/usr/share/doc/libgpp4-doc/html/index.html is in libgpp4-doc 1.3.1-0ubuntu5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.13"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>gpp4: The gpp4 library</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">gpp4
 <span id="projectnumber">1.3.1</span>
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.13 -->
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
$(function() {
initMenu('',false,false,'search.php','Search');
});
</script>
<div id="main-nav"></div>
</div><!-- top -->
<div class="header">
<div class="headertitle">
<div class="title">The gpp4 library </div> </div>
</div><!--header-->
<div class="contents">
<div class="textblock"><h1><a class="anchor" id="introduction"></a>
Introduction</h1>
<p>This distribution is a special version of the CCP4 library, released under the Lesser GNU Public License version 2.1.</p>
<p>The goal of this project – named gpp4 to distinguish it from CCP4 – is to provide a drop-in replacement for the CCP4 libraries, that as carefully as possible will implement the current CCP4 library interface.</p>
<p>The initial motivation to create this public fork the CCP4 library was that the licensing was changed in version 6.0 to be "non-free". At the time, the last version of the CCP4 library covered by a free license was version 5.0.2.</p>
<p>There are several third-party applications, such as Phenix and Coot, that depend on the CCP4 library. However, you could not legally create a derived work containing both CCP4 6.* licensed code and GPL'd code, and distribute the resulting program, since the GPL demands that the derived work be distributed without additional restrictions. The CCP4 6.* license imposed additional restrictions on redistribution - in particular (but not limited to) an indemnity clause.</p>
<p>Version 5.0.2 of the CCP4 library was patched by Ralf Grosse-Kunstleve to address some of the more serious deficiencies of the older libraries and included with the Phenix distribution.</p>
<p>It is this patched version of the CCP4 library that forms the original basis for this distribution, which includes a GNU autotools build environment developed by Paul Emsley and Morten Kjeldgaard.</p>
<p>At this time, the CCP4 has revised its licensing policy, and the CCP4 library is again licensed under the Lesser GNU Public License. However, there is still a very good reason to maintain and develop ggp4, because the CCP4 library is tightly integrated with the entire CCP4 distribution, of currently around 220Mb.</p>
<p>The ggp4 distribution thus serves as a small, standalone version, that can be included in third party software distributions. It is also available through the Ubuntu and Fedora software repositories for easy installation.</p>
<h1><a class="anchor" id="purpose"></a>
Purpose</h1>
<p>The CCP4 software suite is based around a library of routines which cover common tasks, such as file opening, parsing keyworded input, reading and writing of standard data formats, applying symmetry operations, etc. Programs in the suite call these routines which, as well as saving the programmer some effort, ensure that the varied programs in the suite have a similar look-and-feel. </p>
<p>Since 2002, there has been a major effort to re-write much of the CCP4 library into C/C++. The aims are:</p>
<ul>
<li>
<p class="startli">To implement a better representation of the underlying data model. For example, Eugene Krissinel's MMDB library acts on a data structure which represents the various levels of structure of a protein model. The new <a class="el" href="struct_m_t_z.html">MTZ</a> library encapsulates the crystal/dataset hierarchy that is increasingly being used by programs.</p>
<p class="endli"></p>
</li>
<li>
<p class="startli">To maintain support for existing programs. In particular, the existing Fortran APIs will be maintained, although they will now often be only wrappers to functions in the new library. It is hoped that many existing programs will be migrated to using the new library directly.</p>
<p class="endli"></p>
</li>
<li>
To provide support for scripting. It is possible to generate APIs for Python, Tcl and Perl automatically from the core C code. Thus, much of the standard CCP4 functionality wil be available to scripts used e.g. in ccp4i or the molecular graphics project. </li>
</ul>
<p>This incremental approach, maintaining the existing suite while improving the underlying code, puts constraints on what is possible, but is considered more appropriate for a collaborative project like CCP4.</p>
<h1><a class="anchor" id="start"></a>
This documentation</h1>
<p>This documentation is generated automatically by <a href="http://www.doxygen.org/">Doxygen</a> from comment sections in the code. It is therefore detailed and extensive. The library divides roughly into the following sections: </p><dl>
<dt>CMTZ library </dt>
<dd><p class="startdd">See the <a class="el" href="cmtz_page.html">CMTZ library</a> page for C/C++ programmers, and the <a class="el" href="cmtz_f_page.html">Fortran API to CMTZ</a> page for Fortran programmers.</p>
<p class="enddd"></p>
</dd>
<dt>CMAP library </dt>
<dd><p class="startdd">See the <a class="el" href="cmap_page.html">CMAP library</a> page for C/C++ programmers, and the <a class="el" href="cmap_f_page.html">Fortran API to CMAP</a> page for Fortran programmers.</p>
<p class="enddd"></p>
</dd>
<dt>MMDB library </dt>
<dd><p class="startdd">See Eugene's <a href="http://www.ebi.ac.uk/pdbe/docs/cldoc/">documentation</a>.</p>
<p class="enddd"></p>
</dd>
<dt>CSYM library </dt>
<dd><p class="startdd">See the <a class="el" href="csym_page.html">CSYM library</a> page for C/C++ programmers, and the <a class="el" href="csym_f_page.html">Software Library for handling symmetry operations</a> page for Fortran programmers.</p>
<p class="enddd"></p>
</dd>
<dt>CCP4 utility library </dt>
<dd><p class="startdd">See the <a class="el" href="utilities_page.html">CCP4 Library Utilities</a> page for C/C++ programmers.</p>
<p class="enddd"></p>
</dd>
<dt>CCP4 Parser library </dt>
<dd><p class="startdd">See the <a class="el" href="cparser_page.html">CParser library</a> page for details on how to use the CCP4 parser routines from C/C++ programs.</p>
<p class="enddd"></p>
</dd>
<dt>CCP4 resizable arrays </dt>
<dd><p class="startdd">See the <a class="el" href="ccp4_array_page.html">CCP4 resizable array implementation</a> page for information on Kevin Cowtan's resizable array implementation.</p>
<p class="enddd"></p>
</dd>
<dt>Low level disk i/o </dt>
<dd><p class="startdd">See the <a class="el" href="diskio_f_page.html">Fortran API for low level input/output.</a> page for Fortran programmers.</p>
<p class="enddd"></p>
</dd>
</dl>
</div></div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by  <a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.13
</small></address>
</body>
</html>
|