lDDT: docu updates

modules/doc/actions.rst

@@ -13,7 +13,7 @@ you can type ``ost <ACTION> -h`` to get a description on its usage.
 
 Here we list the most prominent actions with simple examples.
 
-.. ost-compare-structures:
+.. _ost compare structures:
 
 Comparing two structures
 --------------------------------------------------------------------------------
@@ -39,13 +39,12 @@ In summary it performs the following steps:
   if 100% sequence identity is expected.
 - Compute scores requested by user (CA-RMSD of oligomer,
   :mod:`QS scores of oligomer <ost.mol.alg.qsscoring>`,
-  :class:`single chain lDDT scores <ost.mol.alg.lDDTScorer>`,
-  :attr:`weighted average of single chain lDDT scores <ost.mol.alg.qsscoring.OligoLDDTScorer.weighted_lddt>`,
+  :class:`single chain lDDT scores <ost.mol.alg.qsscoring.OligoLDDTScorer.sc_lddt>`,
   :attr:`lDDT score of oligomer <ost.mol.alg.qsscoring.OligoLDDTScorer.oligo_lddt>`).
   Note that while the QS score is symmetric (same result when swapping reference
   and model), the lDDT scores are not. Extra atoms in the model for mapped
   chains have no effect on the score, while extra atoms in the reference reduce
-  the score. For the oligomeric variants (weighted-lDDT & oligo-lDDT), we do
+  the score. For oligo_lddt, we do
   :attr:`penalize for extra chains <ost.mol.alg.qsscoring.OligoLDDTScorer.penalize_extra_chains>`
   in both reference and model.
 

modules/mol/alg/doc/lddt.rst

@@ -8,7 +8,7 @@ lDDT
   `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
-  (:ref:`ost-compare-structures`) which utilizes the latest lDDT implementation
+  (: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

@@ -22,7 +22,7 @@ Local Distance Test scores (lDDT, DRMSD)
   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
+  ``compare-structures`` action (:ref:`ost compare structures`) to
   compute lDDT with pre-processing and support for quaternary structures.