lDDT: docu updates

modules/mol/alg/doc/lddt.rst

@@ -7,7 +7,7 @@ lDDT
   The executable that refers to
   `Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_
   is considered deprecated. This documentation still exists for
-  reference but you should consider using the `compare-structures` action
+  reference but you should consider using the ``compare-structures`` action
   (:ref:`ost-compare-structures`) which utilizes the latest lDDT implementation
   that can deal with quaternary structures and compounds beyond the 20
   standard proteinogenic amino acids. 

modules/mol/alg/doc/molalg.rst

@@ -16,6 +16,15 @@ Local Distance Test scores (lDDT, DRMSD)
   proteinogenic amino acids. The old code is still available and documented
   :doc:`here <lddt_deprecated>`.
 
+.. note::
+
+  :class:`lddt.lDDTScorer` provides the raw Python API to compute lDDT but
+  stereochemistry checks as described in
+  `Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_
+  must be done seperately. You may want to check out the
+  ``compare-structures`` action (:ref:`ost-compare-structures`) to
+  compute lDDT with pre-processing and support for quaternary structures.
+
 
 .. autoclass:: ost.mol.alg.lddt.lDDTScorer
   :members:
@@ -25,8 +34,6 @@ Local Distance Test scores (lDDT, DRMSD)
 
 .. autofunction:: ost.mol.alg.lddt.GetDefaultSymmetrySettings
 
-
-
 .. function:: CheckStructure(ent, \
                              bond_table, \
                              angle_table, \