docu updates

actions/ost-compare-structures

@@ -5,13 +5,13 @@ Example: ost compare-structures -m model.pdb -r reference.cif
 
 Loads the structures and performs basic cleanup:
 
- * Assign elements according to the PDB compound dictionary
+ * Assign elements according to the PDB Chemical Component Dictionary
  * Map nonstandard residues to their parent residues as defined by the PDB
-   compound dictionary, e.g. phospho-serine => serine
+   Chemical Component Dictionary, e.g. phospho-serine => serine
  * Remove hydrogens
  * Remove OXT atoms
  * Remove unknown atoms, i.e. atoms that are not expected according to the PDB
-   compound dictionary
+   Chemical Component Dictionary
  * Select for peptide/nucleotide residues
 
 The cleaned structures are optionally dumped using -d/--dump-structures
@@ -51,7 +51,7 @@ enabling -rna/--residue-number-alignment is recommended.
 
 Each score is opt-in and can be enabled with optional arguments.
 
-Example to compute local and per-residue lDDT values as well as QS-score:
+Example to compute global and per-residue lDDT values as well as QS-score:
 
 ost compare-structures -m model.pdb -r reference.cif --lddt --local-lddt \
 --qs-score

modules/doc/actions.rst

@@ -19,7 +19,8 @@ Comparing two structures
 --------------------------------------------------------------------------------
 
 You can compare two structures from the command line with the
-``ost compare-structures`` action.
+``ost compare-structures`` action. This can be considered a command line
+interface to :class:`ost.mol.alg.scoring.Scorer`
 
 .. warning::
 
@@ -47,16 +48,16 @@ Details on the usage (output of ``ost compare-structures --help``):
   Example: ost compare-structures -m model.pdb -r reference.cif
   
   Loads the structures and performs basic cleanup:
-  
-   * Assign elements according to the PDB compound dictionary
+
+   * Assign elements according to the PDB Chemical Component Dictionary
    * Map nonstandard residues to their parent residues as defined by the PDB
-     compound dictionary, e.g. phospho-serine => serine
+     Chemical Component Dictionary, e.g. phospho-serine => serine
    * Remove hydrogens
    * Remove OXT atoms
    * Remove unknown atoms, i.e. atoms that are not expected according to the PDB
-     compound dictionary
+     Chemical Component Dictionary
    * Select for peptide/nucleotide residues
-  
+
   The cleaned structures are optionally dumped using -d/--dump-structures
   
   Output is written in JSON format (default: out.json). In case of no additional
@@ -94,7 +95,7 @@ Details on the usage (output of ``ost compare-structures --help``):
   
   Each score is opt-in and can be enabled with optional arguments.
   
-  Example to compute local and per-residue lDDT values as well as QS-score:
+  Example to compute global and per-residue lDDT values as well as QS-score:
   
   ost compare-structures -m model.pdb -r reference.cif --lddt --local-lddt --qs-score
   

modules/mol/alg/pymod/qsscore.py

@@ -246,7 +246,7 @@ class QSScorer:
         chain_mapper = ChainMapper(ent_1)
         mapping_result = chain_mapper.GetlDDTMapping(ent_2)
         qs_scorer = QSScorer.FromMappingResult(mapping_result)
-        score_result = qs_scorer.GetQSScore(mapping_result.mapping)
+        score_result = qs_scorer.Score(mapping_result.mapping)
         print("score:", score_result.QS_global)
 
     QS-score computation in :func:`QSScorer.Score` implements caching.