docu updates

loop/doc/backbone_loop_score.rst

@@ -9,29 +9,31 @@ The BackboneLoopScorer
 --------------------------------------------------------------------------------
 
 The :class:`BackboneLoopScorer` provides several terms to assess a 
-loop conformations plausibility. To be used, the scorer 
-must be initialized with a seqres. After initialization the structural 
-environment can be set. This environment defines the particles a certain 
-loop interacts with and can be reset/extended at any time in the modelling
-process. All values of the different scores can be set manually. Once the
-scores are set, the scorer can be saved/loaded from/to disk. 
-To define the position of a loop to be scored you need to provide the 
-chain_idx and the start_resnum.
+loop conformations plausibility. All values of the different scores 
+can be set manually. Once the scores are set, the scorer can be 
+saved/loaded from/to disk. Setting the scores can be avoided by 
+just loading the default scorer, which should satisfy most needs. 
+To be used, the scorer must be initialized with a seqres. 
+After initialization the structural environment can be set. 
+This environment defines the particles a certain loop interacts with 
+and can be reset/extended at any time in the modelling process.
+To score a certain loop you must define its exact location in the
+environment using a *chain_idx* and *start_resnum*. 
 
 * chain_idx: Index of chain as it occurs in the sequence list you initialized
              the scorer with (0 in case of a single sequence)
 
 * start_resnum: Residue number defining the position in the SEQRES of chain with
-                index *chain_index*. The numbering start for every chain with
-                the value **1**
+                index *chain_idx*. **The numbering starts for every chain with
+                the value 1**
 
 Following scores are available:
 
-* ClashScore: Calculates a simple clash score of a loop itself and with 
+* **ClashScore:** Calculates a simple clash score of a loop itself and with 
               the set environment. There is no need to define any parameters 
               if you start with an empty scorer.
 
-* CBetaScore: Evaluates a pairwise pseudo interaction energy between CB atoms.
+* **CBetaScore:** Evaluates a pairwise pseudo interaction energy between CB atoms.
               If you start with an empty scorer you need to parametrize the
               energy function by calling the according SetParameter function.
               You can then set an energy value for every possible pair of
@@ -42,7 +44,7 @@ Following scores are available:
               of total interactions.
               
 
-* ReducedScore: Evaluates a pairwise pseude interaction energy between the
+* **ReducedScore:** Evaluates a pairwise pseude interaction energy between the
                 reduced representation of residues.
                 Every residue gets represented by its CA
                 position p and a directional component 
@@ -65,7 +67,7 @@ Following scores are available:
                 parametrization, summed up and finally normalized by the number 
                 of total interactions.                
 
-* TorsionScore: Evaluates pseudo energies based on the identity of three 
+* **TorsionScore:** Evaluates pseudo energies based on the identity of three 
                 consecutive residues and the phi/psi dihedral angles of the 
                 central residue. The group definitions are the same as they
                 are used in the :class:`TorsionSampler`.
@@ -79,7 +81,7 @@ Following scores are available:
                 psi angle get determined with the help of the environment 
                 if set.
 
-* CBPackingScore: Evaluates pseudo energies by counting the number of other 
+* **CBPackingScore:** Evaluates pseudo energies by counting the number of other 
                   CB positions within a certain cutoff radius of the CB position
                   of the residue to be evaluated.
                   If you start with an empty scorer you need to parametrize the
@@ -91,7 +93,7 @@ Following scores are available:
                   parametrization and the final score gets normalized by the
                   number of residues in the loop.
 
-* HBondScore: Evaluates pairwise HBond pseudo energies similar to the one 
+* **HBondScore:** Evaluates pairwise HBond pseudo energies similar to the one 
               defined in the Rosetta energy function. It considers the 
               CA, C and O positions from backbone hbond acceptors in interaction 
               with the N and H positions from the backbone hbond donors. 
@@ -117,7 +119,7 @@ Following scores are available:
               parametrization, summed up and finally normalized by the number 
               of total interactions.
 
-* SSAgreementScore: Evaluates an SSAgreement score. Despite no parameters 
+* **SSAgreementScore:** Evaluates an SSAgreement score. Despite no parameters 
                     being given, the according SetParameters function has 
                     to be called before you can set any SSAgreement scores 
                     since the memory has to be allocated internally. The 
@@ -133,7 +135,7 @@ Following scores are available:
                     The final score gets summed up over all residues in the
                     loop and normalized by the number of residues.
 
-* ContactScore: Evaluates contacts with the environment and within the loop 
+* **ContactScore:** Evaluates contacts with the environment and within the loop 
                 itself. You can set arbitrary contact functions. 
                 They are defined by a score, that gets added when the CA atoms
                 of two specific residues are within a maximal distance.
@@ -142,7 +144,7 @@ Following scores are available:
                 contacts. The returned value gets then normalized by the number
                 of residues in the loop.
 
-* ConstraintScore: Evaluates constraints with the environment and within the 
+* **ConstraintScore:** Evaluates constraints with the environment and within the 
                    loop itself. You can set arbitrary constraint functions.
                    They are defined by a min and max distance and an arbitrary
                    list of score values. If the distance between the CA atoms
@@ -154,7 +156,7 @@ Following scores are available:
                    loop internal constraints. The returned value gets then 
                    normalized by the number of residues in the loop.
 
-* TransOmegaTorsion: Does not really return a score but rather a boolean value.
+* **TransOmegaTorsion:** Does not really return a score but rather a boolean value.
                      It evaluates, whether there are any unfavorable trans omega
                      torsion angles in the loop. If you wish you can decide, 
                      whether you want to allow pre-proline trans omega torsions.
@@ -423,26 +425,14 @@ Following scores are available:
     SSAgreementScore.
 
     :param pred:        The prediction
-    :type pred:         :class:`PsipredPrediction`
-
-    :raises:            :class:`RuntimeError` If the scorer is not yet initialized,
-                        the scorer is initialized for multiple chains or when the
-                        the size of the prediction is inconsistent with the internal
-                        seqres in the scorer.
-
-  .. method:: SetPsipredPrediction(pred)
-
-    Internally sets the psipred prediction, which is necessary to calculate the
-    SSAgreementScore.
-
-    :param pred:        The prediction
-    :type pred:         :class:`list` of :class:`PsipredPrediction`
+    :type pred:         :class:`PsipredPrediction` / :class:`list` of :class:`PsipredPrediction`
 
     :raises:            :class:`RuntimeError` If the scorer is not yet initialized,
                         the number of predictions is inconsistent with the number of
                         internal chains or when one of the predictions sizes is
                         inconsistent with the according internal seqres
 
+
   .. method:: SetEnvironment(env)
 
     Sets structural environment with which loops to be scored interact.