doc: clarify deprecation warning/notes

Now we always have a warning on the deprecated doc with a link to the
new implementation; and a note on the new implementation which starts
with "this is the new implementation" rather than "XXX is deprecated".

modules/mol/alg/doc/lddt_deprecated.rst

@@ -6,7 +6,8 @@ lDDT (deprecated)
 .. warning::
 
   These functions in `ost.mol.alg` are deprecated. Consider using the newer
-  implementation in :class:`ost.mol.alg.lDDTScorer` instead.
+  implementation in
+  :class:`ost.mol.alg.lddt.lDDTScorer <ost.mol.alg.lddt.lDDTScorer>` instead.
 
 .. function:: LocalDistDiffTest(model, distance_list, tolerance_list, \
                                 sequence_separation=0, \

modules/mol/alg/doc/stereochemistry.rst

 :mod:`~ost.mol.alg.stereochemistry` -- Stereochemistry Checks
 --------------------------------------------------------------------------------------
 
-.. warning::
-
-  Stereochemistry checks described in
-  `Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_ are
-  considered deprecated. They have been re-implemented and now support
-  nucleotides. The old code is still available and documented
-  :doc:`here <stereochemistry_deprecated>`.
-
 .. automodule:: ost.mol.alg.stereochemistry
    :members:
    :member-order: bysource

modules/mol/alg/doc/stereochemistry_deprecated.rst

@@ -3,6 +3,11 @@
 Stereochemistry (deprecated)
 ================================================================================
 
+.. warning::
+
+  These functions in `ost.mol.alg` are deprecated.
+  Consider using the newer implementation in
+  :mod:`~ost.mol.alg.stereochemistry` instead.
 
 .. function:: CheckStructure(ent, \
                              bond_table, \

modules/mol/alg/pymod/stereochemistry.py

+"""
+.. note::
+
+  This is a new implementation of the stereochemistry checks, introduced in
+  OpenStructure 2.4, with support for nucleotides. The
+  :doc:`previous stereochemistry checks <stereochemistry_deprecated>` that come
+  with `Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_ are
+  considered deprecated.
+"""
+
 import os
 import json
 import datetime