Merge pull request #71 from rinikerlab/TI_update_traj_centering

Ti update traj centering
rinikerlab · May 26, 2021 · f23a92b · f23a92b
2 parents 268be6a + 118a9c2
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diff --git a/docs/Examples/example_PyGromosPP.html b/docs/Examples/example_PyGromosPP.html
diff --git a/docs/Examples/example_PyGromosPP.ipynb b/docs/Examples/example_PyGromosPP.ipynb
diff --git a/docs/Examples/example_TI_gromos_simulation.html b/docs/Examples/example_TI_gromos_simulation.html
diff --git a/docs/Examples/example_TI_gromos_simulation.ipynb b/docs/Examples/example_TI_gromos_simulation.ipynb
diff --git a/docs/Examples/example_gromos_files.html b/docs/Examples/example_gromos_files.html
diff --git a/docs/Examples/example_gromos_files.ipynb b/docs/Examples/example_gromos_files.ipynb
diff --git a/docs/Examples/example_gromos_simulation.html b/docs/Examples/example_gromos_simulation.html
diff --git a/docs/Examples/example_gromos_simulation.ipynb b/docs/Examples/example_gromos_simulation.ipynb
diff --git a/docs/Examples/example_gromos_trajectories.html b/docs/Examples/example_gromos_trajectories.html
diff --git a/docs/Examples/example_gromos_trajectories.ipynb b/docs/Examples/example_gromos_trajectories.ipynb
diff --git a/docs/Examples/example_hvap.html b/docs/Examples/example_hvap.html
diff --git a/docs/Examples/example_hvap.ipynb b/docs/Examples/example_hvap.ipynb
diff --git a/docs/Examples/example_submission_systems.html b/docs/Examples/example_submission_systems.html
diff --git a/docs/Examples/example_submission_systems.ipynb b/docs/Examples/example_submission_systems.ipynb
diff --git a/docs/Examples/example_topology_creation.html b/docs/Examples/example_topology_creation.html
diff --git a/docs/Examples/example_topology_creation.ipynb b/docs/Examples/example_topology_creation.ipynb
diff --git a/docs/Examples/index.html b/docs/Examples/index.html
@@ -93,6 +93,8 @@
 <li class="toctree-l2"><a class="reference internal" href="example_gromos_files.html">PyGromos File Examples</a></li>
 <li class="toctree-l2"><a class="reference internal" href="example_gromos_simulation.html">SD Simulations with Submission System</a></li>
 <li class="toctree-l2"><a class="reference internal" href="example_gromos_trajectories.html">Gromos Trajectory evaluation with Pygromos and Pandas</a></li>
+<li class="toctree-l2"><a class="reference internal" href="example_submission_systems.html">Submission Systems</a></li>
+<li class="toctree-l2"><a class="reference internal" href="example_topology_creation.html">Topology creation and modifications with PyGromosTools</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../Tutorials/index.html">Tutorials</a></li>
@@ -213,13 +215,7 @@ <h1>Examples<a class="headerlink" href="#examples" title="Permalink to this head
 <li class="toctree-l3"><a class="reference internal" href="example_TI_gromos_simulation.html#Setup-again">Setup again</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="example_TI_gromos_simulation.html#Submission">Submission</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="example_TI_gromos_simulation.html#Direction-B-&gt;A">Direction B-&gt;A</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="example_TI_gromos_simulation.html#id1">Setup:</a></li>
-</ul>
-</li>
-</ul>
-</li>
+<li class="toctree-l2"><a class="reference internal" href="example_TI_gromos_simulation.html#Submission">Submission</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="example_gromos_files.html">PyGromos File Examples</a><ul>
@@ -238,6 +234,9 @@ <h1>Examples<a class="headerlink" href="#examples" title="Permalink to this head
 <li class="toctree-l3"><a class="reference internal" href="example_gromos_files.html#Read-in-ptp-file:">Read in ptp file:</a></li>
 <li class="toctree-l3"><a class="reference internal" href="example_gromos_files.html#delete-full-state">delete full state</a></li>
 <li class="toctree-l3"><a class="reference internal" href="example_gromos_files.html#delete-specific-atoms">delete specific atoms</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="example_gromos_files.html#Write-out-ptp-file">Write out ptp file</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="example_gromos_files.html#Add-atom-or-state-or-overwrite-atominformation-(except-atom.NR)">Add atom or state or overwrite atominformation (except atom.NR)</a></li>
 <li class="toctree-l3"><a class="reference internal" href="example_gromos_files.html#Building-ptp-from-scratch-and-generate-all-possible-state-combinations:">Building ptp from scratch and generate all possible state combinations:</a></li>
 </ul>
@@ -277,6 +276,22 @@ <h1>Examples<a class="headerlink" href="#examples" title="Permalink to this head
 <li class="toctree-l2"><a class="reference internal" href="example_gromos_trajectories.html#Concatenate-and-Copy-multiple-Trajectories">Concatenate and Copy multiple Trajectories</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="example_submission_systems.html">Submission Systems</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="example_submission_systems.html#Local-Submission">Local Submission</a></li>
+<li class="toctree-l2"><a class="reference internal" href="example_submission_systems.html#LSF-Submission">LSF Submission</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="example_submission_systems.html#Queue-Checking:">Queue Checking:</a></li>
+<li class="toctree-l3"><a class="reference internal" href="example_submission_systems.html#Submission:">Submission:</a></li>
+<li class="toctree-l3"><a class="reference internal" href="example_submission_systems.html#Submitting-multiple-jobs">Submitting multiple jobs</a></li>
+<li class="toctree-l3"><a class="reference internal" href="example_submission_systems.html#Killing-a-jobs">Killing a jobs</a></li>
+</ul>
+</li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="example_topology_creation.html">Topology creation and modifications with PyGromosTools</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="example_topology_creation.html#Automatic-System-generation-and-combining-of-topologies">Automatic System generation and combining of topologies</a></li>
+<li class="toctree-l2"><a class="reference internal" href="example_topology_creation.html#Manual-topology-modifications">Manual topology modifications</a></li>
+</ul>
+</li>
 </ul>
 </div>
 </div>

diff --git a/docs/Tutorials/index.html b/docs/Tutorials/index.html
@@ -39,8 +39,8 @@
 
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="Pygromos: OOP in python 3" href="talk_pygromos_and_oop.html" />
-    <link rel="prev" title="Gromos Trajectory evaluation with Pygromos and Pandas" href="../Examples/example_gromos_trajectories.html" /> 
+    <link rel="next" title="Gromos Tutorial Pipeline" href="tutorial_gromos_pipeline.html" />
+    <link rel="prev" title="Topology creation and modifications with PyGromosTools" href="../Examples/example_topology_creation.html" /> 
 </head>
 
 <body class="wy-body-for-nav">
@@ -89,7 +89,6 @@
 <li class="toctree-l1"><a class="reference internal" href="../introduction.html">Welcome to PyGromosTools</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../Examples/index.html">Examples</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Tutorials</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="talk_pygromos_and_oop.html">Pygromos: OOP in python 3</a></li>
 <li class="toctree-l2"><a class="reference internal" href="tutorial_gromos_pipeline.html">Gromos Tutorial Pipeline</a></li>
 </ul>
 </li>
@@ -189,46 +188,6 @@
 <h1>Tutorials<a class="headerlink" href="#tutorials" title="Permalink to this headline">¶</a></h1>
 <div class="toctree-wrapper compound">
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="talk_pygromos_and_oop.html">Pygromos: OOP in python 3</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="talk_pygromos_and_oop.html#Implementations-of-OOP-in-Python3">Implementations of OOP in Python3</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="talk_pygromos_and_oop.html#Definition-of-a-Class">Definition of a Class</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="talk_pygromos_and_oop.html#Magic-functions-(****)">Magic functions (****)</a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="talk_pygromos_and_oop.html#Class-Attributes">Class Attributes</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="talk_pygromos_and_oop.html#Accessibility">Accessibility</a></li>
-<li class="toctree-l4"><a class="reference internal" href="talk_pygromos_and_oop.html#Mutability-of-Class-Attributes">Mutability of Class Attributes</a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="talk_pygromos_and_oop.html#Methods">Methods</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="talk_pygromos_and_oop.html#Levels">Levels</a></li>
-<li class="toctree-l4"><a class="reference internal" href="talk_pygromos_and_oop.html#Overwriting-methods-on-Runtime">Overwriting methods on Runtime</a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="talk_pygromos_and_oop.html#Inheritance">Inheritance</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="talk_pygromos_and_oop.html#Type-Testing-&amp;-implicit-Polymorphism">Type Testing &amp; implicit Polymorphism</a></li>
-</ul>
-</li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="talk_pygromos_and_oop.html#Using-Pygromos">Using Pygromos</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="talk_pygromos_and_oop.html#PyGromos-Wrapper:">PyGromos Wrapper:</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="talk_pygromos_and_oop.html#Example-gromosPP:">Example gromosPP:</a></li>
-<li class="toctree-l4"><a class="reference internal" href="talk_pygromos_and_oop.html#Example-for-gromosXX:">Example for gromosXX:</a></li>
-</ul>
-</li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="talk_pygromos_and_oop.html#PyGromos-Files:">PyGromos Files:</a></li>
-<li class="toctree-l2"><a class="reference internal" href="talk_pygromos_and_oop.html#Additional:-functional-programming---BONUS">Additional: functional programming - BONUS</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="talk_pygromos_and_oop.html#Lambda-functions">Lambda functions</a></li>
-<li class="toctree-l3"><a class="reference internal" href="talk_pygromos_and_oop.html#preimplemented-functions">preimplemented functions</a></li>
-<li class="toctree-l3"><a class="reference internal" href="talk_pygromos_and_oop.html#list/dict---comprehensions">list/dict - comprehensions</a></li>
-<li class="toctree-l3"><a class="reference internal" href="talk_pygromos_and_oop.html#decorators---how-they-work">decorators - how they work</a></li>
-</ul>
-</li>
-</ul>
-</li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_gromos_pipeline.html">Gromos Tutorial Pipeline</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="tutorial_gromos_pipeline.html#Build-initial-files">Build initial files</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="tutorial_gromos_pipeline.html#generate-Topology">generate Topology</a><ul>
@@ -271,8 +230,8 @@ <h1>Tutorials<a class="headerlink" href="#tutorials" title="Permalink to this he
           </div>
           <footer>
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
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+        <a href="../Examples/example_topology_creation.html" class="btn btn-neutral float-left" title="Topology creation and modifications with PyGromosTools" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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