Documentation update

molinfo-vienna · Jan 20, 2024 · f2d5683 · f2d5683
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diff --git a/master/.doctrees/applications/confgen.doctree b/master/.doctrees/applications/confgen.doctree
diff --git a/master/.doctrees/applications/genfraglib.doctree b/master/.doctrees/applications/genfraglib.doctree
diff --git a/master/.doctrees/applications/psdcreate.doctree b/master/.doctrees/applications/psdcreate.doctree
diff --git a/master/.doctrees/applications/psdscreen.doctree b/master/.doctrees/applications/psdscreen.doctree
diff --git a/master/.doctrees/applications/shapescreen.doctree b/master/.doctrees/applications/shapescreen.doctree
diff --git a/master/.doctrees/applications/structgen.doctree b/master/.doctrees/applications/structgen.doctree
diff --git a/master/.doctrees/applications/tautgen.doctree b/master/.doctrees/applications/tautgen.doctree
diff --git a/master/.doctrees/environment.pickle b/master/.doctrees/environment.pickle
diff --git a/master/.doctrees/installation.doctree b/master/.doctrees/installation.doctree
diff --git a/master/_sources/applications/confgen.rst.txt b/master/_sources/applications/confgen.rst.txt
@@ -113,7 +113,7 @@ Other options
   -t [ --num-threads ] [=arg(=4)]
 
     Number of parallel execution threads (default: no multithreading, implicit value: 
-    4 threads, must be >= 0, 0 disables multithreading).
+    number of CPUs, must be >= 0, 0 disables multithreading).
 
   -C [ --conf-gen-preset ] arg
 

diff --git a/master/_sources/applications/genfraglib.rst.txt b/master/_sources/applications/genfraglib.rst.txt
@@ -78,7 +78,7 @@ Other options
   -t [ --num-threads ] [=arg(=4)]
 
     Number of parallel execution threads (default: no multithreading, implicit value: 
-    4 threads, must be >= 0, 0 disables multithreading).
+    number of CPUs, must be >= 0, 0 disables multithreading).
 
   -I [ --input-format ] arg
 

diff --git a/master/_sources/applications/psdcreate.rst.txt b/master/_sources/applications/psdcreate.rst.txt
@@ -76,7 +76,7 @@ Other options
   -t [ --num-threads ] [=arg(=4)]
 
     Number of parallel execution threads (default: no multithreading, implicit value: 
-    4 threads, must be >= 0, 0 disables multithreading).
+    number of CPUs, must be >= 0, 0 disables multithreading).
 
   -I [ --input-format ] arg
 

diff --git a/master/_sources/applications/psdscreen.rst.txt b/master/_sources/applications/psdscreen.rst.txt
@@ -82,25 +82,25 @@ Other options
 
   -m [ --mode ] arg
 
-    Molecule conformation matching mode (FIRST-MATCH, BEST-MATCH, ALL-MATCHES, default: 
+    Molecule conformer matching mode (FIRST-MATCH, BEST-MATCH, ALL-MATCHES, default: 
     FIRST-MATCH).
 
   -s [ --start-index ] arg (=0)
 
-    Screening range start molecule index (zero-based!, default: 0).
+    Screening start molecule index (zero-based, default: 0).
 
   -e [ --end-index ] arg (=0)
 
-    Screening range end molecule index (zero-based and not included in screening!, default: 
-    one after last molecule).
+    Screening end molecule index (zero-based and not included in the 
+    screening run, default: number of molecules in the database).
 
   -n [ --max-num-hits ] arg (=0)
 
     Maxmimum number of hits to report (default: no limit).
 
   -M [ --max-omitted ] arg (=0)
 
-    Maximum number of allowed unmatched features.
+    Allowed maximum number of unmatched features.
 
   -x [ --check-xvols ] [=arg(=1)]
 
@@ -141,7 +141,7 @@ Other options
   -t [ --num-threads ] [=arg(=4)]
 
     Number of parallel execution threads (default: no multithreading, implicit value: 
-    4 threads, must be >= 0, 0 disables multithreading).
+    number of CPUs, must be >= 0, 0 disables multithreading).
 
   -u [ --unique-hits ] [=arg(=1)]
 

diff --git a/master/_sources/applications/shapescreen.rst.txt b/master/_sources/applications/shapescreen.rst.txt
@@ -245,7 +245,7 @@ Other options
   -t [ --num-threads ] [=arg(=4)]
 
     Number of parallel execution threads (default: no multithreading, implicit value: 
-    4 threads, must be >= 0, 0 disables multithreading).
+    number of CPUs, must be >= 0, 0 disables multithreading).
 
   -Q [ --query-format ] arg
 

diff --git a/master/_sources/applications/structgen.rst.txt b/master/_sources/applications/structgen.rst.txt
@@ -111,7 +111,7 @@ Other options
   -t [ --num-threads ] [=arg(=4)]
 
     Number of parallel execution threads (default: no multithreading, implicit value: 
-    4 threads, must be >= 0, 0 disables multithreading).
+    number of CPUs, must be >= 0, 0 disables multithreading).
 
   -m [ --mode ] arg
 

diff --git a/master/_sources/applications/tautgen.rst.txt b/master/_sources/applications/tautgen.rst.txt
@@ -95,7 +95,7 @@ Other options
   -t [ --num-threads ] [=arg(=4)]
 
     Number of parallel execution threads (default: no multithreading, implicit value: 
-    4 threads, must be >= 0, 0 disables multithreading).
+    number of CPUs, must be >= 0, 0 disables multithreading).
 
   -I [ --input-format ] arg
 

diff --git a/master/_sources/installation.rst.txt b/master/_sources/installation.rst.txt
@@ -191,7 +191,7 @@ Mandatory for a successful build is the availability of the `Sphinx <https://www
 plus the listed extensions (see `Build requirements`_). Furthermore, for generating CDPL C++ and Python API-documentation (optional),
 the program `Doxygen <https://www.doxygen.nl>`_ has to be installed.
 
-.. note::
+.. hint::
 
    Sphinx and its extensions can be installed via the Python package installer :program:`pip`.
 

diff --git a/master/applications/confgen.html b/master/applications/confgen.html
@@ -228,7 +228,7 @@ <h2>Other options<a class="headerlink" href="#other-options" title="Permalink to
 <p>-t [ –num-threads ] [=arg(=4)]</p>
 <blockquote>
 <div><p>Number of parallel execution threads (default: no multithreading, implicit value:
-4 threads, must be &gt;= 0, 0 disables multithreading).</p>
+number of CPUs, must be &gt;= 0, 0 disables multithreading).</p>
 </div></blockquote>
 <p>-C [ –conf-gen-preset ] arg</p>
 <blockquote>

diff --git a/master/applications/genfraglib.html b/master/applications/genfraglib.html
@@ -183,7 +183,7 @@ <h2>Other options<a class="headerlink" href="#other-options" title="Permalink to
 <p>-t [ –num-threads ] [=arg(=4)]</p>
 <blockquote>
 <div><p>Number of parallel execution threads (default: no multithreading, implicit value:
-4 threads, must be &gt;= 0, 0 disables multithreading).</p>
+number of CPUs, must be &gt;= 0, 0 disables multithreading).</p>
 </div></blockquote>
 <p>-I [ –input-format ] arg</p>
 <blockquote>

diff --git a/master/applications/psdcreate.html b/master/applications/psdcreate.html
@@ -182,7 +182,7 @@ <h2>Other options<a class="headerlink" href="#other-options" title="Permalink to
 <p>-t [ –num-threads ] [=arg(=4)]</p>
 <blockquote>
 <div><p>Number of parallel execution threads (default: no multithreading, implicit value:
-4 threads, must be &gt;= 0, 0 disables multithreading).</p>
+number of CPUs, must be &gt;= 0, 0 disables multithreading).</p>
 </div></blockquote>
 <p>-I [ –input-format ] arg</p>
 <blockquote>

diff --git a/master/applications/psdscreen.html b/master/applications/psdscreen.html
@@ -191,25 +191,25 @@ <h2>Other options<a class="headerlink" href="#other-options" title="Permalink to
 </div></blockquote>
 <p>-m [ –mode ] arg</p>
 <blockquote>
-<div><p>Molecule conformation matching mode (FIRST-MATCH, BEST-MATCH, ALL-MATCHES, default:
+<div><p>Molecule conformer matching mode (FIRST-MATCH, BEST-MATCH, ALL-MATCHES, default:
 FIRST-MATCH).</p>
 </div></blockquote>
 <p>-s [ –start-index ] arg (=0)</p>
 <blockquote>
-<div><p>Screening range start molecule index (zero-based!, default: 0).</p>
+<div><p>Screening start molecule index (zero-based, default: 0).</p>
 </div></blockquote>
 <p>-e [ –end-index ] arg (=0)</p>
 <blockquote>
-<div><p>Screening range end molecule index (zero-based and not included in screening!, default:
-one after last molecule).</p>
+<div><p>Screening end molecule index (zero-based and not included in the
+screening run, default: number of molecules in the database).</p>
 </div></blockquote>
 <p>-n [ –max-num-hits ] arg (=0)</p>
 <blockquote>
 <div><p>Maxmimum number of hits to report (default: no limit).</p>
 </div></blockquote>
 <p>-M [ –max-omitted ] arg (=0)</p>
 <blockquote>
-<div><p>Maximum number of allowed unmatched features.</p>
+<div><p>Allowed maximum number of unmatched features.</p>
 </div></blockquote>
 <p>-x [ –check-xvols ] [=arg(=1)]</p>
 <blockquote>
@@ -250,7 +250,7 @@ <h2>Other options<a class="headerlink" href="#other-options" title="Permalink to
 <p>-t [ –num-threads ] [=arg(=4)]</p>
 <blockquote>
 <div><p>Number of parallel execution threads (default: no multithreading, implicit value:
-4 threads, must be &gt;= 0, 0 disables multithreading).</p>
+number of CPUs, must be &gt;= 0, 0 disables multithreading).</p>
 </div></blockquote>
 <p>-u [ –unique-hits ] [=arg(=1)]</p>
 <blockquote>

diff --git a/master/applications/shapescreen.html b/master/applications/shapescreen.html
@@ -355,7 +355,7 @@ <h2>Other options<a class="headerlink" href="#other-options" title="Permalink to
 <p>-t [ –num-threads ] [=arg(=4)]</p>
 <blockquote>
 <div><p>Number of parallel execution threads (default: no multithreading, implicit value:
-4 threads, must be &gt;= 0, 0 disables multithreading).</p>
+number of CPUs, must be &gt;= 0, 0 disables multithreading).</p>
 </div></blockquote>
 <p>-Q [ –query-format ] arg</p>
 <blockquote>

diff --git a/master/applications/structgen.html b/master/applications/structgen.html
@@ -222,7 +222,7 @@ <h2>Other options<a class="headerlink" href="#other-options" title="Permalink to
 <p>-t [ –num-threads ] [=arg(=4)]</p>
 <blockquote>
 <div><p>Number of parallel execution threads (default: no multithreading, implicit value:
-4 threads, must be &gt;= 0, 0 disables multithreading).</p>
+number of CPUs, must be &gt;= 0, 0 disables multithreading).</p>
 </div></blockquote>
 <p>-m [ –mode ] arg</p>
 <blockquote>

diff --git a/master/applications/tautgen.html b/master/applications/tautgen.html
@@ -204,7 +204,7 @@ <h2>Other options<a class="headerlink" href="#other-options" title="Permalink to
 <p>-t [ –num-threads ] [=arg(=4)]</p>
 <blockquote>
 <div><p>Number of parallel execution threads (default: no multithreading, implicit value:
-4 threads, must be &gt;= 0, 0 disables multithreading).</p>
+number of CPUs, must be &gt;= 0, 0 disables multithreading).</p>
 </div></blockquote>
 <p>-I [ –input-format ] arg</p>
 <blockquote>

diff --git a/master/cdpl_api_doc/c++_api_doc/BuildInfo_8hpp.html b/master/cdpl_api_doc/c++_api_doc/BuildInfo_8hpp.html
@@ -97,7 +97,7 @@
 <tr class="memitem:a51e57b678c884de89185798ef6128d94"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="BuildInfo_8hpp.html#a51e57b678c884de89185798ef6128d94">CDPL_BUILD_SYSTEM</a>&#160;&#160;&#160;&quot;Linux-4.18.0-394.el8.x86_64&quot;</td></tr>
 <tr class="memdesc:a51e57b678c884de89185798ef6128d94"><td class="mdescLeft">&#160;</td><td class="mdescRight"><em>CDPL</em> build system information.  <a href="BuildInfo_8hpp.html#a51e57b678c884de89185798ef6128d94">More...</a><br /></td></tr>
 <tr class="separator:a51e57b678c884de89185798ef6128d94"><td class="memSeparator" colspan="2">&#160;</td></tr>
-<tr class="memitem:ad86a4e1cf8fdd8816ac991f89da6e44a"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="BuildInfo_8hpp.html#ad86a4e1cf8fdd8816ac991f89da6e44a">CDPL_BUILD_TIME</a>&#160;&#160;&#160;202401180000</td></tr>
+<tr class="memitem:ad86a4e1cf8fdd8816ac991f89da6e44a"><td class="memItemLeft" align="right" valign="top">#define&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="BuildInfo_8hpp.html#ad86a4e1cf8fdd8816ac991f89da6e44a">CDPL_BUILD_TIME</a>&#160;&#160;&#160;202401200001</td></tr>
 <tr class="memdesc:ad86a4e1cf8fdd8816ac991f89da6e44a"><td class="mdescLeft">&#160;</td><td class="mdescRight">The <em>CDPL</em> build time in the format <em>YYYYMMDDHHMM</em>.  <a href="BuildInfo_8hpp.html#ad86a4e1cf8fdd8816ac991f89da6e44a">More...</a><br /></td></tr>
 <tr class="separator:ad86a4e1cf8fdd8816ac991f89da6e44a"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table>
@@ -159,7 +159,7 @@ <h2 class="memtitle"><span class="permalink"><a href="#ad86a4e1cf8fdd8816ac991f8
 <div class="memproto">
       <table class="memname">
         <tr>
-          <td class="memname">#define CDPL_BUILD_TIME&#160;&#160;&#160;202401180000</td>
+          <td class="memname">#define CDPL_BUILD_TIME&#160;&#160;&#160;202401200001</td>
         </tr>
       </table>
 </div><div class="memdoc">

diff --git a/master/cdpl_api_doc/c++_api_doc/BuildInfo_8hpp_source.html b/master/cdpl_api_doc/c++_api_doc/BuildInfo_8hpp_source.html
@@ -110,7 +110,7 @@
 <div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160; </div>
 <div class="line"><a name="l00045"></a><span class="lineno"><a class="line" href="BuildInfo_8hpp.html#a51e57b678c884de89185798ef6128d94">   45</a></span>&#160;<span class="preprocessor">#define CDPL_BUILD_SYSTEM     &quot;Linux-4.18.0-394.el8.x86_64&quot;</span></div>
 <div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160; </div>
-<div class="line"><a name="l00050"></a><span class="lineno"><a class="line" href="BuildInfo_8hpp.html#ad86a4e1cf8fdd8816ac991f89da6e44a">   50</a></span>&#160;<span class="preprocessor">#define CDPL_BUILD_TIME        202401180000</span></div>
+<div class="line"><a name="l00050"></a><span class="lineno"><a class="line" href="BuildInfo_8hpp.html#ad86a4e1cf8fdd8816ac991f89da6e44a">   50</a></span>&#160;<span class="preprocessor">#define CDPL_BUILD_TIME        202401200001</span></div>
 <div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160; </div>
 <div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;<span class="preprocessor">#endif // CDPL_BUILDINFO_HPP</span></div>
 </div><!-- fragment --></div><!-- contents -->