bernd.warken@web.de> + + * chem.am: Add `Last update'. Setup Emacs makefile-automake-mode. + +2015-04-03 Werner LEMBERG <wl@gnu.org> + + * chem.man: Make it work in compatibility mode. + (EL): Fix typo. + +2014-09-25 Bernd Warken <bernd.warken@web.de> + + * chem.pl: New chem version 1.0.5. + + * Makefile.sub: Add .PHONY. Restructure install and uninstall. + +2014-09-03 Bernd Warken <bernd.warken@web.de> + + * chem.pl: New chem version 1.0.4. Change version(). + + * all `chem' source files: Add and improve the copying + information. Remove last update. Add Emacs setting if necessary. + +2014-07-05 Bernd Warken <bernd.warken@web.de> + ________________________________________________________________ + * chem.pl: New chem version 1.0.3 + + * chem.man: Make file doclifter compatible. + +2014-07-04 Bernd Warken <bernd.warken@web.de> + ________________________________________________________________ + * release of chem 1.0.2 + + * chem.man: Remove definition of `.FONT'. + +2014-07-04 Bernd Warken <bernd.warken@web.de> + + * chem.man: Transform into classical man-page style. + +2014-07-04 Bernd Warken <bernd.warken@web.de> + + * chem.man: Remove definition of .Env-var. + +2014-07-03 Bernd Warken <bernd.warken@web.de> + ________________________________________________________________ + * release of chem 1.0.1 + + * chem.man: Add `.mso' for `groffer.man'. + +2014-06-17 Bernd Warken <bernd.warken@web.de> + ________________________________________________________________ + * release of chem 1.0.0 + + * Makefile.sub: Add Emacs final part. + + * ChangeLog: Correct the space characters in this file as Emacs + style. + +2014-03-29 Steffen Nurpmeso <sdaoden@yandex.com> + + * Makefile.sub (uninstall_examples): Remove superfluous `rmdir'. + +2014-03-29 Steffen Nurpmeso <sdaoden@yandex.com> + + * Makefile.sub (install_examples): Use `find', not shell globs. + + Instead of using rm(1) two times with shell globs the expansion of + which will include subdirectories (thus resulting in error + messages), use find(1) and its `-exec' operand. + +2014-03-29 Steffen Nurpmeso <sdaoden@yandex.com> + + * Makefile.sub: Handle examples separately, controlled by + $(make{_,_install_,_uninstall_}examples). + +2013-01-29 Bernd Warken <bernd.warken@web.de> + + * all: Change license into GPL2. + +2013-01-29 Werner LEMBERG <wl@gnu.org> + + * Makefile.sub (MOSTLYCLEANADD): Fix typo. + +2010-12-13 Werner LEMBERG <wl@gnu.org> + + Really fix handling of examples/122. + + * examples/122/README: Renamed to... + * examples/122/README.txt: This. + + * Makefile.sub (all, MOSTLYCLEANADD): Add `examples/122/README'. + (examples/122/README): New target. + (install_data): Fix typo. + +2010-06-02 Larry Jones <lawrence.jones@siemens.com> + + * Makefile.sub (install): Fix handling of examples/122. + It tried to process the CVS subdirectory as a file. + +2009-01-03 Werner LEMBERG <wl@gnu.org> + + * chem.pl: Prepare for groff version 1.20. + +2008-01-04 Werner LEMBERG <wl@gnu.org> + + * chem.man: Insert `\:' in URLs where appropriate. + +2007-02-06 Eric S. Raymond <esr@snark.thyrsus.com> + + * chem.man: Change .UR/.UE and .MT/.ME so the start macro no + longer takes a second argument that is pasted to the end of the + generated text. Instead, the end macro takes an argument that + does the same thing. + +2007-02-02 Werner LEMBERG <wl@gnu.org> + + * chem.man: Further refinements and normalizations. + +2007-02-02 Eric S. Raymond <esr@snark.thyrsus.com> + + * chem.man: Converted to use .SY/.OP/.YS and for cross-viewer + portability. Conversion checked using the protocol described in + tmac/TESTING-HINTS. + +2006-11-10 Bernd Warken <groff-bernd.warken-72@web.de> + ________________________________________________________________ + * release of chem 0.3.1 + + * chem.man: Add information about example files. + +2006-11-10 Werner LEMBERG <wl@gnu.org> + + * chem.man1: Rename back to... + * chem.man: This. + Use @G@, @MACRODIR@, and @DATASUBDIR@. + + * 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 <groff-bernd.warken-72@web.de> + ________________________________________________________________ + * release of chem 0.3.0 + + * chem.man1: Rename `chem.man' to translate some `@...@' + 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 <wl@gnu.org> + + * chem.man: Revised. + +2006-11-08 Bernd Warken <groff-bernd.warken-72@web.de> + ________________________________________________________________ + * release of chem 0.2.0 + + * pic.tmac: Remove this file. Use instead the installed pic.tmac + in $(tmacdir). + + * Makefile.sub, chem.pl: + - Install macros.pic to $(tmacdir)/pic/chem.pic. + - Remove parts with `libdir'. + +2006-11-07 Werner LEMBERG <wl@gnu.org> + + * Makefile.sub: Add and fix $(srcdir) where necessary to make it + compile with srcdir != builddir. Other minor fixes improvements. + +2006-11-07 Bernd Warken <groff-bernd.warken-72@web.de> + ________________________________________________________________ + * release of chem 0.1.2 + + ### `chem' works now with all example files (examples/*.chem and + examples/122/*.chem). + + * examples/122/README: Add some information on the example files. + + * examples/122/chAi_poly_vinyl_chloride.chem: Use .ps with + argument `-2' and recall `.ps +2' at the end of the file. This + stops the size shift in the following files. + + * examples/122/ch6b_dna.chem: Make the file runnable, it works + now. + + * examples/reserpine.chem: Change access to `begin chem'. + + * chem.man: + - Fix the BUGS section. + - Correct the name of the macro file to `macros.pic'. + - Extent section DESCRIPTION and LANGUAGE. + - Moieties and Strings: Rewritten section about moieties and + double quoted strings. + + * chem.pl: + - parameter check: Add filespecs only when non-empty file. + - Set $Last_Type to $OTHER for the `pic' command. + - joinring(), label(), labsave(), reduce(): Remove these functions. + - `[', `]', `{', `}', `define': Make these and the defined + functions commands for `chem' without using the `pic' word. + - @Words: Fix it such that all double quoted strings are + completely in an element. + - `Last: ': Remove this prefix from all commands that are related + to `pic'. + + ### global variables + + * chem.pl: + - $Line: Add this variable to store the unchanged input line. + - %Params: Add the variables from setparams() to this hash. + - %Types: Add BOND, MOL, RING, OTHER from init() to this hash. + - %Put: Move %put to this. + - %Dbl: Move %dbl to this. + - %Labtype: Move %labtype to this. + - %Aromatic: Move $aromatic to this. + - %Dc: Move %dc to this. + - %Nput: Move $nput to this. + - %Define: New hash for storing the names of the `define' + constructs during `chem'. Use the elements in `%Define' as `chem' + commands. + +2006-10-27 Bernd Warken <groff-bernd.warken-72@web.de> + ________________________________________________________________ + * release of chem 0.1.1 + + * chem.pl: + - Add handling of `[' and `]' (extension of chem awk). + - Restrict line break after labels. + + * ChangeLog: Correct the former entry. + +2006-10-26 Bernd Warken <groff-bernd.warken-72@web.de> + ________________________________________________________________ + * release of chem 0.1.0 + + ### Extensions to the chem awk version. + + * chem.pl: + - parameters: -h, --help, -v, --version, -- are added as options. + The minus character - is added as filespec for standard input, it + may be used several times. + - remove the functions `inline', `shiftfields', and `set'. + - Fix the handling of the initialization commands .PS, .cstart, + `begin chem', and `end'. + - Add error massages. + - error(): Add file name. + - Add concatenation of lines with final backslash `\'. + - Add pic.tmac to guarantee that each pic display is centered. + - Warnings and strict are active. + + ### Source files of the chem Perl version + + * chem.pl: Source file for the Perl version of chem. + + * macros.pic: Pic macro file that is loaded by each run of chem. + + * pic.tmac: Macro file for .PS and .PE; taken over from the groff + source file <groff-top-source>/tmac/pic.tmac. + + * Makefile.sub: Make file for the groff system. + + * ChangeLog: This file. + + * chem.man: Manual page for the Perl version of chem. + + * README.txt: File for information on this chem version. + + * examples/*.chem: Self-constructed example files for chem. + + * examples/README.txt: Information on the example files. + + * examples/122/*.chem: Example files from the classical chem book + 122.ps at <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + + * examples/122/README: Information on the example files in this + directory. + +2006-10-16 Bernd Warken <groff-bernd.warken-72@web.de> + + * awk version of chem + chem is a roff preprocessor that generates chemical structure + diagrams suitable for the pic preprocessor. The original version + of chem is an awk script written by Brian Kernighan. This project + is a rewrite of chem in Perl. + +2006-10-15 Bernd Warken <groff-bernd.warken-72@web.de> +________________________________________________________________ +License + +Copyright (C) 2006-2020 Free Software Foundation, Inc. +Written by Bernd Warken <groff-bernd.warken-72@web.de>. + +Copying and distribution of this file, with or without +modification, are permitted provided the copyright notice and this +notice are preserved. + +This file is part of `chem', which is part of the `groff' project. + + +##### Editor settings +Local Variables: +mode: change-log +End: diff --git a/contrib/chem/README.txt b/contrib/chem/README.txt new file mode 100644 index 0000000..06baed2 --- /dev/null +++ b/contrib/chem/README.txt @@ -0,0 +1,50 @@ +'chem' is a 'roff' language to generate chemical structure diagrams. +'@g@chem' is a 'groff' preprocessor that produces output suitable for +the '@g@pic' preprocessor. + +The original version of 'chem' is an 'awk' script written by Brian +Kernighan <http://cm.bell-labs.com/cm/cs/who/bwk/index.html>. The +source files of the 'awk' version of 'chem' are available at +<http://cm.bell-labs.com/netlib/typesetting/chem.gz>. + +This project is a rewrite of 'chem' in Perl for the GNU 'roff' project +'groff'. It was written under Perl v5.8.8, but at least Perl v5.6 is +needed to run the Perl version of 'chem'. + +In comparison to the original 'awk' version of 'chem', the Perl +version does the following changements: +- the options -h, --help, -v, --version to output usage and version +information are added. +- remove some functions 'inline', 'shiftfields', and 'set' and some +variables that are used only once. + +The subdirectory 'examples/' contains example files for chem. They +are written in the 'chem' language. The file names end with .chem. + + +####### License + +Copyright (C) 2006-2020 Free Software Foundation, Inc. +Written by Bernd Warken <groff-bernd.warken-72@web.de>. + +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 (GPL) version 2 as +published by the Free Software Foundation. + +'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. + +The GPL2 license text is available in the internet at +<http://www.gnu.org/licenses/gpl-2.0.html>. + + +##### Editor settings +Local Variables: +fill-column: 72 +mode: text +End: +vim: set textwidth=72: diff --git a/contrib/chem/chem.1.man b/contrib/chem/chem.1.man new file mode 100644 index 0000000..a02242f --- /dev/null +++ b/contrib/chem/chem.1.man @@ -0,0 +1,925 @@ +.TH @g@chem @MAN1EXT@ "@MDATE@" "groff @VERSION@" +.SH Name +@g@chem \- embed chemical structure diagrams in +.I groff +documents +. +. +.\" ==================================================================== +.\" Legal Terms +.\" ==================================================================== +.\" +.\" Copyright (C) 2006-2020 Free Software Foundation, Inc. +.\" +.\" This file is part of chem, which is part of groff, a free software +.\" project. +.\" +.\" You can redistribute it and/or modify it under the terms of the GNU +.\" General Public License version 2 (GPL2) as published by the Free +.\" Software Foundation. +.\" +.\" The license text for GPL2 is available in the internet at +.\" <http://www.gnu.org/licenses/gpl-2.0.html>. +. +. +.\" Save and disable compatibility mode (for, e.g., Solaris 10/11). +.do nr *groff_chem_1_man_C \n[.cp] +.cp 0 +. +.\" Define fallback for groff 1.23's MR macro if the system lacks it. +.nr do-fallback 0 +.if !\n(.f .nr do-fallback 1 \" mandoc +.if \n(.g .if !d MR .nr do-fallback 1 \" older groff +.if !\n(.g .nr do-fallback 1 \" non-groff *roff +.if \n[do-fallback] \{\ +. de MR +. ie \\n(.$=1 \ +. I \%\\$1 +. el \ +. IR \%\\$1 (\\$2)\\$3 +. . +.\} +.rr do-fallback +. +. +.\" ==================================================================== +.SH Synopsis +.\" ==================================================================== +. +.SY @g@chem +.RB [ \-\- ] +.RI [ file\~ .\|.\|.] +.YS +. +. +.SY @g@chem +.B \-h +. +.SY @g@chem +.B \-\-help +.YS +. +. +.SY @g@chem +.B \-v +. +.SY @g@chem +.B \-\-version +.YS +. +. +.\" ==================================================================== +.SH Description +.\" ==================================================================== +. +.I chem +produces chemical structure diagrams. +. +Today's version is best suited for organic chemistry (bonds, rings). +. +The +.I @g@chem +program is a +.I groff +preprocessor like +.IR @g@eqn , +.IR @g@pic , +.IR @g@tbl , +etc. +. +It generates +.I pic +output such that all +.I chem +parts are translated into diagrams of the +.I pic +language. +. +. +.P +If no operands are given, +or if +.I file +is +.RB \[lq] \- \[rq], +.I @g@chem +reads the standard input stream. +. +.B \-h +and +.B \-\-help +display a usage message, +whereas +.B \-v +and +.B \-\-version +display version information; +all exit. +. +. +.P +The program +.I @g@chem +originates from the Perl source file +.IR chem.pl . +. +It tells +.I @g@pic +to include a copy of the macro file +.IR chem.pic . +. +Moreover the +.I groff +source file +.I pic.tmac +is loaded. +. +. +.P +In a style reminiscent of +.I eqn +and +.IR pic , +the +.I chem +diagrams are written in a special language. +. +. +.P +A set of +.I chem +lines looks like this +. +. +.IP +.EX +\&.cstart +.I chem data +\&.cend +.EE +. +. +.P +Lines containing the keywords +.B .cstart +and +.B .cend +start and end the input for +.IR @g@chem , +respectively. +. +In +.I pic +context, i.e., after the call of +.BR .PS , +.I chem +input can optionally be started by the line +.B \%begin\~chem +and ended by the line with the single word +.B end +instead. +. +. +.P +Anything outside these initialization lines is copied through +without modification; +all data between the initialization lines is converted into +.I pic +commands to draw the diagram. +. +. +.P +As an example, +. +.IP +.EX +\&.cstart +CH3 +bond +CH3 +\&.cend +.EE +. +. +.P +prints two +.B CH3 +groups with a bond between them. +. +. +.P +If you want to create just +.I groff +output, you must run +.I @g@chem +followed by +.I groff +with the option +.B \-p +for the activation of +.IR @g@pic : +.IP +.I @g@chem +.RI [ file\~ .\|.\|.\&] +.BR "| groff \-p\~" .\|.\|. +. +. +.\" ==================================================================== +.SH 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 , +\&.\|.\|., +and strings. +. +. +.\" ==================================================================== +.SS "Setting variables" +.\" ==================================================================== +. +There are some variables that can be set by commands. +. +Such commands have two possible forms, either +. +.RS +.P +.I "variable value" +.RE +. +.P +or +. +.RS +.P +.IB "variable " = " value" +.RE +. +.P +This sets the given +.I variable +to the argument +.IR value . +If more arguments are given only the last argument is taken, all other +arguments are ignored. +. +. +.P +There are only a few variables to be set by these commands: +. +.TP +.BI textht " arg" +Set the height of the text to +.IR arg ; +default is 0.16. +. +.TP +.BI cwid " arg" +Set the character width to +.IR arg ; +default is 0.12. +. +.TP +.BI db " arg" +Set the bond length to +.IR arg ; +default is 0.2. +. +.TP +.BI size " arg" +Scale the diagram to make it look plausible at point size +.IR arg ; +default is 10 point. +. +. +.\" ==================================================================== +.SS Bonds +.\" ==================================================================== +. +This +. +.RS +.SY bond +.RI [ direction ] +.RI [ length\ n ] +.RB [ from\ \c +.IR Name | picstuff ] +.YS +.RE +. +.P +draws a single bond in direction from nearest corner of +.IR Name . +.B bond +can also be +.BR "double bond" , +.BR "front bond" , +.BR "back bond" , +etc. +. +(We will get back to +.I Name +soon.) +. +. +.P +.I direction +is the angle in degrees (0\~up, positive clockwise) +or a direction word like +.BR up , +.BR down , +.B sw +(=\~southwest), etc. +. +If no direction is specified, the bond goes in the current direction +(usually that of the last bond). +. +. +.P +Normally the bond begins at the last object placed; this +can be changed by naming a +.B from +place. +. +For instance, to make a simple alkyl chain: +. +.RS +.TS +tab (@); +lb l. +CH3 +bond@(this one goes right from the CH3) +C@(at the right end of the bond) +double bond up@(from the C) +O@(at the end of the double bond) +bond right from C +CH3 +.TE +.RE +. +. +.P +A length in inches may be specified to override the default length. +. +Other +.I pic +commands can be tacked on to the end of a bond command, to created +dotted or dashed bonds or to specify a +.B to +place. +. +. +.\" ==================================================================== +.SS Rings +.\" ==================================================================== +. +There are lots of rings, +but only five- and six-sided rings get much support. +. +.B ring +by itself is a six-sided ring; +.B benzene +is the benzene ring with a circle inside. +.B aromatic +puts a circle into any kind of ring. +. +.RS +.SY ring +.RB [ \%pointing\ ( up | right | left | down )] +.RB [ \%aromatic ] +.RB [ put\ Mol\ at\ \fIn\/\fP ] +.RB [ \%double\ \c +.IR i , j\ \/\c +.IR k , l\ \/\c +\&.\|.\|.\& +.RI [ picstuff ] +.YS +.RE +. +. +.P +The vertices of a ring are numbered 1, 2, \&.\|.\|.\& from the +vertex that points in the natural compass direction. +. +So for a hexagonal ring with the point at the top, the top vertex +is\~1, while if the ring has a point at the east side, that is +vertex\~1. +. +This is expressed as +. +.IP +.EX +R1: ring pointing up +R2: ring pointing right +.EE +. +. +.P +The ring vertices are named +.BR .V1 , +\&.\|.\|., +.BI .V n\fR,\fP +with +.B .V1 +in the pointing direction. +. +So the corners of +.B R1 +are +.B R1.V1 +(the +.IR top ), +.BR R1.V2 , +.BR R1.V3 , +.B R1.V4 +(the +.IR bottom ), +etc., whereas for +.BR R2 , +.B R2.V1 +is the rightmost vertex and +.B R2.V4 +the leftmost. +. +These vertex names are used for connecting bonds or other rings. +. +For example, +. +.IP +.EX +R1: benzene pointing right +R2: benzene pointing right with .V6 at R1.V2 +.EE +. +. +.P +creates two benzene rings connected along a side. +. +. +.P +Interior double bonds are specified as +.B \%double +.IB n1 , "n2 n3" , n4 +.RB .\|.\|. ; +each number pair adds an interior bond. +. +So the alternate form of a benzene ring is +. +.IP +.B "ring double 1,2 3,4 5,6" +. +. +.P +Heterocycles (rings with something other than carbon at a vertex) are +written as +.BI put\ X\ at\ V\fR,\fP +as in +. +.IP +.B "R: ring put N at 1 put O at 2" +. +. +.P +In this heterocycle, +.B R.N +and +.B R.O +become synonyms for +.B R.V1 +and +.BR R.V2 . +. +. +.P +There are two five-sided rings. +. +.B ring5 +is pentagonal with a side that matches the six-sided ring; +it has four natural directions. +. +A +.B \%flatring +is a five-sided ring created by chopping one corner of a six-sided ring +so that it exactly matches the six-sided rings. +. +. +.P +The description of a ring has to fit on a single line. +. +. +.\" ==================================================================== +.SS "Moieties and strings" +.\" ==================================================================== +. +A moiety is a string of characters beginning with a capital letter, +such as N(C2H5)2. +. +Numbers are converted to subscripts (unless they appear to be +fractional values, as in N2.5H). +. +The name of a moiety is determined from the moiety after special +characters have been stripped out: e.g., N(C2H5)2) has the name NC2H52. +. +. +.P +Moieties can be specified in two kinds. +. +Normally a moiety is placed right after the last thing mentioned, +separated by a semicolon surrounded by spaces, e.g., +. +.IP +.B "B1: bond ; OH" +. +.P +Here the moiety is +.BR OH ; +it is set after a bond. +. +. +.P +As the second kind a moiety can be positioned as the first word in a +.IR pic -like +command, e.g., +. +.IP +.B "CH3 at C + (0.5,0.5)" +. +.P +Here the moiety is +.BR CH3 . +It is placed at a position relative to +.BR C , +a moiety used earlier in the chemical structure. +. +. +.P +So moiety names can be specified as +.I chem +positions everywhere in the +.I chem +code. +. +Beneath their printing moieties are names for places. +. +. +.P +The moiety +.B BP +is special. +. +It is not printed but just serves as a mark to be referred to in later +.I chem +commands. +. +For example, +. +.IP +.B "bond ; BP" +. +.P +sets a mark at the end of the bond. +. +This can be used then for specifying a place. +. +The name +.B BP +is derived from +.I branch point +(i.e., line crossing). +. +. +.P +A string within double quotes +.B \(dq +is interpreted as a part of a +.I chem +command. +. +It represents a string that should be printed (without the quotes). +. +Text within quotes +.BR \(dq .\|.\|.\& \(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 : +\&.\|.\|. +. +. +.P +.I Name +is often the name of a moiety like +.BR CH3 , +but it need not to be. +. +Any name that begins with a capital letter and which contains +only letters and numbers is valid: +. +.RS +.TP +.B First: +.B bond +.TQ +\& +.B "bond 30 from First" +.RE +. +. +.\" ==================================================================== +.SS Miscellaneous +.\" ==================================================================== +. +The specific construction +.RS +.TP +.BR bond \~.\|.\|.\&\~ "; moiety" +.RE +.P +is equivalent to +.IP +.EX +bond +moiety +.EE +. +. +.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 \[aq] +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 +.I @g@chem +is a +.I @g@pic +preprocessor, it is possible to include +.I pic +statements in the middle of a diagram to draw things not provided for +by +.I chem +itself. +. +Such +.I pic +statements should be included in +.I chem +code by adding +.B pic +as the first word of this line for clarity. +. +. +.P +The following +.I pic +commands are accepted as +.I chem +commands, so no +.B pic +command word is needed: +. +.IP +.B define +Start the definition of +.I pic +macro within +.IR chem . +. +.RS +.TP +.B [ +Start a block composite. +. +.TP +.B ] +End a block composite. +. +.TP +.B { +Start a macro definition block. +. +.TP +.B } +End a macro definition block. +.RE +. +.P +The macro names from +.B define +statements are stored and their call is accepted as a +.I chem +command as well. +. +. +.\" ==================================================================== +.SS "Wish list" +.\" ==================================================================== +. +.P +This TODO list was collected by Brian Kernighan. +. +. +.P +Error checking is minimal; errors are usually detected and reported in +an oblique fashion by +.IR pic . +. +. +.P +There is no library or file inclusion mechanism, and there is no +shorthand for repetitive structures. +. +. +.P +The extension mechanism is to create +.I pic +macros, but these are tricky to get right and don't have all the +properties of built-in objects. +. +. +.P +There is no in-line chemistry yet +(e.g., +analogous to the +.BR $ .\|.\|. $ +construct of +.IR eqn ). +. +. +.P +There is no way to control entry point for bonds on groups. +. +Normally a bond connects to the carbon atom if entering from +the top or bottom and otherwise to the nearest corner. +. +. +.P +Bonds from substituted atoms on heterocycles do not join at the proper +place without adding a bit of +.IR pic . +. +. +.P +There is no decent primitive for brackets. +. +. +.P +Text (quoted strings) doesn't work very well. +. +. +.P +A squiggle bond is needed. +. +. +.\" ==================================================================== +.SH Files +.\" ==================================================================== +. +.TP +.I @DATASUBDIR@/\:pic/\:chem\:.pic +A collection of +.I pic +macros needed by +.IR @g@chem . +. +.TP +.I @MACRODIR@/\:pic\:.tmac +A macro file which redefines +.BR .PS , +.BR .PE , +and +.B .PF +to center +.I pic +diagrams. +. +.TP +.IR @DOCDIR@/\:\%examples/\:chem/\: * .chem +Example files for +.IR chem . +. +.TP +.IR @DOCDIR@/\:\%examples/\:chem/\:122/\: * .chem +Example files from the +.I chem +article by its authors, +\[lq]CHEM\[em]A Program for Typesetting Chemical Structure Diagrams: +User Manual\[rq] +(CSTR\~#122). +. +. +.\" ==================================================================== +.SH Authors +.\" ==================================================================== +. +The GNU version of +.I chem +was written by +.MT groff\-bernd\:.warken\-72@\:web\:.de +Bernd Warken +.ME . +. +It is based on the documentation of Brian Kernighan's original +.I awk +version of +.IR chem . +. +. +.\" ==================================================================== +.SH "See also" +.\" ==================================================================== +. +\[lq]CHEM\[em]A Program for Typesetting Chemical Diagrams: User +Manual\[rq] +by Jon L.\& Bentley, +Lynn W.\& Jelinski, +and +Brian W.\& Kernighan, +1992, +AT&T Bell Laboratories Computing Science Technical Report No.\& 122 +. +. +.P +.MR groff @MAN1EXT@ , +.MR @g@pic @MAN1EXT@ +. +. +.\" Restore compatibility mode (for, e.g., Solaris 10/11). +.cp \n[*groff_chem_1_man_C] +.do rr *groff_chem_1_man_C +. +. +.\" Local Variables: +.\" fill-column: 72 +.\" mode: nroff +.\" End: +.\" vim: set filetype=groff textwidth=72: diff --git a/contrib/chem/chem.am b/contrib/chem/chem.am new file mode 100644 index 0000000..abee480 --- /dev/null +++ b/contrib/chem/chem.am @@ -0,0 +1,120 @@ +# Automake rules for 'chem' + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. +# Written by Bernd Warken <groff-bernd.warken-72@web.de>. +# Moved to automake by Bertrand Garrigues +# +# 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 (GPL) version 2 as +# published by the Free Software Foundation. +# +# '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. +# +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +chem_srcdir = $(top_srcdir)/contrib/chem +prefixexecbin_SCRIPTS += chem + +# Files installed in $(datasubdir)/pic +chempicdir = $(datasubdir)/pic +dist_chempic_DATA = contrib/chem/chem.pic + + +CHEM_GENEXAMPLES = contrib/chem/examples/README +CHEM_EXAMPLES = \ + contrib/chem/examples/atp.chem \ + contrib/chem/examples/cholesterin.chem \ + contrib/chem/examples/ethamivan.chem \ + contrib/chem/examples/lsd.chem \ + contrib/chem/examples/morphine.chem \ + contrib/chem/examples/penicillin.chem \ + contrib/chem/examples/reserpine.chem + +# Files installed in $(exampledir)/chem +chemexampledir = $(exampledir)/chem +nodist_chemexample_DATA = $(CHEM_GENEXAMPLES) +dist_chemexample_DATA = $(CHEM_EXAMPLES) + +# Files installed in $(exampledir)/chem/122. All the .chem files in 122 are +# lazily installed by the local install target +chemexample122dir = $(chemexampledir)/122 +nodist_chemexample122_DATA = contrib/chem/examples/122/README +EXTRA_DIST += \ + contrib/chem/ChangeLog \ + contrib/chem/chem.1.man \ + contrib/chem/chem.pic \ + contrib/chem/chem.pl \ + contrib/chem/README.txt \ + contrib/chem/examples/README.txt \ + contrib/chem/examples/122/README.txt + +man1_MANS += contrib/chem/chem.1 +MOSTLYCLEANFILES += $(CHEM_GENEXAMPLES) $(nodist_chemexample122_DATA) \ + contrib/chem/README + +# This is strangely built but not installed +all: contrib/chem/README + +contrib/chem/README: $(chem_srcdir)/README.txt + $(AM_V_GEN)$(MKDIR_P) contrib/chem/ \ + && sed -e "s|[@]g[@]|$(g)|g" $? >$@ + +contrib/chem/examples/README: $(chem_srcdir)/examples/README.txt + $(AM_V_GEN)$(MKDIR_P) contrib/chem/examples \ + && sed -e "s|[@]g[@]|$(g)|g" $? >$@ + +contrib/chem/examples/122/README: $(chem_srcdir)/examples/122/README.txt + $(AM_V_GEN)$(MKDIR_P) contrib/chem/examples/122 \ + && sed -e "s|[@]g[@]|$(g)|g" $? >$@ + +chem: $(chem_srcdir)/chem.pl $(SH_DEPS_SED_SCRIPT) + $(AM_V_GEN)$(RM) $@ \ + && sed -f "$(SH_DEPS_SED_SCRIPT)" \ + -e "s|[@]g[@]|$(g)|g" \ + -e "s|[@]BINDIR[@]|$(DESTDIR)$(bindir)|g" \ + -e "s|[@]MACRODIR[@]|$(DESTDIR)$(tmacdir)|g" \ + -e "s|[@]PICDIR[@]|$(DESTDIR)$(datasubdir)/pic|g" \ + -e "s|[@]VERSION[@]|$(VERSION)|g" \ + -e "$(SH_SCRIPT_SED_CMD)" \ + $(chem_srcdir)/chem.pl \ + >$@ \ + && chmod +x $@ + +install-data-local: install_chem_extra +install_chem_extra: + -test -d $(DESTDIR)$(chemexample122dir) \ + || $(mkinstalldirs) $(DESTDIR)$(chemexample122dir); + for i in $(chem_srcdir)/examples/122/*.chem; do \ + n=`echo $$i | sed 's|$(chem_srcdir)/examples/122/||g'`; \ + $(INSTALL_DATA) $$i $(DESTDIR)$(chemexample122dir)/$$n; \ + done + +uninstall-local: uninstall_chem_extra +uninstall_chem_extra: + $(RM) $(DESTDIR)$(exampledir)/chem/122/* + -rmdir $(DESTDIR)$(exampledir)/chem/122 + $(RM) $(DESTDIR)$(exampledir)/chem/* + -rmdir $(DESTDIR)$(exampledir)/chem + -rmdir $(DESTDIR)$(datasubdir)/pic + +dist-hook: dist_chem +dist_chem: + chmod u+w $(distdir)/contrib/chem/examples/122 + for i in $(chem_srcdir)/examples/122/*.chem; do \ + cp -f $$i $(distdir)/contrib/chem/examples/122; \ + done + + +# Local Variables: +# mode: makefile-automake +# fill-column: 72 +# End: +# vim: set autoindent filetype=automake textwidth=72: diff --git a/contrib/chem/chem.pic b/contrib/chem/chem.pic new file mode 100644 index 0000000..33e932c --- /dev/null +++ b/contrib/chem/chem.pic @@ -0,0 +1,89 @@ +# macros for chem + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. +# Written by Brian Kernighan <http://cm.bell-labs.com/cm/cs/who/bwk>, +# modified by Bernd Warken <groff-bernd.warken-72@web.de>. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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. + +# The license text for GPL2 is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +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 +} +# Local Variables: +# mode: Nroff +# End: diff --git a/contrib/chem/chem.pl b/contrib/chem/chem.pl new file mode 100755 index 0000000..5ca3fa2 --- /dev/null +++ b/contrib/chem/chem.pl @@ -0,0 +1,1231 @@ +#! /usr/bin/env perl + +# chem - a groff preprocessor for producing chemical structure diagrams + +my $copyright = 'Copyright (C) 2006-2014, 2022' + . ' Free Software Foundation, Inc.'; +# Written by Bernd Warken <groff-bernd.warken-72@web.de>. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## +# settings +######################################################################## + +my $chem_version = '1.0.6'; +my $groff_version = 'DEVELOPMENT'; + +require v5.6; + + +######################################################################## +# begin +######################################################################## + +use warnings; +use strict; +use Math::Trig; + +# for catfile() +use File::Spec; + +# $Bin is the directory where this script is located +use FindBin; + +my $chem; +my $File_chem_pic; + +my $is_in_source_tree; +{ + $is_in_source_tree = 1 if '@VERSION@' eq '@' . 'VERSION' . '@'; +} + +my %makevar; + +if ($is_in_source_tree) { + my $chem_dir = $FindBin::Bin; + $makevar{'G'} = ''; + $File_chem_pic = File::Spec->catfile($chem_dir, 'chem.pic'); + $chem = 'chem'; +} else { + $groff_version = '@VERSION@'; + $makevar{'G'} = '@g@'; + $makevar{'PICDIR'} = '@PICDIR@'; + $File_chem_pic = File::Spec->catfile($makevar{'PICDIR'}, 'chem.pic'); + $chem = $makevar{'G'} . 'chem'; +} + + +######################################################################## +# check the parameters +######################################################################## + +if (@ARGV) { + # process any FOO=bar switches + # eval '$'.$1.'$2;' while $ARGV[0] =~ /^([A-Za-z_0-9]+=)(.*)/ && shift; + my @filespec = (); + my $dbl_minus; + my $wrong; + foreach (@ARGV) { + next unless $_; + if (/=/) { + # ignore FOO=bar switches + push @filespec, $_ if -f; + next; + } + if ($dbl_minus) { + if (-f $_) { + push @filespec, $_ if -s $_; + } else { + warn "chem: argument $_ is not an existing file.\n"; + $wrong = 1; + } + next; + } + if (/^--$/) { + $dbl_minus = 1; + next; + } + if (/^-$/) { + push @filespec, $_; + next; + } + if (/^-h$/ or '--help' =~ /^$_/) { + &usage(); + exit 0; + } + if (/^-v$/ or '--version' =~ /^$_/) { + &version(); + exit 0; + } + if (-f $_) { + push @filespec, $_ if -s $_; + } else { + $wrong = 1; + if (/^-/) { + warn "chem: wrong option ${_}.\n"; + } else { + warn "chem: argument $_ is not an existing file.\n"; + } + } + } + if (@filespec) { + @ARGV = @filespec; + } else { + exit 0 if $wrong; + @ARGV = ('-'); + } +} else { # @ARGV is empty + @ARGV = ('-') unless @ARGV; +} + + +######################################################################## +# main process +######################################################################## + +my %Dc = ( 'up' => 0, 'right' => 90, 'down' => 180, 'left' => 270, + 'ne' => 45, 'se' => 135, 'sw' => 225, 'nw' => 315, + 0 => 'n', 90 => 'e', 180 => 's', 270 => 'w', + 30 => 'ne', 45 => 'ne', 60 => 'ne', + 120 => 'se', 135 => 'se', 150 => 'se', + 210 => 'sw', 225 => 'sw', 240 => 'sw', + 300 => 'nw', 315 => 'nw', 330 => 'nw', + ); + +my $Word_Count; +my @Words; + +my $Line_No; +my $Last_Name = ''; + +# from init() +my $First_Time = 1; +my $Last_Type; +my $Dir; # direction +my %Types = ( + 'RING' => 'R', + 'MOL' => 'M', + 'BOND' => 'B', + 'OTHER' => 'O' # manifests + ); + +# from setparams() +my %Params; + +# from ring() +my $Nput; +my $Aromatic; +my %Put; +my %Dbl; + +my %Labtype; +my %Define = (); + +my $File_Name = ''; +my $Line = ''; + +&main(); + +{ + my $is_pic = ''; + my $is_chem = ''; + my $former_line = ''; + + ########## + # main() + # + sub main { + my $count_minus = 0; + my @stdin = (); + my $stdin = 0; + + foreach (@ARGV) { + $count_minus++ if /^-$/; + } + + foreach my $arg (@ARGV) { + &setparams(1.0); + next unless $arg; + $Line_No = 0; + $is_pic = ''; + $is_chem = ''; + if ($arg eq '-') { + $File_Name = 'standard input'; + if ($stdin) { + &main_line($_) foreach @stdin; + } else { + $stdin = 1; + if ($count_minus <= 1) { + while (<STDIN>) { + &main_line($_); + } + } else { + @stdin = (); + while (<STDIN>) { + push @stdin, $_; + &main_line($_); + } + } + } +### main() + } else { # $arg is not - + $File_Name = $arg; + open FILE, "<$arg"; + &main_line($_) while <FILE>; + close FILE; + } # if $arg + if ($is_pic) { + printf ".PE\n"; + } + } + } # main() + + + ########## + # main_line() + # + sub main_line { + my $line = $_[0]; +# $Last_Type = $Types{'OTHER'}; +# $Last_Type = ''; + my $stack; + $Line_No++; + chomp $line; + + $line = $former_line . $line if $former_line; + if ($line =~ /^(.*)\\$/) { + $former_line = $1; + return 1; + } else { + $former_line = ''; + } + $Line = $line; + + { + @Words = (); + my $s = $line; + $s =~ s/^\s*//; + $s =~ s/\s+$//; + return 1 unless $s; + $s = " $s"; + $s =~ s/\s+#.*$// if $is_pic; + return 1 unless $s; + $line = $s; + $line =~ s/^\s*|\s*$//g; + my $bool = 1; + while ($bool) { + $s =~ /^([^"]*)\s("[^"]*"?\S*)(.*)$/; + if (defined $1) { + my $s1 = $1; + my $s2 = $2; + $s = $3; + $s1 =~ s/^\s*|\s*$//g; + push @Words, split(/\s+/, $s1) if $s1; + push @Words, $s2; + } + if ($s !~ /\s"/) { + $s =~ s/^\s*|\s*$//g; + push @Words, split(/\s+/, $s) if $s; + $bool = 0; + } + } + +# @Words = split(/\s+/, $s); + return 1 unless @Words; +# foreach my $i (0..$#Words) { +# if ($Words[$i] =~ /^\s*#/) { +# $#Words = $i - 1; +# last; +# } +# } +# return 1 unless @Words; + } + + if ($line =~ /^([\.']\s*PS\s*)|([\.']\s*PS\s.+)$/) { + # .PS + unless ($is_pic) { + $is_pic = 'running'; + print "$line\n"; + } + return 1; + } +### main_line() + if ( $line =~ /^([\.']\s*PE\s*)|([\.']\s*PE\s.+)$/ ) { + # .PE + $is_chem = ''; + if ($is_pic) { + $is_pic = ''; + print "$line\n"; + } + return 1; + } + if ($line =~ /^[\.']\s*cstart\s*$/) { + # line: '.cstart' + if ($is_chem) { + &error("additional '.cstart'; chem is already active."); + return 1; + } + unless ($is_pic) { + &print_ps(); + $is_pic = 'by chem'; + } + $is_chem = '.cstart'; + &init(); + return 1; + } +### main_line() + if ($line =~ /^\s*begin\s+chem\s*$/) { + # line: 'begin chem' + if ($is_pic) { + if ($is_chem) { + &error("additional 'begin chem'; chem is already active."); + return 1; + } + $is_chem = 'begin chem'; + &init(); + } else { + print "$line\n"; + } + return 1; + } + if ($line =~ /^[\.']\s*cend\s*/) { + # line '.cend' + if ($is_chem) { + &error("you end chem with '.cend', but started it with 'begin chem'.") + if $is_chem eq 'begin chem'; + if ($is_pic eq 'by chem') { + &print_pe(); + $is_pic = ''; + } + $is_chem = ''; + } else { + print "$line\n"; + } + return 1; + } + if ($line =~ /^\s*end\s*$/) { + # line: 'end' + if ($is_chem) { + &error("you end chem with 'end', but started it with '.cstart'.") + if $is_chem eq '.cstart'; + if ($is_pic eq 'by chem') { + &print_pe(); + $is_pic = ''; + } + $is_chem = ''; + } else { + print "$line\n"; + } + return 1; + } + +### main_line() + if (! $is_chem) { + print "$line\n"; + return 1; + } + if ($line =~ /^[.']/) { + # groff request line + print "$line\n"; + return 1; + } + + if ($Words[0] eq 'pic') { + # pic pass-through + return 1 if $#Words == 0; + my $s = $line; + $s =~ /^\s*pic\s*(.*)$/; + $s = $1; + print "$s\n" if $s; + $Last_Type = $Types{'OTHER'}; + $Define{ $Words[2] } = 1 if $#Words >= 2 && $Words[1] eq 'define'; + return 1; + } + + if ($Words[0] eq 'textht') { + if ($#Words == 0) { + &error("'textht' needs a single argument."); + return 0; + } + &error("only the last argument is taken for 'textht', " . + "all others are ignored.") + unless $#Words <= 1 or ($#Words == 2 && $Words[1] =~ /^=/); + $Params{'textht'} = $Words[$#Words]; + return 1; + } +### main_line() + if ($Words[0] eq 'cwid') { # character width + if ($#Words == 0) { + &error("'cwid' needs a single argument."); + return 0; + } + &error("only the last argument is taken for 'cwid', " . + "all others are ignored.") + unless $#Words <= 1 or ($#Words == 2 && $Words[1] =~ /^=/); + $Params{'cwid'} = $Words[$#Words]; + return 1; + } + if ($Words[0] eq 'db') { # bond length + if ($#Words == 0) { + &error("'db' needs a single argument."); + return 0; + } + &error("only the last argument is taken for 'db', " . + "all others are ignored.") + unless $#Words <= 1 or ($#Words == 2 && $Words[1] =~ /^=/); + $Params{'db'} = $Words[$#Words]; + return 1; + } + if ($Words[0] eq 'size') { # size for all parts of the whole diagram + my $size; + if ($#Words == 0) { + &error("'size' needs a single argument."); + return 0; + } + &error("only the last argument is taken for 'size', " . + "all others are ignored.") + unless $#Words <= 1 or ($#Words == 2 && $Words[1] =~ /^=/); + if ($Words[$#Words] <= 4) { + $size = $Words[$#Words]; + } else { + $size = $Words[$#Words] / 10; + } + &setparams($size); + return 1; + } + +### main_line() + print "\n#", $Line, "\n"; # debugging, etc. + $Last_Name = ''; +# $Last_Type = $Types{'OTHER'}; +# $Last_Type = ''; + + if ($Words[0] =~ /^[A-Z].*:$/) { + # label; falls thru after shifting left + my $w = $Words[0]; + $Last_Name = $w; + $Last_Name =~ s/:$//; + print "$w"; + shift @Words; + if (@Words) { + print " "; + $line =~ s/^\s*$w\s*//; + } else { + print "\n"; + return 1; + } + } + + if ($Words[0] eq 'define') { + print "$line\n"; + $Define{ $Words[1] } = 1 if $#Words >= 1; + $Last_Type = $Types{'OTHER'}; + return 1; + } + if ($Words[0] =~ /^[\[\]{}]/) { + print "$line\n"; + $Last_Type = $Types{'OTHER'}; + return 1; + } + + if ($Words[0] =~ /^"/) { + print 'Last: ', $line, "\n"; + $Last_Type = $Types{'OTHER'}; + return 1; + } + + if ($Words[0] =~ /bond/) { + &bond($Words[0]); + return 1; + } + + if ($#Words >= 1) { + if ($Words[0] =~ /^(double|triple|front|back)$/ && + $Words[1] eq 'bond') { + my $w = shift @Words; + $Words[0] = $w . $Words[0]; + &bond($Words[0]); + return 1; + } + if ($Words[0] eq 'aromatic') { + my $temp = $Words[0]; + $Words[0] = $Words[1] ? $Words[1] : ''; + $Words[1] = $temp; + } + } + + if ($Words[0] =~ /ring|benz/) { + &ring($Words[0]); + return 1; + } + if ($Words[0] eq 'methyl') { + # left here as an example + $Words[0] = 'CH3'; + } +### main_line() + if ($Words[0] =~ /^[A-Z]/) { + &molecule(); + return 1; + } + if ($Words[0] eq 'left') { + my %left; # not used + $left{++$stack} = &fields(1, $#Words); + printf (("Last: [\n")); + return 1; + } + if ($Words[0] eq 'right') { + &bracket(); + $stack--; + return 1; + } + if ($Words[0] eq 'label') { # prints the vertex numbers in a ring + if ( exists $Labtype{$Words[1]} and + $Labtype{$Words[1]} =~ /^$Types{'RING'}/ ) { + my $v = substr($Labtype{$Words[1]}, 1, 1); + $Words[1] = '' unless $Words[1]; + foreach my $i ( 1..$v ) { + printf "\"\\s-3%d\\s0\" at 0.%d<%s.C,%s.V%d>\n", $i, $v + 2, + $Words[1], $Words[1], $i; + } + } else { + &error("$Words[1] is not a ring."); + } + return 1; + } + + if ( exists $Define{ $Words[0] } ) { + print $line, "\n"; + $Last_Type = $Types{'OTHER'}; + return 1; + } + return 1 unless $line; +# print STDERR "# $Line\n"; +# &error('This is not a chem command. To include a command for pic, ' . +# "add 'pic' as the first word to the command."); + print $line, "\n"; + $Last_Type = $Types{'OTHER'}; + 1; + } # main_line() + +} + +######################################################################## +# functions +######################################################################## + +########## +# atom(<string>) +# +sub atom { + # convert CH3 to atom(...) + my ($s) = @_; + my ($i, $n, $nsub, $cloc, $nsubc, @s); + if ($s eq "\"\"") { + return $s; + } + $n = length($s); + $nsub = $nsubc = 0; + $cloc = index($s, 'C'); + if (! defined($cloc) || $cloc < 0) { + $cloc = 0; + } + @s = split('', $s); + $i = 0; + foreach (@s) { + unless (/[A-Z]/) { + $nsub++; + $nsubc++ if $i < $cloc; + $i++; + } + } + $s =~ s/([0-9]+\.[0-9]+)|([0-9]+)/\\s-3\\d$&\\u\\s+3/g; + if ($s =~ /([^0-9]\.)|(\.[^0-9])/) { # centered dot + $s =~ s/\./\\v#-.3m#.\\v#.3m#/g; + } + sprintf( "atom(\"%s\", %g, %g, %g, %g, %g, %g)", + $s, ($n - $nsub / 2) * $Params{'cwid'}, $Params{'textht'}, + ($cloc - $nsubc / 2 + 0.5) * $Params{'cwid'}, $Params{'crh'}, + $Params{'crw'}, $Params{'dav'} + ); +} # atom() + + +########## +# bond(<type>) +# +sub bond { + my ($type) = @_; + my ($i, $moiety, $from, $leng); + $moiety = ''; + for ($i = 1; $i <= $#Words; $i++) { + if ($Words[$i] eq ';') { + &error("a colon ';' must be followed by a space and a single word.") + if $i != $#Words - 1; + $moiety = $Words[$i + 1] if $#Words > $i; + $#Words = $i - 1; + last; + } + } + $leng = $Params{'db'}; # bond length + $from = ''; + for ($Word_Count = 1; $Word_Count <= $#Words; ) { + if ($Words[$Word_Count] =~ + /(\+|-)?\d+|up|down|right|left|ne|se|nw|sw/) { + $Dir = &cvtdir($Dir); + } elsif ($Words[$Word_Count] =~ /^leng/) { + $leng = $Words[$Word_Count + 1] if $#Words > $Word_Count; + $Word_Count += 2; + } elsif ($Words[$Word_Count] eq 'to') { + $leng = 0; + $from = &fields($Word_Count, $#Words); + last; + } elsif ($Words[$Word_Count] eq 'from') { + $from = &dofrom(); + last; + } elsif ($Words[$Word_Count] =~ /^#/) { + $Word_Count = $#Words + 1; + last; + } else { + $from = &fields($Word_Count, $#Words); + last; + } + } +### bond() + if ($from =~ /( to )|^to/) { # said "from ... to ...", so zap length + $leng = 0; + } elsif (! $from) { # no from given at all + $from = 'from Last.' . &leave($Last_Type, $Dir) . ' ' . + &fields($Word_Count, $#Words); + } + printf "Last: %s(%g, %g, %s)\n", $type, $leng, $Dir, $from; + $Last_Type = $Types{'BOND'}; + $Labtype{$Last_Name} = $Last_Type if $Last_Name; + if ($moiety) { + @Words = ($moiety); + &molecule(); + } +} # bond() + + +########## +# bracket() +# +sub bracket { + my $t; + printf (("]\n")); + if ($Words[1] && $Words[1] eq ')') { + $t = 'spline'; + } else { + $t = 'line'; + } + printf "%s from last [].sw+(%g,0) to last [].sw to last [].nw to last " . + "[].nw+(%g,0)\n", $t, $Params{'dbrack'}, $Params{'dbrack'}; + printf "%s from last [].se-(%g,0) to last [].se to last [].ne to last " . + "[].ne-(%g,0)\n", $t, $Params{'dbrack'}, $Params{'dbrack'}; + if ($Words[2] && $Words[2] eq 'sub') { + printf "\" %s\" ljust at last [].se\n", &fields(3, $#Words); + } +} # bracket() + + +########## +# corner(<dir>) +# +# Return the corner name next to the given angle. +# +sub corner { + my ($d) = @_; + $Dc{ (45 * int(($d + 22.5) / 45)) % 360 }; +} # corner() + + +########## +# cvtdir(<dir>) +# +# Maps "[pointing] somewhere" to degrees. +# +sub cvtdir { + my ($d) = @_; + if ($Words[$Word_Count] eq 'pointing') { + $Word_Count++; + } + if ($Words[$Word_Count] =~ /^[+\\-]?\d+/) { + return ( $Words[$Word_Count++] % 360 ); + } elsif ($Words[$Word_Count] =~ /left|right|up|down|ne|nw|se|sw/) { + return ( $Dc{$Words[$Word_Count++]} % 360 ); + } else { + $Word_Count++; + return $d; + } +} # cvtdir() + + +########## +# dblring(<v>) +# +sub dblring { + my ($v) = @_; + my ($d, $v1, $v2); + # should canonicalize to i,i+1 mod v + $d = $Words[$Word_Count]; + for ($Word_Count++; $Word_Count <= $#Words && + $Words[$Word_Count] =~ /^[1-9]/; $Word_Count++) { + $v1 = substr($Words[$Word_Count], 0, 1); + $v2 = substr($Words[$Word_Count], 2, 1); + if ($v2 == $v1 + 1 || $v1 == $v && $v2 == 1) { # e.g., 2,3 or 5,1 + $Dbl{$v1} = $d; + } elsif ($v1 == $v2 + 1 || $v2 == $v && $v1 == 1) { # e.g., 3,2 or 1,5 + $Dbl{$v2} = $d; + } else { + &error(sprintf("weird %s bond in\n\t%s", $d, $_)); + } + } +} # dblring() + + +########## +# dofrom() +# +sub dofrom { + my $n; + $Word_Count++; # skip "from" + $n = $Words[$Word_Count]; + if (defined $Labtype{$n}) { # "from Thing" => "from Thing.V.s" + return 'from ' . $n . '.' . &leave($Labtype{$n}, $Dir); + } + if ($n =~ /^\.[A-Z]/) { # "from .V" => "from Last.V.s" + return 'from Last' . $n . '.' . &corner($Dir); + } + if ($n =~ /^[A-Z][^.]*\.[A-Z][^.]*$/) { # "from X.V" => "from X.V.s" + return 'from ' . $n . '.' . &corner($Dir); + } + &fields($Word_Count - 1, $#Words); +} # dofrom() + + +########## +# error(<string>) +# +sub error { + my ($s) = @_; + printf STDERR "chem: error in %s on line %d: %s\n", + $File_Name, $Line_No, $s; +} # error() + + +########## +# fields(<n1>, <n2>) +# +sub fields { + my ($n1, $n2) = @_; + if ($n1 > $n2) { + return ''; + } + my $s = ''; + foreach my $i ($n1..$n2) { + if ($Words[$i] =~ /^#/) { + last; + } + $s = $s . $Words[$i] . ' '; + } + $s; +} # fields() + + +########## +# init() +# +sub init { + if ($First_Time) { + 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", + $Params{'lineht'}, $Params{'linewid'}; + $First_Time = 0; + } + printf "Last: 0,0\n"; + $Last_Type = $Types{'OTHER'}; + $Dir = 90; +} # init() + + +########## +# leave(<last>, <d>) +# +sub leave { + my ($last, $d) = @_; + my ($c, $c1); + # return vertex of $last in direction $d + if ( $last eq $Types{'BOND'} ) { + return 'end'; + } + $d %= 360; + if ( $last =~ /^$Types{'RING'}/ ) { + return &ringleave($last, $d); + } + if ( $last eq $Types{'MOL'} ) { + if ($d == 0 || $d == 180) { + $c = 'C'; + } elsif ($d > 0 && $d < 180) { + $c = 'R'; + } else { + $c = 'L'; + } + if (defined $Dc{$d}) { + $c1 = $Dc{$d}; + } else { + $c1 = &corner($d); + } + return sprintf('%s.%s', $c, $c1); + } + if ( $last eq $Types{'OTHER'} ) { + return &corner($d); + } + 'c'; +} # leave() + + +########## +# makering(<type>, <pt>, <v>) +# +sub makering { + my ($type, $pt, $v) = @_; + my ($i, $j, $a, $r, $rat, $fix, $c1, $c2); + if ($type =~ /flat/) { + $v = 6; + # vertices + ; + } + $r = $Params{'ringside'} / (2 * sin(pi / $v)); + printf "\tC: 0,0\n"; + for ($i = 0; $i <= $v + 1; $i++) { + $a = (($i - 1) / $v * 360 + $pt) / 57.29578; # 57. is $deg + printf "\tV%d: (%g,%g)\n", $i, $r * sin($a), $r * cos($a); + } + if ($type =~ /flat/) { + printf "\tV4: V5; V5: V6\n"; + $v = 5; + } + # sides + if ($Nput > 0) { + # hetero ... + for ($i = 1; $i <= $v; $i++) { + $c1 = $c2 = 0; + if ($Put{$i} ne '') { + printf "\tV%d: ellipse invis ht %g wid %g at V%d\n", + $i, $Params{'crh'}, $Params{'crw'}, $i; + printf "\t%s at V%d\n", $Put{$i}, $i; + $c1 = $Params{'cr'}; + } + $j = $i + 1; + if ($j > $v) { + $j = 1; + } +### makering() + if ($Put{$j} ne '') { + $c2 = $Params{'cr'}; + } + printf "\tline from V%d to V%d chop %g chop %g\n", $i, $j, $c1, $c2; + if ($Dbl{$i} ne '') { + # should check i<j + if ($type =~ /flat/ && $i == 3) { + $rat = 0.75; + $fix = 5; + } else { + $rat = 0.85; + $fix = 1.5; + } + if ($Put{$i} eq '') { + $c1 = 0; + } else { + $c1 = $Params{'cr'} / $fix; + } + if ($Put{$j} eq '') { + $c2 = 0; + } else { + $c2 = $Params{'cr'} / $fix; + } + printf "\tline from %g<C,V%d> to %g<C,V%d> chop %g chop %g\n", + $rat, $i, $rat, $j, $c1, $c2; + if ($Dbl{$i} eq 'triple') { + printf "\tline from %g<C,V%d> to %g<C,V%d> chop %g chop %g\n", + 2 - $rat, $i, 2 - $rat, $j, $c1, $c2; + } + } + } +### makering() + } else { + # regular + for ($i = 1; $i <= $v; $i++) { + $j = $i + 1; + if ($j > $v) { + $j = 1; + } + printf "\tline from V%d to V%d\n", $i, $j; + if ($Dbl{$i} ne '') { + # should check i<j + if ($type =~ /flat/ && $i == 3) { + $rat = 0.75; + } else { + $rat = 0.85; + } + printf "\tline from %g<C,V%d> to %g<C,V%d>\n", + $rat, $i, $rat, $j; + if ($Dbl{$i} eq 'triple') { + printf "\tline from %g<C,V%d> to %g<C,V%d>\n", + 2 - $rat, $i, 2 - $rat, $j; + } + } + } + } +### makering() + # punt on triple temporarily + # circle + if ($type =~ /benz/ || $Aromatic > 0) { + if ($type =~ /flat/) { + $r *= .4; + } else { + $r *= .5; + } + printf "\tcircle rad %g at 0,0\n", $r; + } +} # makering() + + +########## +# molecule() +# +sub molecule { + my ($n, $type); + if ($#Words >= 0) { + $n = $Words[0]; + if ($n eq 'BP') { + $Words[0] = "\"\" ht 0 wid 0"; + $type = $Types{'OTHER'}; + } else { + $Words[0] = &atom($n); + $type = $Types{'MOL'}; + } + } + $n =~ s/[^A-Za-z0-9]//g; # for stuff like C(OH3): zap non-alnum + if ($#Words < 1) { + printf "Last: %s: %s with .%s at Last.%s\n", + $n, join(' ', @Words), &leave($type, $Dir + 180), + &leave($Last_Type, $Dir); +### molecule() + } else { + if (! $Words[1]) { + printf "Last: %s: %s with .%s at Last.%s\n", + $n, join(' ', @Words), &leave($type, $Dir + 180), + &leave($Last_Type, $Dir); + } elsif ($#Words >= 1 and $Words[1] eq 'below') { + $Words[2] = '' if ! $Words[2]; + printf "Last: %s: %s with .n at %s.s\n", $n, $Words[0], $Words[2]; + } elsif ($#Words >= 1 and $Words[1] eq 'above') { + $Words[2] = '' if ! $Words[2]; + printf "Last: %s: %s with .s at %s.n\n", $n, $Words[0], $Words[2]; + } elsif ($#Words >= 2 and $Words[1] eq 'left' && $Words[2] eq 'of') { + $Words[3] = '' if ! $Words[3]; + printf "Last: %s: %s with .e at %s.w+(%g,0)\n", + $n, $Words[0], $Words[3], $Params{'dew'}; + } elsif ($#Words >= 2 and $Words[1] eq 'right' && $Words[2] eq 'of') { + $Words[3] = '' if ! $Words[3]; + printf "Last: %s: %s with .w at %s.e-(%g,0)\n", + $n, $Words[0], $Words[3], $Params{'dew'}; + } else { + printf "Last: %s: %s\n", $n, join(' ', @Words); + } + } + + $Last_Type = $type; + if ($Last_Name) { + # $Last_Type = ''; + $Labtype{$Last_Name} = $Last_Type; + } + $Labtype{$n} = $Last_Type; +} # molecule() + + +########## +# print_hash(<hash_or_ref>) +# +# print the elements of a hash or hash reference +# +sub print_hash { + my $hr; + my $n = scalar @_; + if ($n == 0) { + print STDERR "empty hash\n;"; + return 1; + } elsif ($n == 1) { + if (ref($_[0]) eq 'HASH') { + $hr = $_[0]; + } else { + warn 'print_hash(): the argument is not a hash or hash reference;'; + return 0; + } + } else { + if ($n % 2) { + warn 'print_hash(): the arguments are not a hash;'; + return 0; + } else { + my %h = @_; + $hr = \%h; + } + } + +### print_hash() + unless (%$hr) { + print STDERR "empty hash\n"; + return 1; + } + print STDERR "hash (ignore the ^ characters):\n"; + for my $k (sort keys %$hr) { + my $hk = $hr->{$k}; + print STDERR " $k => "; + if (defined $hk) { + print STDERR "^$hk^"; + } else { + print STDERR "undef"; + } + print STDERR "\n"; + } + + 1; +} # print_hash() + + +########## +# print_pe() +# +sub print_pe { + print ".PE\n"; +} # print_pe() + + +########## +# print_ps() +# +sub print_ps { + print ".PS\n"; +} # print_ps() + +########## +# putring(<v>) +# +sub putring { + # collect "put Mol at n" + my ($v) = @_; + my ($m, $mol, $n); + $Word_Count++; + $mol = $Words[$Word_Count++]; + if ($Words[$Word_Count] eq 'at') { + $Word_Count++; + } + $n = $Words[$Word_Count]; + if ($n !~ /^\d+$/) { + $n =~ s/(\d)+$/$1/; + $n = 0 if $n !~ /^\d+$/; + error('use single digit as argument for "put at"'); + } + if ($n >= 1 && $n <= $v) { + $m = $mol; + $m =~ s/[^A-Za-z0-9]//g; + $Put{$n} = $m . ':' . &atom($mol); + } elsif ($n == 0) { + error('argument of "put at" must be a single digit'); + } else { + error('argument of "put at" is too large'); + } + $Word_Count++; +} # putring() + + +########## +# ring(<type>) +# +sub ring { + my ($type) = @_; + my ($typeint, $pt, $verts, $i, $other, $fused, $withat); + $pt = 0; # points up by default + if ($type =~ /([1-8])$/) { + $verts = $1; + } elsif ($type =~ /flat/) { + $verts = 5; + } else { + $verts = 6; + } + $fused = $other = ''; + for ($i = 1; $i <= $verts; $i++) { + $Put{$i} = $Dbl{$i} = ''; + } + $Nput = $Aromatic = $withat = 0; + for ($Word_Count = 1; $Word_Count <= $#Words; ) { + if ($Words[$Word_Count] eq 'pointing') { + $pt = &cvtdir(0); + } elsif ($Words[$Word_Count] eq 'double' || + $Words[$Word_Count] eq 'triple') { + &dblring($verts); + } elsif ($Words[$Word_Count] =~ /arom/) { + $Aromatic++; + $Word_Count++; # handled later +### ring() + } elsif ($Words[$Word_Count] eq 'put') { + &putring($verts); + $Nput++; + } elsif ($Words[$Word_Count] =~ /^#/) { + $Word_Count = $#Words + 1; + last; + } else { + if ($Words[$Word_Count] eq 'with' || $Words[$Word_Count] eq 'at') { + $withat = 1; + } + $other = $other . ' ' . $Words[$Word_Count]; + $Word_Count++; + } + } + $typeint = $Types{'RING'} . $verts . $pt; # RING | verts | dir + if ($withat == 0) { + # join a ring to something + if ( $Last_Type =~ /^$Types{'RING'}/ ) { + # ring to ring + if (substr($typeint, 2) eq substr($Last_Type, 2)) { + # fails if not 6-sided + $fused = 'with .V6 at Last.V2'; + } + } + # if all else fails + $fused = sprintf('with .%s at Last.%s', + &leave($typeint, $Dir + 180), &leave($Last_Type, $Dir)); + } + printf "Last: [\n"; + &makering($type, $pt, $verts); + printf "] %s %s\n", $fused, $other; + $Last_Type = $typeint; + $Labtype{$Last_Name} = $Last_Type if $Last_Name; +} # ring() + + +########## +# ringleave(<last>, <d>) +# +sub ringleave { + my ($last, $d) = @_; + my ($rd, $verts); + # return vertex of ring in direction d + $verts = substr($last, 1, 1); + $rd = substr($last, 2); + sprintf('V%d.%s', int( (($d - $rd) % 360) / (360 / $verts)) + 1, + &corner($d)); +} # ringleave() + + +########## +# setparams(<scale>) +# +sub setparams { + my ($scale) = @_; + $Params{'lineht'} = $scale * 0.2; + $Params{'linewid'} = $scale * 0.2; + $Params{'textht'} = $scale * 0.16; + $Params{'db'} = $scale * 0.2; # bond length + $Params{'cwid'} = $scale * 0.12; # character width + $Params{'cr'} = $scale * 0.08; # rad of invis circles at ring vertices + $Params{'crh'} = $scale * 0.16; # ht of invis ellipse at ring vertices + $Params{'crw'} = $scale * 0.12; # wid + $Params{'dav'} = $scale * 0.015; # vertical shift up for atoms in atom macro + $Params{'dew'} = $scale * 0.02; # east-west shift for left of/right of + $Params{'ringside'} = $scale * 0.3; # side of all rings + $Params{'dbrack'} = $scale * 0.1; # length of bottom of bracket +} # setparams() + + +sub usage { + print <<EOF; +usage: $chem [file ...] +usage: $chem { -h | --help | -v | --version } + +$chem is a groff preprocessor for producing chemical structure +diagrams. It produces input for the $makevar{'G'}pic preprocessor. If +no file operands are given, or if file is "-", the standard input stream +is read. + +Options: + -h, --help Display this message and exit. + -v, --version Display version information and exit. +EOF +} + + +sub version { + print <<EOF; +$chem (groff $groff_version) $chem_version +$copyright +License GPLv2: GNU GPL version 2 +<https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html> +This is free software: you are free to change and redistribute it. +There is NO WARRANTY, to the extent permitted by law. +EOF +} + +1; + +# Local Variables: +# fill-column: 72 +# mode: CPerl +# End: +# vim: set cindent noexpandtab shiftwidth=2 softtabstop=2 textwidth=72: diff --git a/contrib/chem/examples/122/README.txt b/contrib/chem/examples/122/README.txt new file mode 100644 index 0000000..6f3809b --- /dev/null +++ b/contrib/chem/examples/122/README.txt @@ -0,0 +1,57 @@ +This directory contains the examples for the 'chem' language written +in the book: + + Computing Science Technical Report No. 122 + CHEM - A Program for Typesetting Chemical Diagrams: User Manual + by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan + +The book is available in the internet at +<http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +Many of the examples had to be fixed. Unfortunately, the 'chem' akw +version does not run on many of these programs. But the Perl version +of 'chem' works on all examples. + +Most examples do not use the modern chemical display. They have C +atoms added, whereas the modern method omits all C atoms and their +directly appended H atoms. + +The examples are named and sorted by the chapter where they are found +in the book. For example, the file 'ch4c_colon.chem' means a 'chem' +example in chapter 4; according to 'c', it is the third example in +this chapter; the name 'colon' is used to describe the context of the +example. + +You can view the graphical display of the examples by calling + + @g@chem <file> | groff -p ... + + +####### License + +Copyright (C) 2006-2020 Free Software Foundation, Inc. +Written by Bernd Warken <groff-bernd.warken-72@web.de>. + +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 (GPL) version 2 as +published by the Free Software Foundation. + +'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 this program. If not, see <http://www.gnu.org/licenses/>. + +The GPL2 license text is available in the internet at +<http://www.gnu.org/licenses/gpl-2.0.html>. + + +##### Editor settings + +Local Variables: +mode: text +End: diff --git a/contrib/chem/examples/122/ch2a_ethyl.chem b/contrib/chem/examples/122/ch2a_ethyl.chem new file mode 100644 index 0000000..089de73 --- /dev/null +++ b/contrib/chem/examples/122/ch2a_ethyl.chem @@ -0,0 +1,43 @@ +ch2a_ethyl.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + CH3 + bond + CH2 + bond + +# Local Variables: +# fill-column: 72 +# mode: Nroff +# End: +# vim: set textwidth=72: +.cend diff --git a/contrib/chem/examples/122/ch2b_benzene.chem b/contrib/chem/examples/122/ch2b_benzene.chem new file mode 100644 index 0000000..0af1c9f --- /dev/null +++ b/contrib/chem/examples/122/ch2b_benzene.chem @@ -0,0 +1,38 @@ +ch2b_benzene.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + benzene + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch2c_benzene_right.chem b/contrib/chem/examples/122/ch2c_benzene_right.chem new file mode 100644 index 0000000..d9f29b5 --- /dev/null +++ b/contrib/chem/examples/122/ch2c_benzene_right.chem @@ -0,0 +1,36 @@ +ch2c_benzene_right.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 'groff' is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + benzene pointing right # a rotated benzene ring + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4a_stick.chem b/contrib/chem/examples/122/ch4a_stick.chem new file mode 100644 index 0000000..f4caef3 --- /dev/null +++ b/contrib/chem/examples/122/ch4a_stick.chem @@ -0,0 +1,45 @@ +ch4a_stick.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + bond right + bond 60 + bond 120 + bond 60 + bond 120 + bond down + +# Local Variables: +# fill-column: 72 +# mode: Nroff +# End: +# vim: set textwidth=72: +.cend diff --git a/contrib/chem/examples/122/ch4b_methyl_acetate.chem b/contrib/chem/examples/122/ch4b_methyl_acetate.chem new file mode 100644 index 0000000..31625a3 --- /dev/null +++ b/contrib/chem/examples/122/ch4b_methyl_acetate.chem @@ -0,0 +1,47 @@ +ch4b_methyl_acetate.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +CH3 # the 3 is automatically turned into a subscript +bond # the implicit direction is right + # implicit connection is to right side of CH3 +C +double bond 30 # by default, from the substituent C +O +bond 120 from C # must be "from C"; otherwise would leave from O +O +bond right +CH3 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4c_colon.chem b/contrib/chem/examples/122/ch4c_colon.chem new file mode 100644 index 0000000..5e42f6b --- /dev/null +++ b/contrib/chem/examples/122/ch4c_colon.chem @@ -0,0 +1,42 @@ +ch4c_colon.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + CH3 + bond ; C + double bond 30 ; O + bond 120 from C ; O + bond right ; CH3 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4d_HCl.H2O.chem b/contrib/chem/examples/122/ch4d_HCl.H2O.chem new file mode 100644 index 0000000..b6ac99d --- /dev/null +++ b/contrib/chem/examples/122/ch4d_HCl.H2O.chem @@ -0,0 +1,38 @@ +ch4d_HCl.H2O.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + HCl.H2O + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4e_CaSO4.2H2O.chem b/contrib/chem/examples/122/ch4e_CaSO4.2H2O.chem new file mode 100644 index 0000000..b2f8bc0 --- /dev/null +++ b/contrib/chem/examples/122/ch4e_CaSO4.2H2O.chem @@ -0,0 +1,38 @@ +ch4e_CaSO4.2H2O.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + CaSO4.2H2O + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4f_C.chem b/contrib/chem/examples/122/ch4f_C.chem new file mode 100644 index 0000000..d54461f --- /dev/null +++ b/contrib/chem/examples/122/ch4f_C.chem @@ -0,0 +1,48 @@ +ch4f_C.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + bond ; C # 1st definition of C + bond up from C + bond down from C + bond right from C ; C # 2nd definition of C + bond up from C + bond down from C + bond right from C ; C # 3rd definition of C + bond up from C + bond down from C + bond right from C + + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4g_BP.chem b/contrib/chem/examples/122/ch4g_BP.chem new file mode 100644 index 0000000..9c6af4b --- /dev/null +++ b/contrib/chem/examples/122/ch4g_BP.chem @@ -0,0 +1,48 @@ +ch4g_BP.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +# this is the isopropyl group + bond 120 ; BP # BP is right end of this bond + bond -120 from BP + bond right from BP ; C + front bond up ; CH3 + back bond down from C ; D + bond right from C ; BP +# redefine BP to mean the center carbon of this t-butyl group + bond up from BP + bond right from BP + bond down from BP + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4h_methacrylate.chem b/contrib/chem/examples/122/ch4h_methacrylate.chem new file mode 100644 index 0000000..8300d25 --- /dev/null +++ b/contrib/chem/examples/122/ch4h_methacrylate.chem @@ -0,0 +1,65 @@ +ch4h_methacrylate.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + bond dotted + bond right ; BP + bond up from BP ; C + double bond -60 from C ; O + bond 60 length .1 from C ; OCH3 + bond down from BP ; CH3 +# begin second segment of polymer + bond right length .5 from BP ; BP + bond up length .1 from BP ; H + bond down length .1 from BP ; H +# begin third segment of polymer + bond right length .5 from BP ; BP + bond up from BP ; C + double bond -60 from C ; O + bond 60 length .1 from C ; OCH3 + bond down from BP ; CH3 +# begin fourth segment of polymer + bond right length .5 from BP ; BP + bond up length .1 from BP ; H + bond down length .1 from BP ; H +# begin fifth segment of polymer + bond right length .5 from BP ; BP + bond up from BP ; C + double bond -60 from C ; O + bond 60 length .1 from C ; OCH3 + bond down from BP ; CH3 + bond right from BP + bond dotted + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4i_cyclo.chem b/contrib/chem/examples/122/ch4i_cyclo.chem new file mode 100644 index 0000000..866e6f7 --- /dev/null +++ b/contrib/chem/examples/122/ch4i_cyclo.chem @@ -0,0 +1,45 @@ +ch4i_cyclo.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +R3: ring3 +R4: ring4 at R3 + (.75,0) +R5: ring5 at R4 + (.75,0) +R6: ring6 at R5 + (.75,0) +B: benzene at R6 + (.75,0) +R7: ring7 at B + (.75,0) +R8: ring8 at R7 + (.75,0) + + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4j_ring4.chem b/contrib/chem/examples/122/ch4j_ring4.chem new file mode 100644 index 0000000..9caf718 --- /dev/null +++ b/contrib/chem/examples/122/ch4j_ring4.chem @@ -0,0 +1,40 @@ +ch4j_ring4.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + ring4 pointing 45 + +# Local Variables: +# fill-column: 72 +# mode: Nroff +# End: +# vim: set textwidth=72: +.cend diff --git a/contrib/chem/examples/122/ch4k_ring3.chem b/contrib/chem/examples/122/ch4k_ring3.chem new file mode 100644 index 0000000..2a2d856 --- /dev/null +++ b/contrib/chem/examples/122/ch4k_ring3.chem @@ -0,0 +1,40 @@ +ch4k_ring3.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +R: ring3 + back bond 120 from R.V2 ; C2H5 + front bond -120 from R.V3 ; HO + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4l_vertex.chem b/contrib/chem/examples/122/ch4l_vertex.chem new file mode 100644 index 0000000..d9fcb07 --- /dev/null +++ b/contrib/chem/examples/122/ch4l_vertex.chem @@ -0,0 +1,45 @@ +ch4l_vertex.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +R: benzene pointing right + bond left from R.V4 ; HO + bond -150 from R.V3 ; CH3O + bond right from R.V1 ; C + double bond up from C ; O + bond right from C ; N + bond 45 ; C2H5 + bond 135 from N ; C2H5 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4m_double.chem b/contrib/chem/examples/122/ch4m_double.chem new file mode 100644 index 0000000..c5b1373 --- /dev/null +++ b/contrib/chem/examples/122/ch4m_double.chem @@ -0,0 +1,38 @@ +ch4m_double.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + ring double 1,2 3,4 5,6 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4n_triple.chem b/contrib/chem/examples/122/ch4n_triple.chem new file mode 100644 index 0000000..5766f85 --- /dev/null +++ b/contrib/chem/examples/122/ch4n_triple.chem @@ -0,0 +1,38 @@ +ch4n_triple.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + ring8 triple 3,4 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4o_aromatic.chem b/contrib/chem/examples/122/ch4o_aromatic.chem new file mode 100644 index 0000000..aa303c7 --- /dev/null +++ b/contrib/chem/examples/122/ch4o_aromatic.chem @@ -0,0 +1,37 @@ +ch4o_aromatic.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 'groff' is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +R: aromatic ring7 + "+" at R + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4p_cholestanol.chem b/contrib/chem/examples/122/ch4p_cholestanol.chem new file mode 100644 index 0000000..e292bea --- /dev/null +++ b/contrib/chem/examples/122/ch4p_cholestanol.chem @@ -0,0 +1,60 @@ +ch4p_cholestanol.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +R1: ring6 + "R1" at R1 # this puts a label at R1 + front bond -120 from R1.V5 ; HO + # the following line says "fuse the next six- + # membered ring with its 6th vertex joining + # the second vertex of R1" +R2: ring6 with .V6 at R1.V2 + front bond up from R2.V6 ; CH3 + back bond down from R2.V4 ; H + back bond down from R2.V1 ; H + front bond up from R2.V2 ; H +R3: ring6 with .V4 at R2.V2 +R4: flatring with .V5 at R3.V2 + front bond up from R4.V5 ; CH3 + back bond down from R4.V4 ; H # this is the alkyl chain + bond up from R4.V1 ; BP + bond -60 from BP + bond 60 from BP + bond 120 + bond 60 + bond 120 ; BP + bond down from BP + bond 60 from BP + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4q_rings.chem b/contrib/chem/examples/122/ch4q_rings.chem new file mode 100644 index 0000000..bafdd92 --- /dev/null +++ b/contrib/chem/examples/122/ch4q_rings.chem @@ -0,0 +1,46 @@ +ch4q_rings.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +R3: ring3 +R4: ring4 pointing 45 with .V1 at R3.V2 +R5: ring5 pointing down with .V4 at R4.V2 +R6: ring6 pointing 54 with .V6 at R5.V5 + # the following lines specify the labels inside the rings + "3" at R3 + "4" at R4 + "5" at R5 + "6" at R6 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4r_spiro.chem b/contrib/chem/examples/122/ch4r_spiro.chem new file mode 100644 index 0000000..24ec050 --- /dev/null +++ b/contrib/chem/examples/122/ch4r_spiro.chem @@ -0,0 +1,42 @@ +ch4r_spiro.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +R1: ring6 +R2: ring6 with .V1 at R1.V4 +R3: ring5 with .V5 at R2.V3 + back bond 60 from R3.V2 ; OH + front bond 150 from R3.V3 ; OH + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4s_heteroatoms.chem b/contrib/chem/examples/122/ch4s_heteroatoms.chem new file mode 100644 index 0000000..7dc8ba7 --- /dev/null +++ b/contrib/chem/examples/122/ch4s_heteroatoms.chem @@ -0,0 +1,38 @@ +ch4s_heteroatoms.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + ring put N at 2 put S at 4 double 2,3 4,5 6,1 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4t_polycyclic.chem b/contrib/chem/examples/122/ch4t_polycyclic.chem new file mode 100644 index 0000000..fc6b580 --- /dev/null +++ b/contrib/chem/examples/122/ch4t_polycyclic.chem @@ -0,0 +1,49 @@ +ch4t_polycyclic.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +R1: benzene pointing right + bond 30 from R1.V6 ; Br +R2: benzene pointing right with .V5 at R1.V1 +R3: benzene pointing right with .V1 at R2.V3 + bond 150 from R3.V2 ; CO2H +R4: benzene pointing right with .V1 at R1.V3 +# next line names bond B1 so we can refer to its end +B1: bond left from R4.V4 + ring6 put N at 4 double 2,3 4,5 6,1 with .V3 at B1.end +B2: bond right from R2.V1 +R5: benzene with .V5 at B2.end + ring6 put N at 4 double 1,2 3,4 with .V5 at R5.V3 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4u_nicotine.chem b/contrib/chem/examples/122/ch4u_nicotine.chem new file mode 100644 index 0000000..d38a7c8 --- /dev/null +++ b/contrib/chem/examples/122/ch4u_nicotine.chem @@ -0,0 +1,42 @@ +ch4u_nicotine.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + benzene put N at 4 + bond right + ring5 pointing down put N at 1 + bond down from .N ; CH3 # or .V1 + + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4v_histidine.chem b/contrib/chem/examples/122/ch4v_histidine.chem new file mode 100644 index 0000000..33a4e9d --- /dev/null +++ b/contrib/chem/examples/122/ch4v_histidine.chem @@ -0,0 +1,44 @@ +ch4v_histidine.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +R1: flatring pointing down put N at 2 put N at 5 double 1,2 3,4 + H right of R1.V5 + bond right from R1.V4 ; CH2 + bond right ; C + bond up from C ; H + bond down from C ; NH2 + bond right from C ; CO2H + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4w_lsd.chem b/contrib/chem/examples/122/ch4w_lsd.chem new file mode 100644 index 0000000..aa68b00 --- /dev/null +++ b/contrib/chem/examples/122/ch4w_lsd.chem @@ -0,0 +1,50 @@ +ch4w_lsd.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +B: benzene pointing right +F: flatring pointing left put N at 5 double 3,4 with .V1 at B.V2 + H below F.N +R: ring pointing right with .V4 at B.V6 + front bond right from R.V6 ; H +W: ring pointing right with .V2 at R.V6 put N at 1 double 3,4 + bond right from W.N ; CH3 + back bond -60 from W.V5 ; H + bond up from W.V5 ; C + double bond up from C ; O + bond right from C ; N + bond 45 from N ; C2H5 + bond 135 from N ; C2H5 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4x_anisole.chem b/contrib/chem/examples/122/ch4x_anisole.chem new file mode 100644 index 0000000..ec78417 --- /dev/null +++ b/contrib/chem/examples/122/ch4x_anisole.chem @@ -0,0 +1,42 @@ +ch4x_anisole.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +R1: benzene + bond down from R1.V4 ; OCH3 +R2: benzene at R1 + (1.5,0) + bond down from R2.V4 ; O + CH3 right of O + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4y_reserpine.chem b/contrib/chem/examples/122/ch4y_reserpine.chem new file mode 100644 index 0000000..fb5d1ca --- /dev/null +++ b/contrib/chem/examples/122/ch4y_reserpine.chem @@ -0,0 +1,62 @@ +ch4y_reserpine.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. +# Some corrections were added. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + CH3O + bond 60 +R1: benzene +R2: aromatic flatring5 pointing down put N at 1 with .V3 at R1.V2 + H below R2.V1 +R3: ring put N at 3 with .V5 at R2.V5 +R4: ring put N at 1 with .V1 at R3.V3 + back bond -120 from R4.V4 ; H + back bond 60 from R4.V3 ; H +R5: ring with .V1 at R4.V3 + bond -120 ; C + double bond down from C ; O + CH3O left of C + back bond 60 from R5.V3 ; H + back bond down from R5.V4 ; O + CH3 right of O + bond 120 from R5.V3 ; O + bond right length .1 from O ; C + double bond down ; O + bond right length .1 from C +B: benzene pointing right + bond 30 from B.V6 ; OCH3 + bond right from B.V1 ; OCH3 + bond 150 from B.V2 ; OCH3 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch4z1_eqn_glutamic.chem b/contrib/chem/examples/122/ch4z1_eqn_glutamic.chem new file mode 100644 index 0000000..6cecd7c --- /dev/null +++ b/contrib/chem/examples/122/ch4z1_eqn_glutamic.chem @@ -0,0 +1,78 @@ +ch4z1_eqn_glutamic.chem: +.br +.EQ +delim $$ +.EN +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. +# Some corrections were added. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +# a left bracket + bond right length .1 ; BP + bond up length .3 + bond right length .1 + bond down length .3 from BP + bond right length .1 +# this is the mainchain amide structure + bond right length .1 from BP ; NH + bond right ; CH +# label the CH with an alpha, intended for eqn. +# this line says "put the north edge of the alpha at the +# south edge of the CH" + "$alpha$" with .n at CH.s + bond right from CH ; C + double bond up from C ; O + bond right length .1 from C ; BP +# a right bracket + bond up length .3 + bond left length .1 + bond right length .1 from BP + bond down length .3 from BP ; BP + bond left length .1 +# label the degree of polymerization + "$n$" with .w at BP.se +# this is the sidechain + bond up from CH ; CH2 + "$beta$" with .e at CH2.w + bond up from CH2 ; CH2 + "$gamma$" with .e at CH2.w + bond up from CH2 ; C +# this is the benzyl ester part + double bond -60 from C ; O + bond 60 from C ; O + bond right ; CH2C6H5 + +# Local Variables: +# mode: Nroff +# End: +.cend +.EQ +delim off +.EN diff --git a/contrib/chem/examples/122/ch4z2_text.chem b/contrib/chem/examples/122/ch4z2_text.chem new file mode 100644 index 0000000..2000636 --- /dev/null +++ b/contrib/chem/examples/122/ch4z2_text.chem @@ -0,0 +1,53 @@ +ch4z2_text.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + bond 120 dotted + bond 120 length .3 ; BP + back bond -120 length .25 from BP ; H + front bond 120 length .25 from BP ; CH3 + bond 60 length .5 from BP ; BP + bond -60 length .25 from BP ; H +# note the pic move command to position the text + move left .35 ; "(ANTI)" + front bond 60 length .25 from BP ; H +# another positioning of text + move right .35 ; "(SYN)" + bond 120 length .4 from BP ; BP + back bond -120 length .25 from BP ; H + front bond 120 length .25 from BP ; CH3 + bond 60 length .5 from BP + bond 60 dotted + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch5a_size.chem b/contrib/chem/examples/122/ch5a_size.chem new file mode 100644 index 0000000..d4eb33f --- /dev/null +++ b/contrib/chem/examples/122/ch5a_size.chem @@ -0,0 +1,45 @@ +ch5a_size.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +.ps 14 +size 16 +R: ring6 put O at 1 put C at 2 put O at 3 put C at 4 put O at 5 put C at 6 + double bond 60 from R.V2 ; NH + double bond down from R.V4 ; NH + double bond -60 from R.V6 ; HN +size 10 # if you are doing more than one +.ps 10 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch6a_pic.chem b/contrib/chem/examples/122/ch6a_pic.chem new file mode 100644 index 0000000..ad6dea6 --- /dev/null +++ b/contrib/chem/examples/122/ch6a_pic.chem @@ -0,0 +1,43 @@ +ch6a_pic.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +R: ring double 2,3 + line from R.V6 to R.C + line from R.C to R.V4 + X1: 1/2 <R.V5,R.C> + X2: 1/2 <R.C,R.V2> + bond from X1 to X2 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/ch6b_dna.chem b/contrib/chem/examples/122/ch6b_dna.chem new file mode 100644 index 0000000..00abbba --- /dev/null +++ b/contrib/chem/examples/122/ch6b_dna.chem @@ -0,0 +1,59 @@ +ch6b_dna.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +P: [ +R1: flatring pointing up put N at 1 put N at 4 double 5,1 + bond -135 from R1.V4 ; BP + "deoxyribose" rjust with .e at BP.w +R2: ring6 put N at 2 put N at 4 double 1,2 3,4 5,6 with .V6 at R1.V2 + pic Conn: R2.V2.ne #because naming is too restricted in pic + bond up from R2.V1 ; N + bond -60 from N ; H + bond 60 from N ; H +] + # thymine +Q: [ +R3: ring6 put N at 3 put N at 5 double 1,2 + bond up from R3.V1 ; CH3 + bond 120 from R3.V3 ; BP + "deoxyribose" ljust with .w at BP.e + double bond down from R3.V4 ; O + double bond -60 from R3.V6 ; O + bond -120 from R3.V5 ; H +] with .O at P.H + (.3,.3) + bond from Q.O.sw to P.H.ne dotted + bond from Q.H.sw to P.Conn dotted + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/chAa_polymer.chem b/contrib/chem/examples/122/chAa_polymer.chem new file mode 100644 index 0000000..3293454 --- /dev/null +++ b/contrib/chem/examples/122/chAa_polymer.chem @@ -0,0 +1,72 @@ +chAa_polymer.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +# epoxy based on the m-phenyldiamine cured bisphenol-A + size 8 + bond dotted + bond ; N + bond ; CH2 + bond down from N +R1: benzene + bond 120 length .1 from R1.V3 ; N + bond right length .1 from N + bond down length .1 from N +# back to the CH2 + bond right from CH2 ; CH + bond down from CH ; OH + bond right from CH ; CH2 + bond right ; O + bond right + benzene pointing right + bond right ; C + bond up from C ; CH3 + bond down from C ; CH3 + bond right from C + benzene pointing right + bond right ; O + bond right from O ; CH2 + bond right ; CH + bond down from CH ; OH + bond right from CH ; CH2 + bond right ; N + bond right from N + bond dotted + bond down from N +R2: benzene + bond 120 length .1 from R2.V3 ; N + bond right length .1 from N + bond down length .1 from N + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/chAb_vinyl_chloro.chem b/contrib/chem/examples/122/chAb_vinyl_chloro.chem new file mode 100644 index 0000000..dff97fc --- /dev/null +++ b/contrib/chem/examples/122/chAb_vinyl_chloro.chem @@ -0,0 +1,62 @@ +chAb_vinyl_chloro.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + Cl + bond 120 length .25 ; BP + bond 60 length .25 from BP ; Cl +B1: double bond down length .3 from BP + bond 120 length .35 ; BP +# now comes the ring +R1: ring6 double 1,2 3,4 5,6 with .V6 at BP + bond up length .1 from R1.V1 ; H + bond 60 length .1 from R1.V2 ; H + bond 120 from R1.V3 ; O + bond 60 from O ; C + double bond up from C ; O + bond 120 from C +# continue decorating the ring + bond down length .1 from R1.V4 ; H + bond -120 length .1 from R1.V5 ; H +# now go back and do the left hand ring + bond -120 length .35 from B1.end ; BP +R2: ring6 double 1,2 3,4 5,6 with .V2 at BP + bond up length .1 from R2.V1 ; H + bond -60 length .1 from R2.V6 ; H + bond -120 from R2.V5 ; O + bond -60 from O + bond down length .1 from R2.V4 ; H + bond 120 length .1 from R2.V3 ; H + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/chAc_morphine.chem b/contrib/chem/examples/122/chAc_morphine.chem new file mode 100644 index 0000000..c9fbf10 --- /dev/null +++ b/contrib/chem/examples/122/chAc_morphine.chem @@ -0,0 +1,52 @@ +chAc_morphine.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +R1: ring6 double 1,2 + bond -60 from R1.V6 ; HO +R2: ring6 with .V1 at R1.V3 + bond 60 from R2.V2 ; N + bond right from N ; CH3 +R3: benzene with .V1 at R2.V5 + bond -120 from R3.V5 ; HO +# this is the furan ring + bond -135 length .33 from R1.V5 ; O + bond -45 length .33 from R3.V6 +# this is the odd ring + bond up length .1 from N ; BP +B1: bond up length .33 from R1.V4 + bond to BP + + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/chAd_chlorophyll.chem b/contrib/chem/examples/122/chAd_chlorophyll.chem new file mode 100644 index 0000000..e2acb22 --- /dev/null +++ b/contrib/chem/examples/122/chAd_chlorophyll.chem @@ -0,0 +1,69 @@ +chAd_chlorophyll.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + Mg + bond 45 ; N +R1: ring5 pointing up put N at 4 double 1,2 4,5 with .V4 at N + bond up from R1.V1 ; CH3 + bond right from R1.V2 ; CH2CH3 + bond 135 from Mg ; N +R2: ring5 pointing down put N at 3 double 1,2 4,5 with .V3 at N + bond right from R2.V5 ; CH3 + bond 225 from Mg ; N +R3: ring5 pointing down put N at 4 double 3,4 with .V4 at N + bond -45 from Mg ; N +R4: ring5 pointing up put N at 3 double 1,5 with .V3 at N + bond left from R4.V5 ; H3C + bond up from R4.V1 ; CH + double bond right length .1 from CH ; CH2 + double bond 150 length .3 from R1.V3 + bond to R2.V4 +R5: ring5 pointing 72 with .V5 at R2.V2 + double bond 135 from R5.V2 ; O + bond down from R5.V3 ; C + double bond left length .1 from C ; O + bond down from C ; O + CH3 left of O + double bond -25 from R5.V4 + bond down from R3.V1 ; CH2 + CH2 left of CH2 + bond left ; C + double bond -45 ; O + bond -135 from C ; C20H39O + bond left from R3.V2 ; H3C + double bond -150 length .3 from R4.V4 + bond to R3.V3 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/chAe_chair.chem b/contrib/chem/examples/122/chAe_chair.chem new file mode 100644 index 0000000..27b046a --- /dev/null +++ b/contrib/chem/examples/122/chAe_chair.chem @@ -0,0 +1,49 @@ +chAe_chair.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +pic define chair { [ + V1: bond 120 length .25 + V2: bond right length .35 + V3: bond 150 length .35 + V4: bond -60 length .25 + V5: bond left length .35 + V6: bond to V1.start +pic ] } +R1: chair +R2: chair with .V1 at R1.V4.start +bond 60 from R2.V4.start ; CH3 +bond down from R2.V4.start ; OH + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/chAf_arrow.chem b/contrib/chem/examples/122/chAf_arrow.chem new file mode 100644 index 0000000..f135ecb --- /dev/null +++ b/contrib/chem/examples/122/chAf_arrow.chem @@ -0,0 +1,68 @@ +chAf_arrow.chem: +.br +.EQ +delim $$ +.EN +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + + bond length .1 ; BP + bond up length .5 + bond right + bond down length .5 from BP + bond right + bond right from BP ; C + double bond up ; O + bond right from C + benzene pointing right + bond right ; C + double bond up from C ; O + bond right from C ; O + bond right ; CH2 +# this is the statement to make the arrow + line <- from CH2.s down + move down .1 ; "0.085" + CH2CH2CH2 right of CH2 + bond right ; O + bond right length .1 ; BP + bond up length .5 from BP + bond left + bond right length .1 from BP + bond down length .5 from BP ; BP + bond left + "$n$" with .w at BP.se + +# Local Variables: +# mode: Nroff +# End: +.cend +.EQ +delim off +.EN diff --git a/contrib/chem/examples/122/chAg_circle.chem b/contrib/chem/examples/122/chAg_circle.chem new file mode 100644 index 0000000..576c926 --- /dev/null +++ b/contrib/chem/examples/122/chAg_circle.chem @@ -0,0 +1,54 @@ +chAg_circle.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +bond 120 ; C +bond 60 ; C +bond up ; Cl +double bond 120 from C ; C +bond 60 ; C +bond 120 ; C +bond 60 ; C +bond up ; Cl +double bond 120 from C ; C +circle at C rad .08 +bond 60 from C ; C +bond 120 ; C +bond 60 ; C +double bond 120 ; C +bond down ; Cl +bond 60 from C ; C +bond 120 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/chAh_brackets.chem b/contrib/chem/examples/122/chAh_brackets.chem new file mode 100644 index 0000000..7605a38 --- /dev/null +++ b/contrib/chem/examples/122/chAh_brackets.chem @@ -0,0 +1,60 @@ +chAh_brackets.chem: +.br +.EQ +delim $$ +.EN +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# This file is part of 'chem', which is part of 'groff'. + +# 'groff' is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License (GPL) version 2 as +# published by the Free Software Foundation. + +# 'groff' is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +[ + bond right ; CH2 + bond 120 ; (CH2) + "$nothing sub n$" + bond 60 ; .CH2 +] +# now put the arrow in + move right .3 + arrow .5 + move right .3 +# begin second structure +[ + bond right ; CH. + bond 120 ; (CH2) + "$nothing sub n$" + bond 60 ; CH3 +] + +# Local Variables: +# mode: Nroff +# End: +.cend +.EQ +delim $$ +.EN diff --git a/contrib/chem/examples/122/chAi_poly_vinyl_chloride.chem b/contrib/chem/examples/122/chAi_poly_vinyl_chloride.chem new file mode 100644 index 0000000..e4539bb --- /dev/null +++ b/contrib/chem/examples/122/chAi_poly_vinyl_chloride.chem @@ -0,0 +1,141 @@ +chAi_poly_vinyl_chloride.chem: +.br +.ps -2 +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +db = .12 +cwid = .095 +A: [ + bond dotted + bond right ; CH + bond down ; Cl + bond right from CH ; CH2 + bond ; CH + bond down ; Cl + bond right from CH ; CH2 + bond ; C. + bond down ; Cl + bond right from C ; CH2 + bond ; CH2 + bond down ; Cl +] +" (6.13a)" ljust at A.e +arrow down .5 from A.s +[ + CH2 + double bond right ; CHCl +] with .w at last arrow.c +B: [ + bond dotted + bond right ; CH + bond down ; Cl + bond right from CH ; CH2 + bond ; CH + bond down ; Cl + bond right from CH ; CH2 + bond ; C + bond up ; Cl + bond down from C ; CH2 + bond ; CH2Cl + bond right from C ; CH2 + bond ; CH + bond down ; Cl + bond right from CH + bond dotted +] with .n at end of last arrow +" (6.13b)" ljust at B.e +C: [ + bond dotted + bond right ; CH + bond down ; Cl + bond right from CH ; CH2 + bond ; C. + bond down ; Cl + bond right from C ; CH2 + bond ; CH + bond down ; Cl + bond right from CH ; CH2 + bond ; CH2 + bond down ; Cl +] with .n at B.s - (0,.5) +" (6.14a)" ljust at C.e +arrow down .3 from C.s +[ + CH2 + double bond right + CHCl +] with .w at last arrow.s +arrow down .3 from last arrow.s + +D: [ + bond dotted + bond right ; CH + bond down ; Cl + bond right from CH ; CH2 + bond ; C + bond up ; Cl + bond down from C ; CH2 + bond ; CHCl + bond ; CH2 + bond ; CH2Cl + bond right from C ; CH2 + bond ; CH + bond down ; Cl + bond right from CH ; CH2 + bond ; CH + bond down ; Cl + bond right from CH + bond dotted +] with .n at last arrow.s +" (6.14b)" ljust at D.e +E: [ + bond dotted + bond ; CH + bond down ; Cl + bond right from CH ; CH2 + bond ; CH + bond down ; Cl + bond right from CH ; CH2 + bond ; CH + bond down ; Cl + bond right from CH ; CH2 + bond ; CH + bond down ; Cl +] with .e at B.w - (.5,0) + +arrow from E.ne to A.sw +arrow from E.se to C.nw + +# Local Variables: +# mode: Nroff +# End: +.cend +.ps +2 diff --git a/contrib/chem/examples/122/chBa_jump.chem b/contrib/chem/examples/122/chBa_jump.chem new file mode 100644 index 0000000..cd40a3a --- /dev/null +++ b/contrib/chem/examples/122/chBa_jump.chem @@ -0,0 +1,41 @@ +chBa_jump.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +SiO2 # name = SiO2 +move right 1 +CH3CH2NH2.HCl # name = CH3CH2NH2HCl + + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/chBb_bonds.chem b/contrib/chem/examples/122/chBb_bonds.chem new file mode 100644 index 0000000..bc29895 --- /dev/null +++ b/contrib/chem/examples/122/chBb_bonds.chem @@ -0,0 +1,42 @@ +chBb_bonds.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +C +frontbond -170 from C ; H +backbond 10 from C ; CO2H +bond left length .15 from C ; H2N +bond right from C ; CH3 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/122/chBc_rings.chem b/contrib/chem/examples/122/chBc_rings.chem new file mode 100644 index 0000000..950cd0b --- /dev/null +++ b/contrib/chem/examples/122/chBc_rings.chem @@ -0,0 +1,43 @@ +chBc_rings.chem: +.br +.cstart + +# Example file for 'chem': + +# This originates from Computing Science Technical Report No. 122 +# CHEM - A Program for Typesetting Chemical Diagrams: User Manual +# by Jon L. Bentley, Lynn W. Jelinski, Brian W. Kernighan +# <http://cm.bell-labs.com/cm/cs/cstr/122.ps.gz>. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +######################################################################## + +R1: benzene + bond -120 from R1.V5 ; CH3O +R2: ring4 pointing 45 with .V4 at R1.V2 +R3: aromatic ring6 put N at 4 put S at 2 at R2 + (.75,0) +R4: ring5 pointing left at R3 + (.75,0) + label R4 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/README.txt b/contrib/chem/examples/README.txt new file mode 100644 index 0000000..6786705 --- /dev/null +++ b/contrib/chem/examples/README.txt @@ -0,0 +1,47 @@ +This directory contains examples for the 'chem' language. + +You can view the graphical display of the examples by calling + + @g@chem <file> | groff -p ... + +On the displays, you can see rings consisting of several lines and +bonds (lines). All points on rings and bonds that do not have a +notation mean a C atom (carbon) filled with H atoms (hydrogen) such +that the valence of 4 is satisfied. + +For example, suppose you have just a single line without any +characters. That means a bond. It has two points, one at each end of +the line. So each of these points stands for a C atom, the bond +itself connects these 2 C atoms. To fulfill the valence of 4, each +points has to carry additionally 3 H atoms. So the single empty bond +stands for CH3-CH3, though this combination doesn't make much sense +chemically. + + +####### License + +Copyright (C) 2006-2020 Free Software Foundation, Inc. +Written by Bernd Warken <groff-bernd.warken-72@web.de>. + +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 3 of the License, 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. + +The GPL2 license text is available in the internet at +<http://www.gnu.org/licenses/gpl-2.0.html>. + + +##### Editor settings +Local Variables: +fill-column: 72 +mode: text +End: +vim: set textwidth=72: diff --git a/contrib/chem/examples/atp.chem b/contrib/chem/examples/atp.chem new file mode 100644 index 0000000..738c4da --- /dev/null +++ b/contrib/chem/examples/atp.chem @@ -0,0 +1,58 @@ +atp.chem: +.cstart + +# Example file for 'chem': +# ATP or C10_H16_N5_O13_P3 or +# [[[5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy- +# phosphoryl]oxy-hydroxy-phosphoryl]oxyphosphonic acid + +# Found at http://www.chemindustry.com/apps/chemicals. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. +# Written by Bernd Warken <groff-bernd.warken-72@web.de>. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +R1: ring5 pointing left double 1,2 3,4 put N at 2 put N at 5 +B: benzene put N at 2 with .V6 at R1.V3 with .V5 at R1.V4 + bond up ; NH2 + backbond 170 length .7 from R1.V5 +R2: ring5 pointing down with .V2 put O at 1 + bond down at R2.V2 ; H + bond down length .1 at R2.V3 ; H + bond up length .1 at R2.V3 ; OH + bond down length .1 at R2.V4 ; H + bond up length .1 at R2.V4 ; OH + frontbond 70 at R2.V5 + bond 110 ; O + bond right ; P + doublebond up ; O + bond down from P ; OH + bond right from P ; O + bond right ; P + doublebond up ; O + bond down from P ; OH + bond right from P ; O + bond right ; P + doublebond up ; O + bond down from P ; OH + bond right from P ; OH + +# Local Variables: +# fill-column: 72 +# mode: Nroff +# End: +# vim: set textwidth=72: +.cend diff --git a/contrib/chem/examples/cholesterin.chem b/contrib/chem/examples/cholesterin.chem new file mode 100644 index 0000000..12ac076 --- /dev/null +++ b/contrib/chem/examples/cholesterin.chem @@ -0,0 +1,47 @@ +cholesterin.chem: +.cstart + +# Example file for 'chem': +# Cholesterin or C27_H46O or +# 10,13-dimethyl-17-(6-methylheptan-2-yl)-2,3,4,5,6,9,11,12,14,15,16,17- +# dodecahydro-1H-cyclopenta[a]phenanthren-3-ol + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. +# Written by Bernd Warken <groff-bernd.warken-72@web.de>. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +R1: ring6 + bond -120 ; HO +R2: ring6 with .V5 at R1.V3 with .V6 at R1.V2 double 4,5 + bond up at R2.V6 +R3: ring6 with .V5 at R2.V1 with .V4 at R2.V2 +R4: flatring5 pointing up with .V4 at R3.V3 with .V5 at R3.V2 + bond up at R4.V5 + bond up at R4.V1 +B1: bond -60 + bond 60 at B1.start + bond 120 + bond 60 + bond 120 +B2: bond 60 + bond down at B2.start + +# Local Variables: +# fill-column: 72 +# mode: Nroff +# End: +# vim: set textwidth=72: +.cend diff --git a/contrib/chem/examples/ethamivan.chem b/contrib/chem/examples/ethamivan.chem new file mode 100644 index 0000000..a0a8aa2 --- /dev/null +++ b/contrib/chem/examples/ethamivan.chem @@ -0,0 +1,43 @@ +ethamivan.chem: +.cstart + +# Example file for 'chem': +# Ethamivan or Analepticon or C12_H17_N_O3 or +# N,N-diethyl-4-hydroxy-3-methoxy-benzamide + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. +# Written by Bernd Warken <groff-bernd.warken-72@web.de>. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +R: ring pointing left double 2,3 4,5 6,1 + bond left from R.V1 ; O + bond left ; H + bond -150 from R.V6 ; O + bond left + bond 60 from R.V4 +B1: double bond up ; O + bond 120 from B1.start ; N + bond 45 + bond right + bond 135 from N + bond right + +# Local Variables: +# fill-column: 72 +# mode: Nroff +# End: +# vim: set textwidth=72: +.cend diff --git a/contrib/chem/examples/lsd.chem b/contrib/chem/examples/lsd.chem new file mode 100644 index 0000000..4879ea8 --- /dev/null +++ b/contrib/chem/examples/lsd.chem @@ -0,0 +1,46 @@ +lsd.chem: +.cstart + +# Example file for 'chem': +# LSD or Lysergic acid dethylamide or C20_H25_N3O or +# 9,10-Didehydro-N,N-diethyl-6-methyl-ergoline-8-beta-carboxamide + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. +# Written by Bernd Warken <groff-bernd.warken-72@web.de>. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +F: flatring5 pointing left put N at 5 double 3,4 + H below F.N +B: benzene pointing right with .V1 at F.V2 +R1: ring pointing right with .V4 at B.V6 + front bond right from R1.V6 ; H +R2: ring pointing right with .V2 at R1.V6 put N at 1 double 3,4 + bond right from R2.N + back bond -60 from R2.V5 ; H + bond up from R2.V5 +B1: double bond up ; O + bond right from B1.start ; N + bond 45 + bond right + bond 135 from N + bond right + +# Local Variables: +# fill-column: 72 +# mode: Nroff +# End: +# vim: set textwidth=72: +.cend diff --git a/contrib/chem/examples/morphine.chem b/contrib/chem/examples/morphine.chem new file mode 100644 index 0000000..5c236ca --- /dev/null +++ b/contrib/chem/examples/morphine.chem @@ -0,0 +1,51 @@ +morphine.chem: +.cstart + +# Example file for 'chem': +# Morphine or C23_H31_N3O or +# N,N-diethyl-N'-(2-methoxyacridin-9-yl)-pentane-1,4-diamine + +# Found at http://www.chemindustry.com/apps/chemicals. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. +# Written by Bernd Warken <groff-bernd.warken-72@web.de>. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +R1: benzene +R2: benzene with .V6 at R1.V2 with .V5 at R1.V3 put N at 4 +R3: benzene with .V6 at R2.V2 with .V5 at R2.V3 + bond 60 at R3.V2 ; O + bond 120 + bond up at R2.V1 ; N + bond 60 ; H + bond -60 at N +B1: backbond -120 + bond up at B1.start + bond -60 + bond up + bond -60 ; N + bond up + bond -60 + bond -120 at N + bond -60 + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/penicillin.chem b/contrib/chem/examples/penicillin.chem new file mode 100644 index 0000000..ef522bc --- /dev/null +++ b/contrib/chem/examples/penicillin.chem @@ -0,0 +1,52 @@ +penicillin.chem: +.cstart + +# Example file for 'chem': +# Penicillin or C16_H18_N2_O4_S or +# 3,3-dimethyl-6-oxo-7-(2-phenylacetyl)amino-2-thia-5- +# azabicyclo[3.2.0]heptane-4-carboxylic acid + +# Found at http://www.chemindustry.com/apps/chemicals. + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. +# Written by Bernd Warken <groff-bernd.warken-72@web.de>. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +R1: flatring5 pointing up put S at 1 put N at 4 + bond 45 at R1.V2 + bond 135 at R1.V2 + bond 120 at R1.V3 +D1: doublebond 45 ; O + bond 135 at D1.start ; OH + bond left at R1.N + doublebond -135 ; O + bond left at R1.V5 +B1: bond down length .3 + bond -60 at B1.start ; N + bond up ; H + bond -120 at N +D2: doublebond down ; O + bond -60 at D2.start + bond -120 + benzene + +# Local Variables: +# mode: Nroff +# End: +.cend diff --git a/contrib/chem/examples/reserpine.chem b/contrib/chem/examples/reserpine.chem new file mode 100644 index 0000000..d1b4046 --- /dev/null +++ b/contrib/chem/examples/reserpine.chem @@ -0,0 +1,63 @@ +reserpine.chem: +.PS +begin chem + +# Example file for 'chem': +# Reserpine or C33H40N2O9 + +# Copyright (C) 2006-2020 Free Software Foundation, Inc. +# Written by Bernd Warken <groff-bernd.warken-72@web.de>. + +# 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 (GPL) version 2 as +# published by the Free Software Foundation. + +# '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 this program. If not, see <http://www.gnu.org/licenses/>. + +# The GPL2 license text is available in the internet at +# <http://www.gnu.org/licenses/gpl-2.0.html>. + +R1: benzene pointing up + bond -120 from R1.V5 ; O + bond left +R2: flatring5 pointing down double 4,5 with .V2 at R1.V3 with .V3 at R1.V2 put N at 1 + H below R2.V1 +R3: ring put N at 3 with .V5 at R2.V5 +R4: ring put N at 1 with .V1 at R3.V3 + back bond -120 from R4.V4 ; H + back bond 60 from R4.V3 ; H +R5: ring with .V1 at R4.V3 + bond -120 +D1: double bond down ; O + bond left from D1.start ; O + bond left + back bond 60 from R5.V3 ; H + back bond down from R5.V4 ; O + bond down from O + bond 120 from R5.V3 ; O + bond 50 from O +D2: double bond up ; O + bond right length .1 from D2.start +B: benzene pointing right + bond 45 from B.V6 ; O + bond right + bond right from B.V1 ; O + bond right + bond 135 from B.V2 ; O + bond right + +# Local Variables: +# fill-column: 72 +# mode: Nroff +# End: +# vim: set textwidth=72: +end +.PE |