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authorNorbert Preining <norbert@preining.info>2019-09-02 13:46:59 +0900
committerNorbert Preining <norbert@preining.info>2019-09-02 13:46:59 +0900
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+ TeXtopo v1.5
+ >>
+ >> A LaTeX package for shaded membrane protein topology plots.
+ >>
+ >> PHD topology predictions are a mighty tool to localize trans-
+ >> membrane domains and the protruding loops. SwissProt database
+ >> files provide sequence feature informations, such as mutation
+ >> sites, important domains, or secondary modifications. Making
+ >> these data visible in a sophisticated topology plot is an
+ >> enormous effort when using a standard drawing software.
+ >>
+ >> TeXtopo is a LaTeX2e macro package that provides two new envi-
+ >> ronments: (a) the textopo environment is used for plotting to-
+ >> pology data of membrane proteins derived from PHD predictions,
+ >> from SwissProt database files or from manually entered data
+ >> containing sequence and transmembrane domain information, and
+ >> (b) the helical wheel environment draws transmembrane domains
+ >> as seen from above or beneath the cell membrane.
+ >>
+ >> Both kinds of plots can be richly decorated with special sha-
+ >> ding for domains of interest, with labels and legends. TeXtopo
+ >> is fully compatible with TeXshade (v1.3 and up) -- the compre-
+ >> hensive alignment shading package for the TeX community. This
+ >> allows one to apply calculated shading based on sequence con-
+ >> servation and functional aspects of the residue sidechains.
+ >>
+ Copyright (C) 2000-2011 Eric Beitz
+
+
+
+ FOR THE HASTY READER
+
+ Be sure to use a docstrip version 2.4 or later!
+ Otherwise you will not be able to tex the documentation!
+
+
+
+1 - FILES DISTRIBUTED WITH THIS PACKAGE
+
+ textopo.ins Batch file, run through LaTeX
+ textopo.dtx Docstrip archive, run twice through LaTeX
+ textopo.txt This file
+
+
+ (a) FILES THAT WILL BE GENERATED FROM TEXTOPO.INS
+
+ textopo.sty LaTeX package
+ textopo.def Standard definitions
+ AQPpro.MSF Example protein alignment file (.MSF-format)
+ AQPpro1.shd Shading information calculated from AQPpro.MSF
+ AQP2spec.ALN Example protein alignment file (.ALN-format)
+ AQP1.phd Example PHD secondary structure file
+ AQP1.tpo Topology data extracted from AQP1.phd
+ AQP1.SP SwissProt database file
+ AQP1.swp Information extracted from AQP1.SP
+ biotex.sty Style file which organizes the BioTeX Bundle
+
+
+ (b) FILE THAT WILL BE GENERATED FROM TEXTOPO.DTX
+
+ textopo.dvi Package documentation
+
+
+
+2 - INSTALLATION
+
+ (a) EXTRACTING FILES FROM THE DOCSTRIP ARCHIVE
+
+ All files provided by TeXtopo are compacted to one single file,
+ namely "textopo.dtx". To extract the archive run "textopo.ins"
+ - which contains the corresponding instructions - through LaTeX.
+ A list of the generated files is given above, see 1(a).
+
+ AGAIN: Be sure to use a docstrip version 2.4 or later! Otherwise
+ you will not be able to tex the documentation!
+
+
+ (b) THE DOCUMENTATION
+
+ The file "textopo.dtx" further contains the package documentation.
+ Therefore, run this file through LaTeX now. As you will recognize
+ two runs are needed to make proper references within the document.
+
+ TeXtopo needs lots of LaTeX's memory, so adjust your parameter set-
+ tings to make TeXtopo feel comfortable. The documentation is a
+ good test for this. (If you have problems TeXing the doc, you can
+ download an on-line version [PDF-, DVI-, or PostScript format] at
+ http://homepages.uni-tuebingen.de/beitz/)
+
+ The resulting file "textopo.dvi" can be viewed and printed using a
+ DVI-viewer which is able to display embedded PostScript. Another
+ possibility is to run "textopo.dvi" through DVIPS, a DVI to Post-
+ Script converter, and finally view and print the converted file
+ which will be most likely "textopo.ps" with GhostView from the GNU
+ free software foundation.
+
+ TeXtopo makes use of "color.sty" by David Carlisle. This style is
+ part of the Standard LaTeX Graphics Bundle. Usually, the bundle is
+ present in a comprehensive LaTeX installation. If this is not the
+ case for your system you have to download the package from a CTAN-
+ server, e.g. ftp.dante.de.
+
+
+ (c) MAKING TEXTOPO.STY AVAILABLE FOR YOUR LATEX SYSTEM
+
+ In the final step, copy at least the files "textopo.sty" and
+ "biotex.sty" to a directory searched by TeX in order to make these
+ files available for all documents you produce in the future. The
+ remaining files are example files which are not necessary for run-
+ ning TeXtopo. Nevertheless, it would be a good idea to keep all the
+ files together.
+
+
+
+
+3 - CONTACT
+
+ E-Mail: ebeitz@pharmazie.uni-kiel.de
+ WWW: http://www.pharmazie.uni-kiel.de/chem/
+ (On-line documentation and updates)
+ Address: Eric Beitz, University of Kiel, Pharmaceutical Chemistry,
+ Gutenbergstrasse 76, D-24118 Kiel (Germany)
+
+
+
+4 - AGREEMENT
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program 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.
+
+ In order to receive a copy of the GNU General Public License write to
+ the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+ Boston, MA 02111-1307, USA.