diff options
Diffstat (limited to 'Master/texmf-dist/doc/latex/textopo/textopo.txt')
| -rw-r--r-- | Master/texmf-dist/doc/latex/textopo/textopo.txt | 140 |
1 files changed, 140 insertions, 0 deletions
diff --git a/Master/texmf-dist/doc/latex/textopo/textopo.txt b/Master/texmf-dist/doc/latex/textopo/textopo.txt new file mode 100644 index 00000000000..5c19de110cc --- /dev/null +++ b/Master/texmf-dist/doc/latex/textopo/textopo.txt @@ -0,0 +1,140 @@ + TeXtopo v1.4 + >> + >> 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) 2000-2005 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: eric.beitz@uni-tuebingen.de + WWW: http://homepages.uni-tuebingen.de/beitz/ + (On-line documentation and updates) + Address: Eric Beitz, Universit"at T"ubingen, Pharmazeutische Chemie, + Auf der Morgenstelle 8, D-72076 T"ubingen (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. |