Shinsaku Fujita and Nobuya Tanaka,
``XyM Notation for Electronic Communication of
Organic Chemical Structures,''
J. Chemical Information and Computer Sciences
39, 903--914 (1999)
or the corresponding on-line article (CI990018X) appearing in
Journal of Chemical Information & Computer Sciences ASAP Table of Contents:
http://pubs.acs.org/subscribe/journals/jcisd8/browse_asap.html
Direct link to CI990018X
http://dx.doi.org/10.1021/CI990018X
xymtx500a.doc
On-line document for XyMTeX in English
Copyright (C) 1993, 1996, 1998, 2001, 2002, 2004, 2005, 2009, 2010 by Shinsak Fujita.
All rights reserved.
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xymtx500.doc
On-line document for XyMTeX in English
Copyright (C) 1993, 1996, 1998, 2001, 2002, 2004, 2005, 2009, 2010 by Shinsak Fujita.
All rights reserved.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
xymtx406.doc
On-line document for XyMTeX in English
Copyright (C) 1993, 1996, 1998, 2001, 2002, 2004, 2005, 2009 by Shinsak Fujita.
All rights reserved.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
xymtx405.doc
On-line document for XyMTeX in English
Copyright (C) 1993, 1996, 1998, 2001, 2002, 2004, 2005, 2009 by Shinsak Fujita.
All rights reserved.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
xymtx404.doc
On-line document for XyMTeX in English
Copyright (C) 1993, 1996, 1998, 2001, 2002, 2004, 2005, 2009 by Shinsak Fujita.
All rights reserved.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
xymtx403.doc
On-line document for XyMTeX in English
Copyright (C) 1993, 1996, 1998, 2001, 2002, 2004,2005 by Shinsak Fujita.
All rights reserved.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
xymtx402.doc
On-line document for XyMTeX in English
Copyright (C) 1993, 1996, 1998, 2001, 2002, 2004 by Shinsak Fujita.
All rights reserved.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
xymtx401.doc
On-line document for XyMTeX in English
Copyright (C) 1993, 1996, 1998, 2001, 2002, 2004 by Shinsak Fujita.
All rights reserved.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
xymtx400.doc
On-line document for XyMTeX in English
Copyright (C) 1993, 1996, 1998, 2001, 2002 by Shinsak Fujita.
All rights reserved.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
xymtx300.doc
On-line document for XyMTeX in English
Copyright (C) 1993, 1996, 1998, 2001, 2002 by Shinsak Fujita.
All rights reserved.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
xymtx201.doc
On-line document for XyMTeX in English
Copyright (C) 1993, 1996, 1998,2001 by Shinsak Fujita. All rights reserved.
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renamed and revised: xymtex2.doc
Copyright (C) 1993, 1996, 1998 by Shinsak Fujita. All rights reserved.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
renamed and revised: xymtex1.doc
Copyright (C) 1993, 1996 by Shinsak Fujita. All rights reserved.
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`XyMTeX' is a macro package for drawing chemical structural formulas.
In the previous versions (\leq version 5.00),
subscripts or superscripts without a pair of braces (e.g., $a^\star$) result in
errors, while those with a pair of braces (e.g., $a^{\star}$) work well.
The present version 5.00a (bug fixed) provides corrections
for chemist.sty and chemtimes.sty, so that such different descriptions
for math symbols and Greek letters are allowed, e.g., $a^\star$ and $a^{\star}$.
(1) Setting up
The XyMTeX system has been frozen with ZIP. Set up according to the software
situation of your computer.
The following is only one example. Let the frozen package
(xymtx500a.zip) be placed in the c:\temp directory,
where the package is melt with an appropriate software for melting.
Thereby, the directory <\xymtex> is automatically created as the
subdirectory of the c:\temp directory. And the following hierarchy of
directories and files is generated.
(For full document directories, visit the original deposit of the latest version at
http://xymtex.com/ (Shonan Institute of Chemoinformatics and Mathematical
Chemistry)).
c---\temp---\xymtex ---\base -- xymtex.sty, xymtexps.sty, xymtexpdf.sty,
| hetaromh.sty, hetarom.sty, ccycle.sty,
| chemstr.sty, carom.sty, lowcycl.sty, aliphat.sty,
| hcycle.sty, locant.sty, polymers.sty, chemist.sty
| methylen.sty, fusering.sty,
| sizeredc.sty, steroid.sty, bondcolor, assurelatexmode
| lewisstruc.sty, chemtimes.sty
| (dtx files and ins files)
|
|---\chemist---chemist.sty, assurechemist.sty
| (dtx files and ins files)
|
|---\xymtxps---xymtx-ps.sty, chmst-ps.sty
| (dtx files and ins files)
|
|---\xymtxpdf---xymtx-pdf.sty, chmst-pdf.sty
| (dtx files and ins files)
|
|---\doc---
| |--\doc101--- xymtex.pdf (on-line document)
| |
| |--\doc200---xymtx200.pdf (on-line document)
| |
| |--\doc300---xymtx300.pdf (on-line document)
| |
| |--\doc401---xymtx401.pdf (on-line document)
| |
| |--\doc402403---xymtx402403.pdf (on-line document)
| |
| |--\doc404---xymtx404.pdf (on-line document)
| |
| |--\doc405406
| | |--xymtx405A.pdf (on-line document)
| | |--xymtx405406B.pdf (on-line document)
| | |--xymtx405406C.pdf (on-line document)
| |
| |--\doc500
| | |--xymtx500.pdf (on-line document)
| | |--xymtx500PS.pdf (on-line document)
|
|---\readme---
| |---xymtx500a.doc (this document)
| |
| |---xymtx500a.jpn (on-line document in Japanese)
| |
| |---readm500a.doc (notes in English)
| |
| |---readm500a.jpn (notes in Japanese)
|
Each of the package (sty) files in the \xymtex directory contains the macro
codes of XymTeX commands. The specification of XyMTeX commands can be printed out
after making a driving file. For the chemstr package as an example, commands
to be typed in a prompt line are as follows:
c:\temp> latex chemstr.ins
c:\temp> latex chemstr.drv
Thereby, you will obtain chemstr.dvi, which is a document of the chemstr package.
The on-line manuals of the old versions (pdf files) stored in respective directories
are effective even to the present version 5.00a. The directory \doc500 contains
two on-line documents, xymtx500.pdf and xymtx500PS.pdf, which have the same contents
but are differently processed:
xymtx500.pdf ---- processed by elatex and converted into PDF by dvipdfmx
xymtx500PS.pdf ---- processed by elatex and converted into PS by dvips, then
further converted into PDF by Adobe Distiller.
They can be browsed with Adobe Reader.
(2) Designating a serach path
Do this task according to the situtation of your computer.
The path searching tool (kpathsea) supported by usual TeX distributions has already decided
several input directories (named ``tex'' or others). Hence, you should only place the resulting
``xymtex'' directry generated from xymtx500.zip in such an appropriate directory named
``tex'' or others (e.g., c:\usr\local\share\texmf\tex\latex).
(3) Writing your manuscript
According to remarkable expansion of computer capacities, all of the package files of
the XyMTeX system can be loaded simultaneously in a tex file. You can adopt one of
the three modes of the XyMTeX system.
-1) For using the LaTeX picture environment and epic (TeX/LaTeX mode):
\documentclass{article}
\usepackage{xymtex}
\usepackage{chemist}
-2) For using under PostScript-compatible mode due to PSTricks techniques:
\documentclass{article}
\usepackage{xymtxps}
\usepackage{chmst-ps}
-3) For using under PDF-compatible mode due to pgf techniques:
\documentclass{article}
\usepackage{xymtxpdf}
\usepackage{chmst-pdf}
The include packages (chemist.sty, chmst-ps.sty, chemtimes.sty, chmst-pdf) should be
loaded separately after xymtex.sty, xymtexps.sty, or xymtexpdf.sty is loaded.
(4) Running LaTeX2e (or pLaTeX2e in Japanese)
You should use XyMTeX commands within LaTeX to creat a dvi file. Note that,
as for the PDF-compatible mode, you should use elatex (or eplatex in Japanese)
during LaTeX processing.
(5) PDF-compatible mode: Conversion of the dvi file into a PDF file (by e.g., dvipdfmx)
(5') PostScript-compatible mode:
--a) Conversion of the dvi file into a PostScript file (by e.g., dvips)
--b) Conversion of the PostScript file into a PDF file (by e.g., Adobe Distiller)
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