[med-svn] r10459 - trunk/packages/king/trunk/debian

Fri Apr 20 14:06:24 UTC 2012

Author: tille
Date: 2012-04-20 14:06:24 +0000 (Fri, 20 Apr 2012)
New Revision: 10459

Added:
   trunk/packages/king/trunk/debian/king.doc-base.chiropraxis
   trunk/packages/king/trunk/debian/king.doc-base.extratools
   trunk/packages/king/trunk/debian/king.doc-base.format-kinemage
   trunk/packages/king/trunk/debian/king.doc-base.hacking-king
   trunk/packages/king/trunk/debian/king.doc-base.kinemage-format
   trunk/packages/king/trunk/debian/king.doc-base.king
   trunk/packages/king/trunk/debian/king.lintian-overrides
Log:
Doc-base matters ...


Added: trunk/packages/king/trunk/debian/king.doc-base.chiropraxis
===================================================================

--- trunk/packages/king/trunk/debian/king.doc-base.chiropraxis	                        (rev 0)
+++ trunk/packages/king/trunk/debian/king.doc-base.chiropraxis	2012-04-20 14:06:24 UTC (rev 10459)
@@ -0,0 +1,13 @@
+Document: chiropraxis
+Title: The Chiropraxis tools manual
+Author: Ian W. Davis
+Abstract: BACKRUB Tool: Protein chiropraxis
+ The BACKRUB tool is used to adjust short segments of protein backbone
+ without disturbing the surrounding structure. It allows you select one
+ residue, and rotate it around the axis between its neighboring C-alphas.
+ Using BACKRUB requires that chiropraxis.jar be present in the plugins/
+ folder.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/king/chiropraxis-manual.pdf

Added: trunk/packages/king/trunk/debian/king.doc-base.extratools
===================================================================
--- trunk/packages/king/trunk/debian/king.doc-base.extratools	                        (rev 0)
+++ trunk/packages/king/trunk/debian/king.doc-base.extratools	2012-04-20 14:06:24 UTC (rev 10459)
@@ -0,0 +1,14 @@
+Document: extratools
+Title: The Extratools manual
+Author: Ian W. Davis, Vincent B. Chen, and Daniel A. Keedy
+Abstract: The KiNG Tools
+ This manual describes the KiNG tools available in the ’extratools’ and
+ ’rdcvis’ packages. It is roughly laid out in order of the tools menu in
+ KiNG, with tools in the main menu in this chapter, and a separate
+ chapter for the ’Data analysis’, ’Kin editing’, ’Structural biology’,
+ ’Export’ (File menu), and ’Specialty’ tools. Also see the KiNG manual
+ for descriptions of other tools.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/king/extratools-manual.pdf

Added: trunk/packages/king/trunk/debian/king.doc-base.format-kinemage
===================================================================
--- trunk/packages/king/trunk/debian/king.doc-base.format-kinemage	                        (rev 0)
+++ trunk/packages/king/trunk/debian/king.doc-base.format-kinemage	2012-04-20 14:06:24 UTC (rev 10459)
@@ -0,0 +1,23 @@
+Document: format-kinemage
+Title: The Kinemage File Format, v1.0
+Author: Ian W. Davis, Jane S. Richardson, David C. Richardson
+Abstract: The Kinemage File Format
+ This document describes the syntax and semantics of the core
+ feature-set of the kinemage file format. Since even the core features
+ are extensive, the description has been broken into two logical halves.
+ The first section describes the semantics and high-level syntax of
+ kinemage files—all the information typically needed to author a new
+ kinemage file from scratch. The second section formally describes the
+ low-level syntax that underlies the entire format, which is important
+ for programmers writing kinemage parsers.
+ .
+ This document does not cover the philosophy, rationale, or history of
+ the kinemage format, nor is it a tutorial in using or creating
+ kinemages. It assumes the user has some experience viewing and
+ interacting with existing kinemages and now wants either (1) to create a
+ new kinemage file by hand or programmatically, starting from scratch, or
+ (2) modify an existing kinemage file by hand at the plain-text level.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/king/format-kinemage.pdf

Added: trunk/packages/king/trunk/debian/king.doc-base.hacking-king
===================================================================
--- trunk/packages/king/trunk/debian/king.doc-base.hacking-king	                        (rev 0)
+++ trunk/packages/king/trunk/debian/king.doc-base.hacking-king	2012-04-20 14:06:24 UTC (rev 10459)
@@ -0,0 +1,23 @@
+Document: hacking-king
+Title: Hacking KiNG
+Author: Ian W. Davis
+Abstract: Hacking KiNG
+ This document is intended to provide a field guide to the code for KiNG
+ and its associated libraries, Driftwood and Chiropraxis. For more
+ information, please see the relevant Javadocs, and ultimately, the code
+ itself. In particular, most of the references for the various published
+ algorithms are somewhere in the Javadocs. Some parts of the code are
+ better commented than others, but it’s mostly pretty comprehensible. If
+ not, you can often use the incomprehensible parts without having to
+ understand how they work.
+ .
+ The first part of this discussion will provide an overview of all the
+ code, starting with driftwood, building chiropraxis on top of that, and
+ finally building king on top of them both. The second part will cover
+ the organizational principles behind the layout of code and resources,
+ compiling and building, maintaining documentation, and distributing
+ finished applications.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/king/hacking-king.pdf

Added: trunk/packages/king/trunk/debian/king.doc-base.kinemage-format
===================================================================
--- trunk/packages/king/trunk/debian/king.doc-base.kinemage-format	                        (rev 0)
+++ trunk/packages/king/trunk/debian/king.doc-base.kinemage-format	2012-04-20 14:06:24 UTC (rev 10459)
@@ -0,0 +1,14 @@
+Document: kinemage-format
+Title: Kinemage format from Mage's help
+Author: Dr. David Richardson <dcr at kinemage.biochem.duke.edu>, Ian Davis <iwd at duke.edu>
+Abstract: Kinemage format from Mage's help
+ This description of the kinemage format, which is taken from Mage's
+ internal help, is very terse and may be incomplete in places. A more
+ complete treatment in included in the KiNG documentation as
+ format-kinemage.pdf, which covers all of the core functionality that
+ Mage and KiNG share.
+Section: Science/Biology
+
+Format: html
+Files: /usr/share/doc/king/kinemage-format.html
+Index: /usr/share/doc/king/kinemage-format.html

Added: trunk/packages/king/trunk/debian/king.doc-base.king
===================================================================
--- trunk/packages/king/trunk/debian/king.doc-base.king	                        (rev 0)
+++ trunk/packages/king/trunk/debian/king.doc-base.king	2012-04-20 14:06:24 UTC (rev 10459)
@@ -0,0 +1,17 @@
+Document: king
+Title: The KiNG manual
+Author: Ian W. Davis, Vincent B. Chen
+Abstract: The KiNG manual
+ KiNG (Kinemage, Next Generation) is an interactive system for
+ three-dimensional vector graphics. It supports a set of graphics
+ primitives that make it suitable for many types of graphs, plots, and
+ other illustrations; although its first use was to display
+ macromolecular structures for biophysical research.  Mage JavaMage, KiNG
+ builds on, and the thekinemage (kinetic image) concept to deliver a
+ full-featured Java application with a user-friendly interface and
+ integrated editing features. It also operates as a Java applet to
+ promote easy access to kinemages from a web browser.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/king/king-manual.pdf

Added: trunk/packages/king/trunk/debian/king.lintian-overrides
===================================================================
--- trunk/packages/king/trunk/debian/king.lintian-overrides	                        (rev 0)
+++ trunk/packages/king/trunk/debian/king.lintian-overrides	2012-04-20 14:06:24 UTC (rev 10459)
@@ -0,0 +1,2 @@
+# When using jarwrapper the JAR file should be executable, shouldn't it?
+king: executable-not-elf-or-script usr/share/java/king-2.20.110601.jar


