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‎_modules/diffpy/structure.html‎

Lines changed: 24 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -90,16 +90,26 @@ <h1>Source code for diffpy.structure</h1><div class="highlight"><pre>
9090
<span class="c1">#</span>
9191
<span class="c1">##############################################################################</span>
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93-
<span class="sd">&quot;&quot;&quot;classes related to structure of materials</span>
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<span class="sd">Classes:</span>
95-
<span class="sd"> Atom</span>
96-
<span class="sd"> Lattice</span>
97-
<span class="sd"> Structure</span>
98-
<span class="sd"> PDFFitStructure</span>
93+
<span class="sd">&quot;&quot;&quot;</span>
94+
<span class="sd">Crystal structure container and parsers for structure formats.</span>
95+
96+
<span class="sd">Classes related to the structure of materials:</span>
97+
<span class="sd"> * Atom</span>
98+
<span class="sd"> * Lattice</span>
99+
<span class="sd"> * Structure</span>
100+
<span class="sd"> * PDFFitStructure</span>
101+
102+
<span class="sd">Other classes:</span>
103+
<span class="sd"> * SpaceGroup</span>
104+
<span class="sd"> * SymOp</span>
105+
<span class="sd"> * ExpandAsymmetricUnit</span>
106+
<span class="sd"> * GeneratorSite</span>
107+
<span class="sd"> * SymmetryConstraints</span>
108+
99109
<span class="sd">Exceptions:</span>
100-
<span class="sd"> StructureFormatError</span>
101-
<span class="sd"> LatticeError</span>
102-
<span class="sd"> SymmetryError</span>
110+
<span class="sd"> * StructureFormatError</span>
111+
<span class="sd"> * LatticeError</span>
112+
<span class="sd"> * SymmetryError</span>
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<span class="sd">&quot;&quot;&quot;</span>
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105115
<span class="c1"># Interface definitions ------------------------------------------------------</span>
@@ -114,29 +124,26 @@ <h1>Source code for diffpy.structure</h1><div class="highlight"><pre>
114124
<span class="c1"># package version</span>
115125
<span class="kn">from</span> <span class="nn">diffpy.structure.version</span> <span class="kn">import</span> <span class="n">__version__</span>
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117-
<span class="sd">&quot;&quot;&quot;Crystal structure container and parsers for structure formats.&quot;&quot;&quot;</span>
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119127
<span class="c1"># top level routines</span>
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121129

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<div class="viewcode-block" id="loadStructure">
123131
<a class="viewcode-back" href="../../api/diffpy.structure.html#diffpy.structure.loadStructure">[docs]</a>
124132
<span class="k">def</span> <span class="nf">loadStructure</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">fmt</span><span class="o">=</span><span class="s2">&quot;auto&quot;</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
125-
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
126-
<span class="sd"> Load new structure object from the specified file.</span>
133+
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Load new structure object from the specified file.</span>
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128135
<span class="sd"> Parameters</span>
129136
<span class="sd"> ----------</span>
130137

131138
<span class="sd"> filename : str</span>
132139
<span class="sd"> Path to the file to be loaded.</span>
133-
<span class="sd"> fmt : str, optional</span>
134-
<span class="sd"> Format of the structure file such as &#39;cif&#39; or &#39;xyz&#39;. Must be</span>
140+
<span class="sd"> fmt : str, Optional</span>
141+
<span class="sd"> Format of the structure file such as &#39;cif&#39; or &#39;xyz&#39;. Must be</span>
135142
<span class="sd"> one of the formats listed by the `parsers.inputFormats` function.</span>
136143
<span class="sd"> When &#39;auto&#39;, all supported formats are tried in a sequence.</span>
137-
<span class="sd"> kw : misc, optional</span>
144+
<span class="sd"> kw : Optional</span>
138145
<span class="sd"> Extra keyword arguments that are passed to `parsers.getParser`</span>
139-
<span class="sd"> function. These configure the dedicated Parser object that</span>
146+
<span class="sd"> function. These configure the dedicated Parser object that</span>
140147
<span class="sd"> is used to read content in filename.</span>
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142149
<span class="sd"> Returns</span>

‎_modules/diffpy/structure/_legacy_importer.html‎

Lines changed: 12 additions & 42 deletions
Original file line numberDiff line numberDiff line change
@@ -95,33 +95,23 @@ <h1>Source code for diffpy.structure._legacy_importer</h1><div class="highlight"
9595
<span class="sd">Support import of old camel-case module names with DeprecationWarning.</span>
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9797
<span class="sd">The imported camel-case modules are aliases for the current module</span>
98-
<span class="sd">instances. Their `__name__` attributes are thus all in lower-case.</span>
98+
<span class="sd">instances. Their `__name__` attributes are thus all in lower-case.</span>
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<span class="sd">This module is deprecated and will be removed in the future.</span>
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<span class="sd">Note</span>
101+
<span class="sd">----</span>
102+
<span class="sd">this module must be only imported from `diffpy.Structure`.</span>
101103

102-
<span class="sd">NOTE: this module must be only imported from `diffpy.Structure`.</span>
104+
<span class="sd">Warning</span>
105+
<span class="sd">-------</span>
106+
<span class="sd">This module is deprecated and will be removed in the future.</span>
103107
<span class="sd">&quot;&quot;&quot;</span>
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105109

110+
<span class="kn">import</span> <span class="nn">importlib.abc</span>
106111
<span class="kn">import</span> <span class="nn">sys</span>
107112
<span class="kn">from</span> <span class="nn">warnings</span> <span class="kn">import</span> <span class="n">warn</span>
108113

109-
<span class="kn">import</span> <span class="nn">six</span>
110-
111-
<span class="k">if</span> <span class="n">six</span><span class="o">.</span><span class="n">PY2</span><span class="p">:</span>
112-
<span class="kn">import</span> <span class="nn">importlib</span>
113-
114-
<span class="k">class</span> <span class="nc">mock_importlib_abc</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
115-
<span class="n">MetaPathFinder</span> <span class="o">=</span> <span class="nb">object</span>
116-
<span class="n">Loader</span> <span class="o">=</span> <span class="nb">object</span>
117-
118-
<span class="n">importlib</span><span class="o">.</span><span class="n">abc</span> <span class="o">=</span> <span class="n">mock_importlib_abc</span>
119-
<span class="n">sys</span><span class="o">.</span><span class="n">modules</span><span class="o">.</span><span class="n">setdefault</span><span class="p">(</span><span class="s2">&quot;importlib.abc&quot;</span><span class="p">,</span> <span class="n">mock_importlib_abc</span><span class="p">)</span>
120-
<span class="k">del</span> <span class="n">mock_importlib_abc</span>
121-
122-
<span class="kn">import</span> <span class="nn">importlib.abc</span>
123-
124-
<span class="n">WMSG</span> <span class="o">=</span> <span class="s2">&quot;Module </span><span class="si">{!r}</span><span class="s2"> is deprecated. Use </span><span class="si">{!r}</span><span class="s2"> instead.&quot;</span>
114+
<span class="n">WMSG</span> <span class="o">=</span> <span class="s2">&quot;Module </span><span class="si">{!r}</span><span class="s2"> is deprecated. Use </span><span class="si">{!r}</span><span class="s2"> instead.&quot;</span>
125115

126116
<span class="c1"># ----------------------------------------------------------------------------</span>
127117

@@ -144,16 +134,7 @@ <h1>Source code for diffpy.structure._legacy_importer</h1><div class="highlight"
144134
<span class="n">spec</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">fullname</span>
145135
<span class="n">spec</span><span class="o">.</span><span class="n">loader</span> <span class="o">=</span> <span class="n">MapRenamedStructureModule</span><span class="p">()</span>
146136
<span class="k">return</span> <span class="n">spec</span></div>
147-
148-
149-
<span class="k">if</span> <span class="n">six</span><span class="o">.</span><span class="n">PY2</span><span class="p">:</span>
150-
151-
<span class="k">def</span> <span class="nf">find_module</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fullname</span><span class="p">,</span> <span class="n">path</span><span class="p">):</span>
152-
<span class="c1"># only handle submodules of diffpy.Structure</span>
153-
<span class="n">loader</span> <span class="o">=</span> <span class="kc">None</span>
154-
<span class="k">if</span> <span class="n">fullname</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">prefix</span><span class="p">):</span>
155-
<span class="n">loader</span> <span class="o">=</span> <span class="n">MapRenamedStructureModule</span><span class="p">()</span>
156-
<span class="k">return</span> <span class="n">loader</span></div>
137+
</div>
157138

158139

159140

@@ -165,9 +146,7 @@ <h1>Source code for diffpy.structure._legacy_importer</h1><div class="highlight"
165146
<div class="viewcode-block" id="MapRenamedStructureModule">
166147
<a class="viewcode-back" href="../../../api/diffpy.structure.html#diffpy.structure._legacy_importer.MapRenamedStructureModule">[docs]</a>
167148
<span class="k">class</span> <span class="nc">MapRenamedStructureModule</span><span class="p">(</span><span class="n">importlib</span><span class="o">.</span><span class="n">abc</span><span class="o">.</span><span class="n">Loader</span><span class="p">):</span>
168-
<span class="w"> </span><span class="sd">&quot;&quot;&quot;</span>
169-
<span class="sd"> Loader for old camel-case module names.</span>
170-
149+
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Loader for old camel-case module names.</span>
171150
<span class="sd"> Import the current module and alias it under the old name.</span>
172151
<span class="sd"> &quot;&quot;&quot;</span>
173152

@@ -185,16 +164,7 @@ <h1>Source code for diffpy.structure._legacy_importer</h1><div class="highlight"
185164
<a class="viewcode-back" href="../../../api/diffpy.structure.html#diffpy.structure._legacy_importer.MapRenamedStructureModule.exec_module">[docs]</a>
186165
<span class="k">def</span> <span class="nf">exec_module</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">module</span><span class="p">):</span>
187166
<span class="k">return</span></div>
188-
189-
190-
<span class="k">if</span> <span class="n">six</span><span class="o">.</span><span class="n">PY2</span><span class="p">:</span>
191-
<span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">namedtuple</span>
192-
193-
<span class="n">ModuleSpec</span> <span class="o">=</span> <span class="n">namedtuple</span><span class="p">(</span><span class="s2">&quot;ModuleSpec&quot;</span><span class="p">,</span> <span class="s2">&quot;name&quot;</span><span class="p">)</span>
194-
195-
<span class="k">def</span> <span class="nf">load_module</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fullname</span><span class="p">):</span>
196-
<span class="n">spec</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">ModuleSpec</span><span class="p">(</span><span class="n">fullname</span><span class="p">)</span>
197-
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">create_module</span><span class="p">(</span><span class="n">spec</span><span class="p">)</span></div>
167+
</div>
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199169

200170

‎_modules/diffpy/structure/apps/anyeye.html‎

Lines changed: 41 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -91,24 +91,37 @@ <h1>Source code for diffpy.structure.apps.anyeye</h1><div class="highlight"><pre
9191
<span class="c1">#</span>
9292
<span class="c1">##############################################################################</span>
9393

94-
<span class="sd">&quot;&quot;&quot;anyeye view structure file in atomeye</span>
95-
<span class="sd">Usage: anyeye [options] strufile</span>
94+
<span class="sd">&quot;&quot;&quot;</span>
95+
<span class="sd">Anyeye view structure file in atomeye.</span>
96+
97+
<span class="sd">Usage: ``anyeye [options] strufile``</span>
9698

97-
<span class="sd">anyeye understands more structure formats than atomeye. It converts strufile</span>
98-
<span class="sd">to a temporary XCFG file which is opened in atomeye. Supported file formats:</span>
99-
<span class="sd"> inputFormats</span>
99+
<span class="sd">Anyeye understands more `Structure` formats than atomeye. It converts `strufile`</span>
100+
<span class="sd">to a temporary XCFG file which is opened in atomeye. See supported file formats:</span>
101+
<span class="sd">``inputFormats``</span>
100102

101103
<span class="sd">Options:</span>
102-
<span class="sd"> -f, --formula override chemical formula in strufile, formula defines</span>
103-
<span class="sd"> elements in the same order as in strufile, e.g, Na4Cl4</span>
104-
<span class="sd"> -w, --watch watch input file for changes</span>
105-
<span class="sd"> --viewer=VIEWER the structure viewer program, by default &quot;atomeye&quot;.</span>
106-
<span class="sd"> The program will be executed as &quot;VIEWER structurefile&quot;</span>
107-
<span class="sd"> --formats=FORMATS comma separated list of file formats that are understood</span>
108-
<span class="sd"> by the VIEWER, by default &quot;xcfg,pdb&quot;. Files of other</span>
109-
<span class="sd"> formats will be converted to the first listed format.</span>
110-
<span class="sd"> -h, --help display this message and exit</span>
111-
<span class="sd"> -V, --version show script version and exit</span>
104+
<span class="sd"> -f, --formula</span>
105+
<span class="sd"> Override chemical formula in `strufile`. The formula defines</span>
106+
<span class="sd"> elements in the same order as in `strufile`, e.g., ``Na4Cl4``.</span>
107+
108+
<span class="sd"> -w, --watch</span>
109+
<span class="sd"> Watch input file for changes.</span>
110+
111+
<span class="sd"> --viewer=VIEWER</span>
112+
<span class="sd"> The structure viewer program, by default &quot;atomeye&quot;.</span>
113+
<span class="sd"> The program will be executed as &quot;VIEWER structurefile&quot;.</span>
114+
115+
<span class="sd"> --formats=FORMATS</span>
116+
<span class="sd"> Comma-separated list of file formats that are understood</span>
117+
<span class="sd"> by the VIEWER, by default ``&quot;xcfg,pdb&quot;``. Files of other</span>
118+
<span class="sd"> formats will be converted to the first listed format.</span>
119+
120+
<span class="sd"> -h, --help</span>
121+
<span class="sd"> Display this message and exit.</span>
122+
123+
<span class="sd"> -V, --version</span>
124+
<span class="sd"> Show script version and exit.</span>
112125
<span class="sd">&quot;&quot;&quot;</span>
113126

114127
<span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">print_function</span>
@@ -132,7 +145,7 @@ <h1>Source code for diffpy.structure.apps.anyeye</h1><div class="highlight"><pre
132145
<div class="viewcode-block" id="usage">
133146
<a class="viewcode-back" href="../../../../diffpy.structure.apps.html#diffpy.structure.apps.anyeye.usage">[docs]</a>
134147
<span class="k">def</span> <span class="nf">usage</span><span class="p">(</span><span class="n">style</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
135-
<span class="w"> </span><span class="sd">&quot;&quot;&quot;show usage info, for style==&quot;brief&quot; show only first 2 lines&quot;&quot;&quot;</span>
148+
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Show usage info, for ``style==&quot;brief&quot;`` show only first 2 lines.&quot;&quot;&quot;</span>
136149
<span class="kn">import</span> <span class="nn">os.path</span>
137150

138151
<span class="n">myname</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
@@ -164,7 +177,17 @@ <h1>Source code for diffpy.structure.apps.anyeye</h1><div class="highlight"><pre
164177
<span class="k">def</span> <span class="nf">loadStructureFile</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="s2">&quot;auto&quot;</span><span class="p">):</span>
165178
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Load structure from specified file.</span>
166179

167-
<span class="sd"> Return a tuple of (Structure, fileformat).</span>
180+
<span class="sd"> Parameters</span>
181+
<span class="sd"> ----------</span>
182+
<span class="sd"> filename : str</span>
183+
<span class="sd"> Path to the structure file.</span>
184+
<span class="sd"> format : str, Optional</span>
185+
<span class="sd"> File format, by default &quot;auto&quot;.</span>
186+
187+
<span class="sd"> Returns</span>
188+
<span class="sd"> -------</span>
189+
<span class="sd"> tuple</span>
190+
<span class="sd"> A tuple of (Structure, fileformat).</span>
168191
<span class="sd"> &quot;&quot;&quot;</span>
169192
<span class="kn">from</span> <span class="nn">diffpy.structure</span> <span class="kn">import</span> <span class="n">Structure</span>
170193

@@ -250,7 +273,7 @@ <h1>Source code for diffpy.structure.apps.anyeye</h1><div class="highlight"><pre
250273
<div class="viewcode-block" id="parseFormula">
251274
<a class="viewcode-back" href="../../../../diffpy.structure.apps.html#diffpy.structure.apps.anyeye.parseFormula">[docs]</a>
252275
<span class="k">def</span> <span class="nf">parseFormula</span><span class="p">(</span><span class="n">formula</span><span class="p">):</span>
253-
<span class="w"> </span><span class="sd">&quot;&quot;&quot;parse chemical formula and return a list of elements&quot;&quot;&quot;</span>
276+
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Parse chemical formula and return a list of elements&quot;&quot;&quot;</span>
254277
<span class="c1"># remove all blanks</span>
255278
<span class="n">formula</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;\s&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">,</span> <span class="n">formula</span><span class="p">)</span>
256279
<span class="k">if</span> <span class="ow">not</span> <span class="n">re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">&quot;^[A-Z]&quot;</span><span class="p">,</span> <span class="n">formula</span><span class="p">):</span>

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