source: trunk/sphinxdocs/build/html/_modules/G2phase.html @ 1123

Last change on this file since 1123 was 1123, checked in by toby, 12 years ago

add import and export routines to sphinx
  • Property svn:mime-type set to text/html
File size: 12.6 KB
Line 
1
2
3<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
6
7<html xmlns="http://www.w3.org/1999/xhtml">
8  <head>
9    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
10   
11    <title>G2phase &mdash; GSAS-II 0.2.0 documentation</title>
12   
13    <link rel="stylesheet" href="../_static/default.css" type="text/css" />
14    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
15   
16    <script type="text/javascript">
17      var DOCUMENTATION_OPTIONS = {
18        URL_ROOT:    '../',
19        VERSION:     '0.2.0',
20        COLLAPSE_INDEX: false,
21        FILE_SUFFIX: '.html',
22        HAS_SOURCE:  true
23      };
24    </script>
25    <script type="text/javascript" src="../_static/jquery.js"></script>
26    <script type="text/javascript" src="../_static/underscore.js"></script>
27    <script type="text/javascript" src="../_static/doctools.js"></script>
28    <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
29    <link rel="top" title="GSAS-II 0.2.0 documentation" href="../index.html" />
30    <link rel="up" title="Module code" href="index.html" /> 
31  </head>
32  <body>
33    <div class="related">
34      <h3>Navigation</h3>
35      <ul>
36        <li class="right" style="margin-right: 10px">
37          <a href="../genindex.html" title="General Index"
38             accesskey="I">index</a></li>
39        <li class="right" >
40          <a href="../py-modindex.html" title="Python Module Index"
41             >modules</a> |</li>
42        <li><a href="../index.html">GSAS-II 0.2.0 documentation</a> &raquo;</li>
43          <li><a href="index.html" accesskey="U">Module code</a> &raquo;</li> 
44      </ul>
45    </div> 
46
47    <div class="document">
48      <div class="documentwrapper">
49        <div class="bodywrapper">
50          <div class="body">
51           
52  <h1>Source code for G2phase</h1><div class="highlight"><pre>
53<span class="c"># -*- coding: utf-8 -*-</span>
54<span class="c">########### SVN repository information ###################</span>
55<span class="c"># $Date: 2013-10-03 13:11:47 -0500 (Thu, 03 Oct 2013) $</span>
56<span class="c"># $Author: toby $</span>
57<span class="c"># $Revision: 1077 $</span>
58<span class="c"># $URL: https://subversion.xor.aps.anl.gov/pyGSAS/trunk/imports/G2phase.py $</span>
59<span class="c"># $Id: G2phase.py 1077 2013-10-03 18:11:47Z toby $</span>
60<span class="c">########### SVN repository information ###################</span>
61<span class="c">#</span>
62<span class="sd">&#39;&#39;&#39;</span>
63<span class="sd">*Module G2phase: PDB and .EXP*</span>
64<span class="sd">------------------------------------</span>
65
66<span class="sd">A set of short routines to read in phases using routines that were</span>
67<span class="sd">previously implemented in GSAS-II: PDB and GSAS .EXP file formats</span>
68
69<span class="sd">&#39;&#39;&#39;</span>
70
71<span class="kn">import</span> <span class="nn">sys</span>
72<span class="kn">import</span> <span class="nn">traceback</span>
73<span class="kn">import</span> <span class="nn">GSASIIIO</span> <span class="kn">as</span> <span class="nn">G2IO</span>
74<span class="kn">import</span> <span class="nn">GSASIIpath</span>
75<span class="n">GSASIIpath</span><span class="o">.</span><span class="n">SetVersionNumber</span><span class="p">(</span><span class="s">&quot;$Revision: 1077 $&quot;</span><span class="p">)</span>
76
77<div class="viewcode-block" id="PDB_ReaderClass"><a class="viewcode-back" href="../imports.html#G2phase.PDB_ReaderClass">[docs]</a><span class="k">class</span> <span class="nc">PDB_ReaderClass</span><span class="p">(</span><span class="n">G2IO</span><span class="o">.</span><span class="n">ImportPhase</span><span class="p">):</span>
78    <span class="s">&#39;Routines to import Phase information from a PDB file&#39;</span>
79    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
80        <span class="nb">super</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span> <span class="c"># fancy way to say ImportPhase.__init__</span>
81            <span class="n">extensionlist</span><span class="o">=</span><span class="p">(</span><span class="s">&#39;.pdb&#39;</span><span class="p">,</span><span class="s">&#39;.ent&#39;</span><span class="p">,</span><span class="s">&#39;.PDB&#39;</span><span class="p">,</span><span class="s">&#39;.ENT&#39;</span><span class="p">),</span>
82            <span class="n">strictExtension</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
83            <span class="n">formatName</span> <span class="o">=</span> <span class="s">&#39;PDB&#39;</span><span class="p">,</span>
84            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">&#39;Original Protein Data Bank (.pdb file) import&#39;</span>
85            <span class="p">)</span>
86    <span class="c"># I don&#39;t know enough to validate the contents</span>
87    <span class="c">#def ContentsValidator(self, filepointer):</span>
88    <span class="c">#    filepointer.seek(0) # rewind the file pointer</span>
89    <span class="c">#    return True</span>
90
91    <span class="k">def</span> <span class="nf">Reader</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">filepointer</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">unused</span><span class="p">):</span>
92        <span class="k">try</span><span class="p">:</span>
93            <span class="bp">self</span><span class="o">.</span><span class="n">Phase</span> <span class="o">=</span> <span class="n">G2IO</span><span class="o">.</span><span class="n">ReadPDBPhase</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
94            <span class="k">return</span> <span class="bp">True</span>
95        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
96            <span class="k">print</span> <span class="s">&#39;PDB read error:&#39;</span><span class="p">,</span><span class="n">detail</span> <span class="c"># for testing</span>
97            <span class="n">traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
98            <span class="k">return</span> <span class="bp">False</span>
99</div>
100<div class="viewcode-block" id="EXP_ReaderClass"><a class="viewcode-back" href="../imports.html#G2phase.EXP_ReaderClass">[docs]</a><span class="k">class</span> <span class="nc">EXP_ReaderClass</span><span class="p">(</span><span class="n">G2IO</span><span class="o">.</span><span class="n">ImportPhase</span><span class="p">):</span>
101    <span class="s">&#39; Routines to import Phase information from GSAS .EXP files&#39;</span>
102    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
103        <span class="nb">super</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">__class__</span><span class="p">,</span><span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span> <span class="c"># fancy way to say ImportPhase.__init__</span>
104            <span class="n">extensionlist</span><span class="o">=</span><span class="p">(</span><span class="s">&#39;.EXP&#39;</span><span class="p">,</span><span class="s">&#39;.exp&#39;</span><span class="p">),</span>
105            <span class="n">strictExtension</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
106            <span class="n">formatName</span> <span class="o">=</span> <span class="s">&#39;GSAS .EXP&#39;</span><span class="p">,</span>
107            <span class="n">longFormatName</span> <span class="o">=</span> <span class="s">&#39;GSAS Experiment (.EXP file) import&#39;</span>
108            <span class="p">)</span>
109    <span class="k">def</span> <span class="nf">ContentsValidator</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filepointer</span><span class="p">):</span>
110        <span class="n">filepointer</span><span class="o">.</span><span class="n">seek</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> <span class="c"># rewind the file pointer</span>
111        <span class="c"># first 13 characters should be VERSION tag -- I think</span>
112        <span class="k">try</span><span class="p">:</span>
113            <span class="k">if</span> <span class="n">filepointer</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="mi">13</span><span class="p">)</span> <span class="o">==</span> <span class="s">&#39;     VERSION &#39;</span><span class="p">:</span>
114                <span class="k">return</span> <span class="bp">True</span>
115        <span class="k">except</span><span class="p">:</span> <span class="k">pass</span>
116        <span class="k">return</span> <span class="bp">False</span>
117
118    <span class="k">def</span> <span class="nf">Reader</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">filename</span><span class="p">,</span><span class="n">filepointer</span><span class="p">,</span> <span class="n">ParentFrame</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="o">**</span><span class="n">unused</span><span class="p">):</span>
119        <span class="k">try</span><span class="p">:</span>
120            <span class="bp">self</span><span class="o">.</span><span class="n">Phase</span> <span class="o">=</span> <span class="n">G2IO</span><span class="o">.</span><span class="n">ReadEXPPhase</span><span class="p">(</span><span class="n">ParentFrame</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
121            <span class="k">return</span> <span class="bp">True</span>
122        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">detail</span><span class="p">:</span>
123            <span class="k">print</span> <span class="s">&#39;GSAS .EXP read error:&#39;</span><span class="p">,</span><span class="n">detail</span> <span class="c"># for testing</span>
124            <span class="n">traceback</span><span class="o">.</span><span class="n">print_exc</span><span class="p">(</span><span class="nb">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
125            <span class="k">return</span> <span class="bp">False</span></div>
126</pre></div>
127
128          </div>
129        </div>
130      </div>
131      <div class="sphinxsidebar">
132        <div class="sphinxsidebarwrapper">
133            <p class="logo"><a href="../index.html">
134              <img class="logo" src="../_static/G2_html_logo.png" alt="Logo"/>
135            </a></p>
136<div id="searchbox" style="display: none">
137  <h3>Quick search</h3>
138    <form class="search" action="../search.html" method="get">
139      <input type="text" name="q" />
140      <input type="submit" value="Go" />
141      <input type="hidden" name="check_keywords" value="yes" />
142      <input type="hidden" name="area" value="default" />
143    </form>
144    <p class="searchtip" style="font-size: 90%">
145    Enter search terms or a module, class or function name.
146    </p>
147</div>
148<script type="text/javascript">$('#searchbox').show(0);</script>
149        </div>
150      </div>
151      <div class="clearer"></div>
152    </div>
153    <div class="related">
154      <h3>Navigation</h3>
155      <ul>
156        <li class="right" style="margin-right: 10px">
157          <a href="../genindex.html" title="General Index"
158             >index</a></li>
159        <li class="right" >
160          <a href="../py-modindex.html" title="Python Module Index"
161             >modules</a> |</li>
162        <li><a href="../index.html">GSAS-II 0.2.0 documentation</a> &raquo;</li>
163          <li><a href="index.html" >Module code</a> &raquo;</li> 
164      </ul>
165    </div>
166    <div class="footer">
167        &copy; Copyright 2013, Von Dreele and Toby for Argonne National Laboratory.
168      Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.2.
169    </div>
170  </body>
171</html>
Note: See TracBrowser for help on using the repository browser.