cleanup of sidechain reconstruction script

sidechain/doc/index.rst

@@ -33,7 +33,7 @@ The simplest usage of the module is provided by the :func:`Reconstruct` function
 
 .. method:: Reconstruct(prot, keep_sidechains=False, build_disulfids, \
                         rotamer_model="frm", consider_hbonds=True, \
-                        rotamer_library=None, add_polar_hydrogens=False)
+                        rotamer_library=None)
 
   The function takes a structure and reconstructs its sidechains given the input 
   parameters.
@@ -61,10 +61,6 @@ The simplest usage of the module is provided by the :func:`Reconstruct` function
   :param rotamer_library: A rotamer library to extract the 
                           rotamers from.
 
-  :param add_polar_hydrogens:   All polar hydrogens will be constructed if  
-                            **consider_hbonds** is True.
-                            If this flag is activated, they'll be added to the
-                            structure.
 
   :type prot:           :class:`ost.mol.EntityHandle`
   :type keep_sidechains: :class:`bool`
@@ -72,7 +68,6 @@ The simplest usage of the module is provided by the :func:`Reconstruct` function
   :type rotamer_model:  :class:`str`
   :type consider_hbonds: :class:`bool`
   :type rotamer_library: :class:`BBDepRotamerLib` / :class:`RotamerLib`
-  :type add_polar_hydrogens: :class:`bool`
 
 
 Sidechain Module Functionality