doc: remove warnings about duplicate object description

modules/bindings/doc/tmtools.rst

@@ -154,6 +154,7 @@ The advantage is that no intermediate files need to be  generated.
 
 
 .. method:: WrappedTMAlign(pos1, pos2, seq1, seq2 [fast=False, rna=False])
+  :noindex:
 
   Similar as described above, but directly feeding in raw data.
 

modules/db/doc/db.rst

@@ -115,6 +115,7 @@ use an indexer to keep track of where to find data for a certain entry.
 
 
   .. method:: GetDataRange(name, chain_name)
+    :noindex:
 
     Get the range for a chain of an assembly
 

modules/gui/doc/layout.rst

@@ -112,6 +112,7 @@ how to add a  widget to the MDI area:
     :type  name: :class:`QWindowState`
 
   .. method:: AddPersistentWidget(title, name, widget, width, height, x, y)
+    :noindex:
 
      Add a widget whose geometry is preserved across application relaunches
      For widgets that are volatile, use #AddWidget()
@@ -258,6 +259,7 @@ and finally display it in the right side bar:
     :type  limit: :class:`int`
 
   .. method:: AddWidgetToPool(name, widget)
+    :noindex:
 
      Add a widget to the widget pool. Same as :meth:`AddWidgetToPool`
      

modules/mol/alg/doc/lddt_deprecated.rst

@@ -61,6 +61,7 @@ lDDT (deprecated)
             model and of all the checked distances
 
 .. function:: LocalDistDiffTest(model, reference_list, distance_list, settings)
+  :noindex:
 
   Wrapper around :func:`LocalDistDiffTest` above.
 
@@ -80,6 +81,7 @@ lDDT (deprecated)
 
 .. function:: LocalDistDiffTest(model, target, cutoff, max_dist, \
                                 local_lddt_property_string="")
+  :noindex:
 
   Wrapper around :func:`LocalDistDiffTest` above using:
   *distance_list* = :func:`CreateDistanceList` with *target* and *max_dist* as
@@ -104,6 +106,7 @@ lDDT (deprecated)
 
 .. function:: LocalDistDiffTest(alignment, tolerance, radius, ref_index=0, \
                                 mdl_index=1)
+  :noindex:
 
   Calculates the Local Distance Difference Test score (see previous function)
   starting from an alignment between a reference structure and a model. The

modules/mol/mm/doc/simulation.rst

@@ -32,6 +32,7 @@ mapped back to the attached structure at any time.
                         :class:`Topology` fails
 
 .. class:: Simulation(topology,entity,settings)
+  :noindex:
 
   Second constructor that takes a :class:`Topology`, a consistent
   :class:`ost.mol.EntityHandle` and a :class:`Settings` as input.

modules/mol/mm/doc/topology.rst

@@ -130,6 +130,7 @@ The Topology Class
                         contains OBC scalings but the **other** not
 
   .. method:: Merge(ent, other, other_ent)
+    :noindex:
 
     Merges in another :class:`Topology` and adds all their particles and 
     interactions. Assuming the actual :class:`Topology` contains n particles, 
@@ -1191,6 +1192,7 @@ The Topology Class
 
 
   .. method:: GetHarmonicBondIndices(index)
+    :noindex:
 
     :param index:       Index of particle
     :type index:        :class:`int`
@@ -1203,6 +1205,7 @@ The Topology Class
 
 
   .. method:: GetHarmonicAngleIndices(index)
+    :noindex:
 
     :param index:       Index of particle
     :type index:        :class:`int`
@@ -1215,6 +1218,7 @@ The Topology Class
 
 
   .. method:: GetUreyBradleyAngleIndices(index)
+    :noindex:
 
     :param index:       Index of particle
     :type index:        :class:`int`
@@ -1228,6 +1232,7 @@ The Topology Class
 
 
   .. method:: GetPeriodicDihedralIndices(index)
+    :noindex:
 
     :param index:       Index of particle
     :type index:        :class:`int`
@@ -1263,6 +1268,7 @@ The Topology Class
 
 
   .. method:: GetCMapIndices(index)
+    :noindex:
 
     :param index:       Index of particle
     :type index:        :class:`int`

modules/seq/alg/doc/seqalg.rst

@@ -941,8 +941,8 @@ etc.) to be set, which is the case if you load a file in hhm format.
     :param filename:    Filename of db
     :type filename:     :class:`str`
 
-
 .. method:: AddAAPseudoCounts(profile, db, a=0.9, b=4.0, c=1.0)
+  :noindex:
 
   Adds pseudo counts to the emission probabilities in *profile* by utilizing 
   context profiles as described in 

modules/seq/base/doc/seq.rst

@@ -526,6 +526,7 @@ an alignment:
     :rtype:  :class:`AlignedColumn`
 
   .. method:: __getitem__(slice)
+    :noindex:
 
     :return: Columns defined by by pythonic slicing.
     :rtype:  :class:`AlignedRegion`