document missing functions

modelling/doc/monte_carlo.rst

@@ -330,7 +330,7 @@ functionality of :class:`CloserBase`.
                          of :class:`~promod3.loop.TorsionSampler`
   :type seed:           :class:`int`
 
-  .. method:: Close(actual_positions,closed_positions)
+  .. method:: Close(actual_positions, closed_positions)
     
     :param actual_positions: Conformation to be closed.
     :param closed_positions: Closed conformation gets stored in here.
@@ -357,7 +357,7 @@ functionality of :class:`CloserBase`.
   :type n_stem:         :class:`ost.mol.ResidueHandle`
   :type c_stem:         :class:`ost.mol.ResidueHandle`
 
-  .. method:: Close(actual_positions,closed_positions)
+  .. method:: Close(actual_positions, closed_positions)
     
     :param actual_positions: Conformation to be closed.
     :param closed_positions: Closed conformation gets stored in here.
@@ -384,7 +384,7 @@ functionality of :class:`CloserBase`.
   :type c_stem:         :class:`ost.mol.ResidueHandle`
   :type seed:           :class:`int`
 
-  .. method:: Close(actual_positions,closed_positions)
+  .. method:: Close(actual_positions, closed_positions)
     
     :param actual_positions: Conformation to be closed.
     :param closed_positions: Closed conformation gets stored in here.
@@ -404,7 +404,18 @@ functionality of :class:`CloserBase`.
                         adapt.
   :type c_stem:         :class:`ost.mol.ResidueHandle`
 
-  :returns:             Whether closing was successful
+
+  .. method:: Close(actual_positions, closed_positions)
+
+    :param actual_positions: Conformation to be closed (or in this case
+                             transformed in space).
+    :param closed_positions: Closed (transformed) conformation gets stored in 
+                             here.
+
+    :type actual_positions: :class:`~promod3.loop.BackboneList`
+    :type closed_positions: :class:`~promod3.loop.BackboneList`
+
+    :returns:           Whether closing was successful
 
 
 .. class:: CTerminalCloser(n_stem)
@@ -416,7 +427,17 @@ functionality of :class:`CloserBase`.
                         adapt.
   :type n_stem:         :class:`ost.mol.ResidueHandle`
 
-  :returns:             Whether closing was successful
+  .. method:: Close(actual_positions,closed_positions)
+
+    :param actual_positions: Conformation to be closed (or in this case
+                             transformed in space).
+    :param closed_positions: Closed (transformed) conformation gets stored in 
+                             here.
+
+    :type actual_positions: :class:`~promod3.loop.BackboneList`
+    :type closed_positions: :class:`~promod3.loop.BackboneList`
+
+    :returns:           Whether closing was successful
 
 
 .. class:: DeNovoCloser