Removed loop part from meld

meld/doc/CMakeLists.txt

 set(MELD_RST
 index.rst
-loop.rst
 rawmodel.rst
 )
 

meld/doc/index.rst

@@ -4,10 +4,10 @@
 .. module:: promod3.meld
   :synopsis: Coordinate modeling and sampling
   
-This module contains functions and classes to model protein structures from sequence.
+This module contains functions and classes to build raw-models for protein
+structures from templates.
 
 .. toctree:: 
   :maxdepth: 2
-  
-  loop
+
   rawmodel

meld/doc/loop.rst

-Loop Modeling
-================================================================================
-
-.. currentmodule:: sm.meld
-
-
-Loop Modeling API
---------------------------------------------------------------------------------
-
-.. class:: LoopCandidate(gap, bb_list)
-
-  A loop candidate holds the coordinates of the four backbone atoms for a given 
-  peptide fragment as well as the sequence.
-  
-  :param gap: The structural gap 
-  :type gap: :class:`StructuralGap`
-  
-  :param bb_list: List of peptide backbone coordinates
-  :type bb_list: :class:`BackboneList`
-  
-  .. method:: InsertInto(entity)
-
-    Inserts the loop candidate into the given entity. This honours the start and 
-    end point stored in the gap. Missing residues and atoms will be inserted 
-    into the structure.
-    
-    
-    :param entity:
-    :type  entity: :class:`~ost.mol.EntityHandle`
-    :returns: True on success, false if the insertion failed
-    :rtype: bool
-
-  .. method:: RmsdTo(entity)
-  
-    Calculates the RMSD to the corresponding backbone fragment in *entity*. 
-    Raises a RuntimeError if not all backbone atoms exist.
-    
-    :param entity:
-    :type  entity: :class:`~ost.mol.EntityHandle`
-    :rtype: float
-
-  .. method:: ToEntity()
-    
-    Returns an entity holding this backbone fragment. Residue numbers go from 
-    gap.start to gap.end.
-    
-    :rtype: :class:`~ost.mol.EntityHandle`
-
-
-  .. attribute:: allatom_score
-     
-    If set, the allatom_score of this fragment
-  
-  
-  
-  .. attribute:: clash_bb_score
-     
-    The clash score of the loop candidate with sidechain atoms
-  
-  
-  
-  .. attribute:: clash_score
-  
-    The sum of backbone and sidechain clash scores
-  
-  
-  
-  .. attribute:: clash_sc_score
-    
-    Clash score with sidechain atoms
-  
-  
-  
-  .. attribute:: coords
-   
-    Access to the actual coordinates
-    
-    :type: :class:`BackboneList`
-  
-  
-  
-  .. attribute:: correl
-    
-    Correlation with density
-  
-  
-  
-  .. attribute:: gap
-    
-    The structural gap
-  
-  
-  
-  .. attribute:: packing_score
-    
-    Packing score of this loop candidate
-  
-  
-  
-  .. attribute:: reduced_score
-   
-    Reduced score
-  
-  
-  
-  .. attribute:: score
-    
-    Total score of this loop candidate.
-  
-  
-  
-  .. attribute:: torsion_score
-    
-    Torsion score of this loop candidate
-  
-
-.. class:: LoopCandidates(model)
-  
-  A list of loop candidates with a few helper methods to make your life easier. 
-  The candidates are supposed to be loop candidates for the same gap. However, 
-  they are not required to have the same start and end position, e.g. due to 
-  extension of the gap. 
-  
-  :param model: The model the candidates are for.
-  
-  :type model: :class:`~ost.mol.EntityHandle`
-
-  .. method:: Add(candidate)
-  
-    Add a new candidate
-    :param candidate:
-    :type  candidate: :class:`LoopCandidate`
-
-  .. method:: SortByCorrel([, increasing])
-    
-    Sort loop candidates by correlation score
-    
-    :param increasing: If true, the candidates are sorted in increasing order
-    :type  increasing: bool
-
-  .. method:: SortByScore([, increasing])
-
-    Sort loop canditates by total score
-    
-    :param increasing: If true, the candidates are sorted in increasing order
-    :type  increasing: bool
-
-
-  .. attribute:: model
-    
-    The model the candidates are for
-  
-    :type: :class:`~ost.mol.EntityHandle`