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JelfsMaterialsGroup · Jul 20, 2018 · d7b0835 · d7b0835
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Showing 8 changed files with 1,756 additions and 38 deletions.
diff --git a/docs/_modules/pywindow/molecular.html b/docs/_modules/pywindow/molecular.html
@@ -910,19 +910,19 @@ <h1>Source code for pywindow.molecular</h1><div class="highlight"><pre>
 
 <span class="sd">    .. code-block:: python</span>
 
-<span class="sd">        pywindow.MolecularSystem.load_file(`filepath`)</span>
+<span class="sd">        pywindow.molecular.MolecularSystem.load_file(`filepath`)</span>
 
 <span class="sd">    2. Using RDKit molecule object as an input:</span>
 
 <span class="sd">    .. code-block:: python</span>
 
-<span class="sd">        pywindow.MolecularSystem.load_rdkit_mol(rdkit.Chem.rdchem.Mol)</span>
+<span class="sd">        pywindow.molecular.MolecularSystem.load_rdkit_mol(rdkit.Chem.rdchem.Mol)</span>
 
 <span class="sd">    3. Using a dictionary (or another :attr:`MoleculeSystem.system`) as input:</span>
 
 <span class="sd">    .. code-block:: python</span>
 
-<span class="sd">        pywindow.MolecularSystem.load_system({...})</span>
+<span class="sd">        pywindow.molecular.MolecularSystem.load_system({...})</span>
 
 <span class="sd">    Attributes</span>
 <span class="sd">    ----------</span>
@@ -1076,7 +1076,7 @@ <h1>Source code for pywindow.molecular</h1><div class="highlight"><pre>
 
 <span class="sd">        .. code-block:: python</span>
 
-<span class="sd">            pywindow.MolecularSystem.swap_atom_keys({&#39;he&#39;: &#39;H&#39;})</span>
+<span class="sd">            pywindow.molecular.MolecularSystem.swap_atom_keys({&#39;he&#39;: &#39;H&#39;})</span>
 
 <span class="sd">        Parameters</span>
 <span class="sd">        ----------</span>

diff --git a/docs/_modules/pywindow/trajectory.html b/docs/_modules/pywindow/trajectory.html
diff --git a/docs/genindex.html b/docs/genindex.html
@@ -181,6 +181,12 @@ <h2 id="A">A</h2>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="pywindow.html#pywindow.trajectory.DLPOLY.analysis_output">analysis_output (pywindow.trajectory.DLPOLY attribute)</a>
+
+      <ul>
+        <li><a href="pywindow.html#pywindow.trajectory.XYZ.analysis_output">(pywindow.trajectory.XYZ attribute)</a>
+</li>
+      </ul></li>
       <li><a href="pywindow.html#pywindow.utilities.angle_between_vectors">angle_between_vectors() (in module pywindow.utilities)</a>
 </li>
       <li><a href="pywindow.html#pywindow.utilities.asphericity">asphericity() (in module pywindow.utilities)</a>
@@ -289,18 +295,32 @@ <h2 id="E">E</h2>
 <h2 id="F">F</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="pywindow.html#pywindow.trajectory.XYZ.filename">filename (pywindow.trajectory.XYZ attribute)</a>
+</li>
+      <li><a href="pywindow.html#pywindow.trajectory.DLPOLY.filepath">filepath (pywindow.trajectory.DLPOLY attribute)</a>
+
+      <ul>
+        <li><a href="pywindow.html#pywindow.trajectory.XYZ.filepath">(pywindow.trajectory.XYZ attribute)</a>
+</li>
+      </ul></li>
       <li><a href="pywindow.html#pywindow.utilities.find_average_diameter">find_average_diameter() (in module pywindow.utilities)</a>
 </li>
       <li><a href="pywindow.html#pywindow.utilities.find_windows">find_windows() (in module pywindow.utilities)</a>
-</li>
-      <li><a href="pywindow.html#pywindow.utilities.find_windows_new">find_windows_new() (in module pywindow.utilities)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="pywindow.html#pywindow.utilities.find_windows_new">find_windows_new() (in module pywindow.utilities)</a>
+</li>
       <li><a href="pywindow.html#pywindow.utilities.frac2cart_all">frac2cart_all() (in module pywindow.utilities)</a>
 </li>
       <li><a href="pywindow.html#pywindow.utilities.fractional_from_cartesian">fractional_from_cartesian() (in module pywindow.utilities)</a>
 </li>
+      <li><a href="pywindow.html#pywindow.trajectory.DLPOLY.frames">frames (pywindow.trajectory.DLPOLY attribute)</a>
+
+      <ul>
+        <li><a href="pywindow.html#pywindow.trajectory.XYZ.frames">(pywindow.trajectory.XYZ attribute)</a>
+</li>
+      </ul></li>
       <li><a href="pywindow.html#pywindow.molecular.Molecule.full_analysis">full_analysis() (pywindow.molecular.Molecule method)</a>
 </li>
   </ul></td>
@@ -486,7 +506,13 @@ <h2 id="S">S</h2>
 </li>
       </ul></li>
       <li><a href="pywindow.html#pywindow.trajectory.DLPOLY.save_frames">save_frames() (pywindow.trajectory.DLPOLY method)</a>
+
+      <ul>
+        <li><a href="pywindow.html#pywindow.trajectory.PDB.save_frames">(pywindow.trajectory.PDB method)</a>
 </li>
+        <li><a href="pywindow.html#pywindow.trajectory.XYZ.save_frames">(pywindow.trajectory.XYZ method)</a>
+</li>
+      </ul></li>
       <li><a href="pywindow.html#pywindow.utilities.shift_com">shift_com() (in module pywindow.utilities)</a>
 </li>
   </ul></td>
@@ -500,7 +526,13 @@ <h2 id="S">S</h2>
       <li><a href="pywindow.html#pywindow.molecular.MolecularSystem.system">system (pywindow.molecular.MolecularSystem attribute)</a>
 </li>
       <li><a href="pywindow.html#pywindow.molecular.MolecularSystem.system_id">system_id (pywindow.molecular.MolecularSystem attribute)</a>
+
+      <ul>
+        <li><a href="pywindow.html#pywindow.trajectory.DLPOLY.system_id">(pywindow.trajectory.DLPOLY attribute)</a>
+</li>
+        <li><a href="pywindow.html#pywindow.trajectory.XYZ.system_id">(pywindow.trajectory.XYZ attribute)</a>
 </li>
+      </ul></li>
       <li><a href="pywindow.html#pywindow.molecular.MolecularSystem.system_to_molecule">system_to_molecule() (pywindow.molecular.MolecularSystem method)</a>
 </li>
   </ul></td>

diff --git a/docs/objects.inv b/docs/objects.inv