-
Notifications
You must be signed in to change notification settings - Fork 0
/
release_notes.html
239 lines (224 loc) · 16.4 KB
/
release_notes.html
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
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Release Notes — CDPKit 1.2.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/tabs.css" type="text/css" />
<link rel="stylesheet" href="_static/css/custom.css" type="text/css" />
<link rel="shortcut icon" href="_static/favicon.svg"/>
<link rel="canonical" href="https://cdpkit.org/release_notes.html" />
<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="_static/doctools.js"></script>
<script src="_static/tabs.js"></script>
<script src="_static/docs-versions-menu.js"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Acknowledgements" href="acknowledgements.html" />
<link rel="prev" title="Python API" href="cdpl_api_doc/python_api_doc/index.html" />
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" style="background: #aaaaaa" >
<a href="index.html">
<img src="_static/logo.svg" class="logo" alt="Logo"/>
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="applications/index.html">Applications</a></li>
<li class="toctree-l1"><a class="reference internal" href="cdpl_python_tutorial/index.html">CDPL Python Tutorial</a></li>
<li class="toctree-l1"><a class="reference internal" href="cdpl_python_cookbook/index.html">CDPL Python Cookbook</a></li>
<li class="toctree-l1"><a class="reference internal" href="cdpl_api_doc/index.html">CDPL API Documentation</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Release Notes</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#release-v1-1-1">Release V1.1.1</a></li>
<li class="toctree-l2"><a class="reference internal" href="#release-v1-1-0">Release V1.1.0</a></li>
<li class="toctree-l2"><a class="reference internal" href="#release-v1-0-0">Release V1.0.0</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="acknowledgements.html">Acknowledgements</a></li>
<li class="toctree-l1"><a class="reference internal" href="bibliography.html">Bibliography</a></li>
<li class="toctree-l1"><a class="reference internal" href="genindex.html">Index</a></li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" style="background: #aaaaaa" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">CDPKit</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html" class="icon icon-home"></a> »</li>
<li>Release Notes</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/release_notes.rst.txt" rel="nofollow"> View page source</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<section id="release-notes">
<span id="index-0"></span><h1>Release Notes<a class="headerlink" href="#release-notes" title="Permalink to this heading"></a></h1>
<section id="release-v1-1-1">
<h2>Release V1.1.1<a class="headerlink" href="#release-v1-1-1" title="Permalink to this heading"></a></h2>
<p class="rubric">Improvements</p>
<ul class="simple">
<li><p>Significantly improved the generation of 2D coordinates for macrocyclic structures</p></li>
</ul>
<p class="rubric">Bug Fixes</p>
<ul class="simple">
<li><p>Fixed an issue with the generation of conformers under application of a fixed substructure template where the generated
conformers sometimes displayed the mirror image of the specified 3D template structure</p></li>
<li><p>The command line tools <a class="reference internal" href="applications/structgen.html"><span class="doc">structgen</span></a> and <a class="reference internal" href="applications/confgen.html"><span class="doc">confgen</span></a> erroneously
used the already reserved letter <strong>p</strong> as shortcut for the option <em>–fixed-substr-min-atoms</em>. The new shortcut is <strong>~</strong></p></li>
</ul>
<p class="rubric">Miscellaneous Changes</p>
<ul class="simple">
<li><p>Rewrote code that uses the boost filesystem library to use C++17 equivalents</p></li>
<li><p>Compiling CDPKit now requires a compiler with C++17 support</p></li>
</ul>
</section>
<section id="release-v1-1-0">
<h2>Release V1.1.0<a class="headerlink" href="#release-v1-1-0" title="Permalink to this heading"></a></h2>
<p class="rubric">New Functionality and Features</p>
<ul class="simple">
<li><p>The tool <a class="reference internal" href="applications/tautgen.html"><span class="doc">tautgen</span></a> provides two new tautomer generation modes <code class="docutils literal notranslate"><span class="pre">BEST_SCORING</span></code> and <code class="docutils literal notranslate"><span class="pre">BEST_SCORING_UNIQUE</span></code>
(the new default mode) for generating only the chemically most reasonable tautomers</p></li>
<li><p>New option in class <em>Chem::TautomerGenerator</em> that allows to suppress the output of generated tautomers
which represent just a different resonance structure of a previously reported tautomeric form</p></li>
<li><p>New <a class="reference internal" href="applications/structgen.html"><span class="doc">structgen</span></a> feature that allows to enforce a particular 3D structure for defined parts of the input molecules</p></li>
<li><p>New <a class="reference internal" href="applications/confgen.html"><span class="doc">confgen</span></a> feature that allows to specify substructures of the input molecules that
shall adopt a particular conformation which is then kept ‘fixed’ during conformer generation
(more information and examples can be found <a class="reference internal" href="applications/confgen.html#confgen-notes-v1-1"><span class="std std-ref">here</span></a>)</p></li>
<li><p>Conformer generator settings now allow to specify rotatable bond count dependent values for RMSD threshold, energy window and
max. output ensemble size</p></li>
<li><p>The pharmacophore screening application <a class="reference internal" href="applications/psdscreen.html"><span class="doc">psdscreen</span></a> provides a new option <em>–unique-hits</em>
which enforces that a database molecule matched by multiple query pharmacophores is saved only once to the output hit list</p></li>
<li><p>New Python example script for database preparation</p></li>
<li><p>New Python example script demonstrating how the torsion driving functionality can be used for conformer sampling</p></li>
<li><p>The visual molecule and reaction data inspection tool <a class="reference internal" href="applications/chox.html"><span class="doc">ChOX</span></a> now allows to display atom and bond configuration labels</p></li>
<li><p>The 2D molecule structure rendering code (implemented by class <em>Vis::StructureView2D</em>) now
allows to display atom and bond configuration labels</p></li>
<li><p>Full implementation of the CIP sequence rule stack for the correct labeling of atom and bond stereocenters (new class <em>Chem::CIPConfigurationLabeler</em>)</p></li>
<li><p>Support for reading/writing molecular structures in XYZ format (classes <em>Chem::XYZMoleculeReader</em> and <em>Chem::XYZMolecularGraphWriter</em>)</p></li>
<li><p>New command line application <a class="reference internal" href="applications/isogen.html"><span class="doc">isogen</span></a> for the enumeration of R/S and E/Z stereoisomers of molecules</p></li>
<li><p>New class <em>Chem::StereoisomerGenerator</em> for the exhaustive enumeration of R/S and E/Z stereoisomers</p></li>
<li><p>New 2D drawing primitives (classes <em>Vis::Path2D</em> and <em>Vis::PathPrimitive2D</em>) and support for clipping operations (class <em>Vis::ClipPathPrimitive2D</em>)</p></li>
<li><p>New class <em>Chem::BemisMurckoAnalyzer</em> for the extraction of Bemis-Murcko scaffolds</p></li>
<li><p>New functions for the alignment conformers</p></li>
<li><p>New utility functions <em>Chem::calcBasicProperties()</em> that ease the recurring task of initializing <em>Chem::MolecularGraph</em>
and <em>Chem::Reaction</em> instances for further processing</p></li>
</ul>
<p class="rubric">Improvements</p>
<ul class="simple">
<li><p>Overhaul of the tautomer generation code for increased efficiency and flexibility</p></li>
<li><p>The output conformer ensemble compilation process now strives for higher energetic diversity among the picked conformers which, on average,
leads to higher accuracy in the reproduction of experimental structures (benchmarking results can be found <a class="reference internal" href="applications/confgen.html#confgen-notes-v1-1"><span class="std std-ref">here</span></a>)</p></li>
<li><p>Update of the torsion library used for systematic conformer generation (more information can be found <a class="reference internal" href="applications/confgen.html#confgen-notes-v1-1"><span class="std std-ref">here</span></a>)</p></li>
<li><p>Systematic conformer sampling speed optimizations</p></li>
<li><p>Reduction of the memory footprint of the conformer generation procedure which could become unacceptably large
under some circumstances</p></li>
<li><p>Documentation updates and corrections</p></li>
<li><p>Refactoring of stereochemistry related code</p></li>
<li><p>Cleanup of the CDPL Python bindings code</p></li>
<li><p>When deep copying <em>Chem::Reaction</em> or <em>Chem::Molecule</em> instances, values of properties referencing atoms and/or bonds (e.g. stereodescriptors, SSSR)
now get automatically translated to values referencing the corresponding atoms/bonds of the copying target</p></li>
<li><p>Cleanup of CDPL C++ header files</p></li>
<li><p>Added support for building CDPL Python bindings <strong class="program">pip</strong> installer wheel files under Windows</p></li>
<li><p>Added support for building manylinux2014 compliant CDPL Python bindings <strong class="program">pip</strong> installer wheel files</p></li>
<li><p>Build system cleanup</p></li>
</ul>
<p class="rubric">Bug Fixes</p>
<ul class="simple">
<li><p>Fixed bugs in classes <em>Chem::MaxCommonAtomSubstructureSearch</em> and <em>Chem::MaxCommonBondSubstructureSearch</em> that led to a
loss of expected matches</p></li>
<li><p>Fix for a bug in the SMARTS parser that lead to the storage of wrong bond directions</p></li>
<li><p>Bond direction specifications (up/down) in SMILES and SMARTS strings are now correctly interpreted</p></li>
<li><p>Fixed a bug that may lead to the generation of conformers with wrong geometries at exocyclic double bonds</p></li>
<li><p>Fixed a bug in the <a class="reference internal" href="applications/shapescreen.html"><span class="doc">shapescreen</span></a> tool that lead to the calculation of erroneous similarity scores
when option <em>–score-only</em> was set</p></li>
<li><p>Fix for a minor bug that affected the indentation of SD-file property entries</p></li>
<li><p>Function overload resolution order fixes in the <em>CDPL.Math</em> Python package</p></li>
<li><p>Prevented the throwing of exceptions when the env. variable <strong>LC_ALL</strong> has not been initialized</p></li>
</ul>
<p class="rubric">API Changes</p>
<ul class="simple">
<li><p>New getter/setter method pair in class <em>Chem::TautomerGenerator</em> for suppressing the output of generated tautomers
which represent just a different resonance structure of a previously reported tautomer</p></li>
<li><p>Data structures with names <em>ForceField::MMFF94XXXInteractionData</em> were renamed into <em>ForceField::MMFF94XXXInteractionList</em>
(XXX = force field interaction type)</p></li>
<li><p>New class <em>ForceField::ElasticPotential</em> plus elastic potential energy and gradient calculation functions</p></li>
<li><p>New class <em>Chem::CIPConfigurationLabeler</em> for the labeling of atom and bond stereocenters</p></li>
<li><p>New class <em>Chem::StereoisomerGenerator</em> for the exhaustive enumeration of R/S and E/Z stereoisomers</p></li>
<li><p>New classes <em>Chem::XYZMoleculeReader</em> and <em>Chem::XYZMolecularGraphWriter</em> implementing reading and writing
of molecule data in XYZ format</p></li>
<li><p>New 2D drawing primitives (classes <em>Vis::Path2D</em> and <em>Vis::PathPrimitive2D</em>) and support for clipping operations
(class <em>Vis::ClipPathPrimitive2D</em>)</p></li>
<li><p>New class <em>Chem::BemisMurckoAnalyzer</em> for the extraction of Bemis-Murcko scaffolds</p></li>
<li><p>New <em>CDPL::Chem</em> functions for the alignment conformers</p></li>
<li><p>Python exports of <em>Util::Map</em> and <em>Util::MultiMap</em> do not provide the properties <em>keys</em>, <em>values</em>, and <em>entries</em> anymore.
They were replaced by the corresponding methods <em>keys()</em>, <em>values()</em> and <em>items()</em></p></li>
<li><p>The <em>MolProp::getAtomCount()</em> function has been extended by a <em>strict</em> argument which, if set to <code class="docutils literal notranslate"><span class="pre">false</span></code>, instructs
the accounting procedure to regard the meaning of generic atom types (e.g. any halogen)</p></li>
<li><p>New utility functions <em>Chem::calcBasicProperties()</em> for a more comfortable initialization of <em>Chem::MolecularGraph</em>
and <em>Chem::Reaction instances</em> for further processing</p></li>
<li><p>Code in class <em>GRAIL::GRAILDescriptorCalculator</em> now calculates a shorter GRAIL descriptor (35 elements) with
not further subdivided H-bond donor/acceptor feature types</p></li>
<li><p>Class <em>GRAIL::GRAILDescriptorCalculator</em> was renamed into <em>GRAIL::GRAILXDescriptorCalculator</em></p></li>
</ul>
</section>
<section id="release-v1-0-0">
<h2>Release V1.0.0<a class="headerlink" href="#release-v1-0-0" title="Permalink to this heading"></a></h2>
<blockquote>
<div><p><strong>- Initial release -</strong></p>
</div></blockquote>
</section>
</section>
</div>
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="cdpl_api_doc/python_api_doc/index.html" class="btn btn-neutral float-left" title="Python API" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
<a href="acknowledgements.html" class="btn btn-neutral float-right" title="Acknowledgements" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>
<hr/>
<div role="contentinfo">
<p>© Copyright 2024, Thomas Seidel and Oliver Wieder.</p>
</div>
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
</body>
</html>