Doc update for scores (lower better usually, higher better for prof. scores)

modelling/doc/loop_candidates.rst

@@ -182,6 +182,7 @@ The LoopCandidates class
     Calculates and returns a given score for each loop candidate. 
     See :meth:`~promod3.scoring.BackboneOverallScorer.Calculate` for a
     detailed description of the arguments and possible exceptions.
+    Note that (unless otherwise noted) a lower "score" is better!
 
     :param scorer: Scorer object with set environment for the particular loop
                    modelling problem.
@@ -230,6 +231,9 @@ The LoopCandidates class
     *structure_db* (see :meth:`ost.seq.ProfileHandle.GetAverageScore` for
     details, *prof.null_model* is used for weighting).
 
+    Note that for profile scores a higher "score" is better! So take care when
+    combining this to other scores, where it is commonly the other way around.
+
     This requires that each candidate has a connected fragment info into the
     given *structure_db* (e.g. :meth:`FillFromDatabase` must have been called
     with this DB).

scoring/doc/all_atom_scorers.rst

@@ -85,7 +85,8 @@ AllAtomScorer base class
   .. method:: CalculateScore(start_resnum, num_residues, chain_idx=0)
 
     Calculates score for the desired loop (extracted from environment) against
-    the set environment.
+    the set environment. Unless otherwise noted in the scorer, a lower "score"
+    is better!
 
     Note that the structural data of the loop is expected to be in the linked
     environment before calling this! This behavior is different from the

scoring/doc/backbone_scorers.rst

@@ -35,7 +35,8 @@ BackboneOverallScorer class
 
   .. method:: Calculate(key, bb_list, start_resnum, chain_idx=0)
 
-    Calculate score(s) for one or many loop(s).
+    Calculate score(s) for one or many loop(s) with
+    :meth:`BackboneScorer.CalculateScore`.
 
     :param key: Key for desired scorer.
     :type key:  :class:`str`
@@ -111,7 +112,8 @@ BackboneScorer base class
 
     Calculates score for the given loop internally and against the set
     environment. Data in the environment, which overlaps with the given
-    *bb_list* is ignored.
+    *bb_list* is ignored. Unless otherwise noted in the scorer, a lower "score"
+    is better!
 
     :param bb_list: Loop for which to calculate the given score
     :type bb_list:  :class:`~promod3.loop.BackboneList`