doc: fix sphinx warnings about duplicate object description

modules/io/doc/io.rst

@@ -549,13 +549,7 @@ Loading Density Maps
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. function:: LoadImage(filename)
-
-  Load density map from disk with the extension being guessed by the function.
-
-  :param filename: The filename
-  :type  filename: string
-
-.. function:: LoadImage(filename, format)
+              LoadImage(filename, format)
 
   Load density map from disk. If no format is given, the function guesses the 
   filetype based on the extension of the file. If the extension is unknown or not present the
@@ -589,12 +583,8 @@ Loading Density Maps
 Saving Density Maps
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. function:: SaveImage(image,filename)
-
-  Save density map to disk with the function guessing the 
-  filetype based on the file extension.
-
-.. function:: SaveImage(image,filename, format)
+.. function:: SaveImage(image, filename)
+              SaveImage(image, filename, format)
 
   Save density map to disk. If no format is set, the function guesses the 
   filetype based on the file extension.

modules/mol/base/doc/editors.rst

@@ -192,6 +192,7 @@ The basic functionality of editors is implemented in the EditorBase class.
     :returns:         :class:`AtomHandle`
 
   .. method:: InsertAltAtom(residue, atom, alt_group)
+    :noindex:
 
     Insert new atom with alternative position indicator
 
@@ -336,6 +337,7 @@ The basic functionality of editors is implemented in the EditorBase class.
     :type new_numbers: :class:`ResNumList`
 
   .. method:: RenumberChain(chain, start, keep_spacing)
+    :noindex:
 
     Renumber residues of the given chain
               
@@ -409,29 +411,14 @@ Euclidian space.
      atoms positions.
      
      :param transform: The transformation to be applied
-     :type  transform: :class:`geom.Mat4`
-
-  .. method:: ApplyTransform(transform)
-  
-     Apply a transformation to the entity. The transformation is applied to all 
-     atoms positions.
-     
-     :param transform: The transformation to be applied
-     :type  transform: :class:`Transform`
+     :type  transform: :class:`geom.Mat4` or :class:`Transform`
      
   .. method:: SetTransform(transform)
   
      Set the entity transformation. See also :meth:`ApplyTransform`
      
      :param transform: The transformation to be applied
-     :type  transform: :class:`geom.Mat4`
-
-  .. method:: SetTransform(transform)
-  
-     Set the entity transformation. See also :meth:`ApplyTransform`
-     
-     :param transform: The transformation to be applied
-     :type  transform: :class:`Transform`
+     :type  transform: :class:`geom.Mat4` or :class:`Transform`
   
   .. method:: FixTransform()
   
@@ -544,6 +531,7 @@ using an :class:`ICSEditor` is undefined and vice versa.
 
 
   .. method:: SetTorsionAngle(atom1, atom2, atom3, atom4, angle, update_others=True)
+    :noindex:
     
     Set the angles of the given atoms. All connectors at the third atom (A3) will be adjusted accordingly. 
     If you only want to adjust the bond between A3 and A4, and leave 
@@ -587,6 +575,7 @@ using an :class:`ICSEditor` is undefined and vice versa.
 
 
   .. method:: RotateTorsionAngle(atom1, atom2, atom3, atom4, angle, update_others=True)
+    :noindex:
     
     Rotate torsion angle
     

modules/mol/base/doc/entity.rst

@@ -2343,7 +2343,7 @@ Other Entity-Related Functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. function:: CreateViewFromAtoms(atom_list)
-.. function:: CreateViewFromAtomList(atom_list)
+              CreateViewFromAtomList(atom_list)
 
   Returns a view made up of the atoms in *atom_list*. All atoms are required to
   be atoms of the same entity. Duplicate atoms are only added to the view once.