embed PV in documentation

doc/conf.py

@@ -125,7 +125,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = []
+html_static_path = [ '_static' ]
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.

doc/ext/pvsample.py

@@ -3,12 +3,13 @@
 from sphinx.util.compat import make_admonition
 from sphinx.util.nodes import set_source_info
 from sphinx.locale import _
+import os
 
 class PVSample(nodes.Admonition, nodes.Element):
     pass
 
 RAW_CODE_PRELUDE='''
-<script type='text/javascript' src='/bio-pv.min.js'></script>
+<script type='text/javascript' src='%s/bio-pv.min.js'></script>
 
 <style>
 #viewer {
@@ -22,7 +23,7 @@ class PVSample(nodes.Admonition, nodes.Element):
 }
 #viewer-wrap {
   text-align:center;
-  width: 100%;
+  width: 100%%;
 }
 </style>
 
@@ -42,8 +43,13 @@ def run(self):
 
         literal = nodes.literal_block(code, code)
         literal['language' ] = 'html'
+        print env.docname
+        doc_dir = os.path.dirname(env.docname)
+        relative_static_path = os.path.relpath(env.config.html_static_path[0],
+                                               doc_dir)
 
-        raw_html_code = nodes.raw(code, RAW_CODE_PRELUDE + code, 
+        prelude = RAW_CODE_PRELUDE % relative_static_path
+        raw_html_code = nodes.raw(code, prelude + code, 
                                   format='html')
         set_source_info(self, literal)
         set_source_info(self, raw_html_code)

doc/samples/ensemble/index.rst

@@ -1,15 +1,15 @@
 Display an NMR ensemble
 =================================================
 
-In this sample we are going to use the *loadAllModels* option of the PDB parser to load all structures present in a multi-model PDB file. The models are then displayed together in the viewer.
+In this sample we are going to use the *loadAllModels* option of the :func:`PDB parser<pv.io.fetchPdb>` to load all structures present in a multi-model PDB file. The models are then displayed together in the viewer using the :func:`cartoon render mode <pv.Viewer.cartoon>`.
 
 .. pv-sample::
 
   <script>
   var viewer = pv.Viewer(document.getElementById('viewer'), 
                         { width : 300, height : 300, antialias : true });
 
-  pv.io.fetchPdb('/pdbs/1nmr.pdb', function(structures) {
+  pv.io.fetchPdb('http://www.rcsb.org/pdb/files/2mjx.pdb', function(structures) {
       // put this in the viewerReady block to make sure we don't try to add the 
       // object before the viewer is ready. In case the viewer is completely 
       // loaded, the function will be immediately executed.
@@ -19,8 +19,9 @@ In this sample we are going to use the *loadAllModels* option of the PDB parser
           viewer.cartoon('structure_' + (index++), s); 
         });
         // adjust center of view and zoom such that all structures can be seen.
-        viewer.centerOn(structures[0]);
-        viewer.setZoom(70);
+        var rotation = pv.viewpoint.principalAxes(viewer.all()[0]);
+        viewer.setRotation(rotation)
+        viewer.autoZoom();
       });
   },  { loadAllModels : true });
   </script>