document some more properties

modules/index.rst

@@ -28,7 +28,7 @@ For Starters
 
 **Installation**: `install from binary <http://www.openstructure.org/download/>`_ | :doc:`install from source <install>`
 
-**Tutorial Style**: :doc:`introduction <intro>` | :doc:`molecules intro <intro-01>` | :doc:`images intro <intro-02>` | :doc:`graphics intro <intro-03>`
+**Tutorial Style**: :doc:`introduction <intro>` | :doc:`molecules intro <intro-01>` | :doc:`images intro <intro-02>` | :doc:`graphics intro <intro-03>` 
 
 
 
@@ -36,7 +36,7 @@ For Starters
 Molecules
 --------------------------------------------------------------------------------
 
-**Overview**: :doc:`molecules intro <intro-01>` | :doc:`mol overview <mol/base/mol>` | :doc:`graphical entity<gfx/entity>` | :doc:`entity <mol/base/entity>`
+**Overview**: :doc:`molecules intro <intro-01>` | :doc:`mol overview <mol/base/mol>` | :doc:`graphical entity<gfx/entity>` | :doc:`entity <mol/base/entity>` | :doc:`queries <mol/base/query>`
 
 **Input/Output**: :ref:`loading and saving molecules <mol-io>`
 

modules/mol/base/doc/entity.rst

@@ -500,7 +500,14 @@ The Handle Classes
   .. attribute:: sec_structure
   
     The secondary structure of the residue.
-    
+  
+  .. attribute:: is_ligand
+  
+    Whether the residue is a ligand. When loading PDB structures, this property 
+    is set based on the HET records. This also means, that this property will 
+    most likely not be set properly for all except PDB files coming from 
+    pdb.org.
+
   .. method:: FindAtom(atom_name)
 
     Get atom by atom name. See also :attr:`atoms`

modules/mol/base/doc/query.rst

@@ -197,6 +197,10 @@ index is the same for views and handles.
 
 **rbfac** (float): average B (temperature) factor of residue
 
+**ligand** (bool) Whether the residue is a ligand. For official PDB files, the ligand property is set based on HET records.
+
+**water** (bool) Whether the residue is water.
+
 Properties of Atoms
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^