deploy: daaf57d

Author: sbillinge

_modules/diffpy/structure.html

@@ -106,17 +106,16 @@ <h1>Source code for diffpy.structure</h1><div class="highlight"><pre>
 
 <span class="kn">from</span> <span class="nn">diffpy.structure.atom</span> <span class="kn">import</span> <span class="n">Atom</span>
 <span class="kn">from</span> <span class="nn">diffpy.structure.lattice</span> <span class="kn">import</span> <span class="n">Lattice</span>
+<span class="kn">from</span> <span class="nn">diffpy.structure.parsers</span> <span class="kn">import</span> <span class="n">getParser</span>
 <span class="kn">from</span> <span class="nn">diffpy.structure.pdffitstructure</span> <span class="kn">import</span> <span class="n">PDFFitStructure</span>
 <span class="kn">from</span> <span class="nn">diffpy.structure.structure</span> <span class="kn">import</span> <span class="n">Structure</span>
 <span class="kn">from</span> <span class="nn">diffpy.structure.structureerrors</span> <span class="kn">import</span> <span class="n">LatticeError</span><span class="p">,</span> <span class="n">StructureFormatError</span><span class="p">,</span> <span class="n">SymmetryError</span>
 
-<span class="c1"># obtain version information</span>
-
-<span class="sd">&quot;&quot;&quot;Crystal structure container and parsers for structure formats.&quot;&quot;&quot;</span>
-
 <span class="c1"># package version</span>
 <span class="kn">from</span> <span class="nn">diffpy.structure.version</span> <span class="kn">import</span> <span class="n">__version__</span>
 
+<span class="sd">&quot;&quot;&quot;Crystal structure container and parsers for structure formats.&quot;&quot;&quot;</span>
+
 <span class="c1"># top level routines</span>
 
 
@@ -147,7 +146,6 @@ <h1>Source code for diffpy.structure</h1><div class="highlight"><pre>
 <span class="sd">        Return a more specific PDFFitStructure type for &#39;pdffit&#39;</span>
 <span class="sd">        and &#39;discus&#39; formats.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="kn">from</span> <span class="nn">diffpy.structure.parsers</span> <span class="kn">import</span> <span class="n">getParser</span>
 
     <span class="n">p</span> <span class="o">=</span> <span class="n">getParser</span><span class="p">(</span><span class="n">fmt</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">)</span>
     <span class="n">rv</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">parseFile</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>

_modules/diffpy/structure/apps/anyeye.html

@@ -118,7 +118,7 @@ <h1>Source code for diffpy.structure.apps.anyeye</h1><div class="highlight"><pre
 <span class="kn">import</span> <span class="nn">signal</span>
 <span class="kn">import</span> <span class="nn">sys</span>
 
-<span class="kn">from</span> <span class="nn">diffpy.structure</span> <span class="kn">import</span> <span class="n">StructureFormatError</span>
+<span class="kn">from</span> <span class="nn">diffpy.structure.structureerrors</span> <span class="kn">import</span> <span class="n">StructureFormatError</span>
 
 <span class="c1"># parameter dictionary</span>
 <span class="n">pd</span> <span class="o">=</span> <span class="p">{</span>

_modules/diffpy/structure/apps/transtru.html

@@ -113,7 +113,8 @@ <h1>Source code for diffpy.structure.apps.transtru</h1><div class="highlight"><p
 
 <span class="kn">import</span> <span class="nn">sys</span>
 
-<span class="kn">from</span> <span class="nn">diffpy.structure</span> <span class="kn">import</span> <span class="n">Structure</span><span class="p">,</span> <span class="n">StructureFormatError</span>
+<span class="kn">from</span> <span class="nn">diffpy.structure</span> <span class="kn">import</span> <span class="n">Structure</span>
+<span class="kn">from</span> <span class="nn">diffpy.structure.structureerrors</span> <span class="kn">import</span> <span class="n">StructureFormatError</span>
 
 
 <div class="viewcode-block" id="usage">

_modules/diffpy/structure/parsers.html

@@ -109,9 +109,9 @@ <h1>Source code for diffpy.structure.parsers</h1><div class="highlight"><pre>
 <span class="sd">    outputFormats   -- list of available output formats</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
-<span class="kn">from</span> <span class="nn">diffpy.structure</span> <span class="kn">import</span> <span class="n">StructureFormatError</span>
 <span class="kn">from</span> <span class="nn">diffpy.structure.parsers.parser_index_mod</span> <span class="kn">import</span> <span class="n">parser_index</span>
 <span class="kn">from</span> <span class="nn">diffpy.structure.parsers.structureparser</span> <span class="kn">import</span> <span class="n">StructureParser</span>
+<span class="kn">from</span> <span class="nn">diffpy.structure.structureerrors</span> <span class="kn">import</span> <span class="n">StructureFormatError</span>
 
 <span class="c1"># silence pyflakes checker</span>
 <span class="k">assert</span> <span class="n">StructureParser</span>

_modules/diffpy/structure/parsers/p_auto.html

@@ -99,8 +99,8 @@ <h1>Source code for diffpy.structure.parsers.p_auto</h1><div class="highlight"><
 
 <span class="kn">import</span> <span class="nn">os</span>
 
-<span class="kn">from</span> <span class="nn">diffpy.structure</span> <span class="kn">import</span> <span class="n">StructureFormatError</span>
 <span class="kn">from</span> <span class="nn">diffpy.structure.parsers</span> <span class="kn">import</span> <span class="n">StructureParser</span><span class="p">,</span> <span class="n">parser_index</span>
+<span class="kn">from</span> <span class="nn">diffpy.structure.structureerrors</span> <span class="kn">import</span> <span class="n">StructureFormatError</span>
 
 
 <div class="viewcode-block" id="P_auto">

_modules/diffpy/structure/parsers/p_cif.html

@@ -104,8 +104,9 @@ <h1>Source code for diffpy.structure.parsers.p_cif</h1><div class="highlight"><p
 <span class="kn">import</span> <span class="nn">numpy</span>
 <span class="kn">import</span> <span class="nn">six</span>
 
-<span class="kn">from</span> <span class="nn">diffpy.structure</span> <span class="kn">import</span> <span class="n">Atom</span><span class="p">,</span> <span class="n">Lattice</span><span class="p">,</span> <span class="n">Structure</span><span class="p">,</span> <span class="n">StructureFormatError</span>
+<span class="kn">from</span> <span class="nn">diffpy.structure</span> <span class="kn">import</span> <span class="n">Atom</span><span class="p">,</span> <span class="n">Lattice</span><span class="p">,</span> <span class="n">Structure</span>
 <span class="kn">from</span> <span class="nn">diffpy.structure.parsers</span> <span class="kn">import</span> <span class="n">StructureParser</span>
+<span class="kn">from</span> <span class="nn">diffpy.structure.structureerrors</span> <span class="kn">import</span> <span class="n">StructureFormatError</span>
 
 <span class="c1"># ----------------------------------------------------------------------------</span>
 
@@ -550,7 +551,7 @@ <h1>Source code for diffpy.structure.parsers.p_cif</h1><div class="highlight"><p
                 <span class="k">break</span>
             <span class="n">idx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">labelindex</span><span class="p">[</span><span class="n">lb</span><span class="p">]</span>
             <span class="n">a</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">stru</span><span class="p">[</span><span class="n">idx</span><span class="p">]</span>
-            <span class="k">if</span> <span class="ow">not</span> <span class="n">lb</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">anisotropy</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">lb</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">anisotropy</span><span class="p">:</span>
                 <span class="n">a</span><span class="o">.</span><span class="n">anisotropy</span> <span class="o">=</span> <span class="kc">True</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">anisotropy</span><span class="p">[</span><span class="n">lb</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
             <span class="k">for</span> <span class="n">fset</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">prop_setters</span><span class="p">,</span> <span class="n">values</span><span class="p">):</span>
@@ -634,7 +635,7 @@ <h1>Source code for diffpy.structure.parsers.p_cif</h1><div class="highlight"><p
         <span class="c1"># setup anisotropy according to symmetry requirements</span>
         <span class="c1"># unless it was already explicitly set</span>
         <span class="k">for</span> <span class="n">ca</span><span class="p">,</span> <span class="n">uisotropy</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stru</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">eau</span><span class="o">.</span><span class="n">Uisotropy</span><span class="p">):</span>
-            <span class="k">if</span> <span class="ow">not</span> <span class="n">ca</span><span class="o">.</span><span class="n">label</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">anisotropy</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">ca</span><span class="o">.</span><span class="n">label</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">anisotropy</span><span class="p">:</span>
                 <span class="n">ca</span><span class="o">.</span><span class="n">anisotropy</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">uisotropy</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">anisotropy</span><span class="p">[</span><span class="n">ca</span><span class="o">.</span><span class="n">label</span><span class="p">]</span> <span class="o">=</span> <span class="n">ca</span><span class="o">.</span><span class="n">anisotropy</span>
         <span class="c1"># build a nested list of new atoms:</span>

_modules/diffpy/structure/parsers/p_discus.html

@@ -100,8 +100,9 @@ <h1>Source code for diffpy.structure.parsers.p_discus</h1><div class="highlight"
 
 <span class="kn">import</span> <span class="nn">six</span>
 
-<span class="kn">from</span> <span class="nn">diffpy.structure</span> <span class="kn">import</span> <span class="n">Lattice</span><span class="p">,</span> <span class="n">PDFFitStructure</span><span class="p">,</span> <span class="n">StructureFormatError</span>
+<span class="kn">from</span> <span class="nn">diffpy.structure</span> <span class="kn">import</span> <span class="n">Lattice</span><span class="p">,</span> <span class="n">PDFFitStructure</span>
 <span class="kn">from</span> <span class="nn">diffpy.structure.parsers</span> <span class="kn">import</span> <span class="n">StructureParser</span>
+<span class="kn">from</span> <span class="nn">diffpy.structure.structureerrors</span> <span class="kn">import</span> <span class="n">StructureFormatError</span>
 
 
 <div class="viewcode-block" id="P_discus">

_modules/diffpy/structure/parsers/p_pdb.html

@@ -106,8 +106,9 @@ <h1>Source code for diffpy.structure.parsers.p_pdb</h1><div class="highlight"><p
 <span class="kn">import</span> <span class="nn">six</span>
 <span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">pi</span>
 
-<span class="kn">from</span> <span class="nn">diffpy.structure</span> <span class="kn">import</span> <span class="n">Structure</span><span class="p">,</span> <span class="n">StructureFormatError</span>
+<span class="kn">from</span> <span class="nn">diffpy.structure</span> <span class="kn">import</span> <span class="n">Structure</span>
 <span class="kn">from</span> <span class="nn">diffpy.structure.parsers</span> <span class="kn">import</span> <span class="n">StructureParser</span>
+<span class="kn">from</span> <span class="nn">diffpy.structure.structureerrors</span> <span class="kn">import</span> <span class="n">StructureFormatError</span>
 
 
 <div class="viewcode-block" id="P_pdb">