ligand scoring: integrate refactored ligand scoring

modules/mol/alg/doc/molalg.rst

@@ -115,10 +115,20 @@ Local Distance Test scores (lDDT, DRMSD)
 .. currentmodule:: ost.mol.alg
 
 
-:mod:`ligand_scoring <ost.mol.alg.ligand_scoring>` -- Ligand scoring functions
---------------------------------------------------------------------------------
+:mod:`ligand_scoring <ost.mol.alg.ligand_scoring_base>` -- Ligand scoring functions
+-----------------------------------------------------------------------------------
+
+.. automodule:: ost.mol.alg.ligand_scoring_base
+   :members:
+   :member-order: bysource
+   :synopsis: Scoring of ligands
+
+.. automodule:: ost.mol.alg.ligand_scoring_lddtpli
+   :members:
+   :member-order: bysource
+   :synopsis: Scoring of ligands
 
-.. automodule:: ost.mol.alg.ligand_scoring
+.. automodule:: ost.mol.alg.ligand_scoring_scrmsd
    :members:
    :member-order: bysource
    :synopsis: Scoring of ligands

modules/mol/alg/pymod/CMakeLists.txt

@@ -29,7 +29,6 @@ set(OST_MOL_ALG_PYMOD_MODULES
   scoring.py
   chain_mapping.py
   stereochemistry.py
-  ligand_scoring.py
   dockq.py
   contact_score.py
   ligand_scoring_base.py

modules/mol/alg/pymod/ligand_scoring_base.py

@@ -83,7 +83,7 @@ class LigandScorer:
     expected with entities loaded from PDB files, as the `is_ligand` flag is
     probably not set properly.
 
-    Here is a snippet example of how to use this code::
+    Here is an example of how to use setup a scorer code::
 
         from ost.mol.alg.ligand_scoring_scrmsd import SCRMSDScorer
         from ost.mol.alg import Molck, MolckSettings
@@ -370,7 +370,7 @@ class LigandScorer:
         and the whole process is repeated until there are no ligands to
         assign anymore.
 
-        :rtype: :class:`list`: of :class:`tuple` (trg_lig_idx, mdl_lig_idx)
+        :rtype: :class:`list` of :class:`tuple` (trg_lig_idx, mdl_lig_idx)
         """
         if self._assignment is None:
             self._assignment = list()
@@ -1065,9 +1065,10 @@ def ComputeSymmetries(model_ligand, target_ligand, substructure_match=False,
     :type max_symmetries: :class:`int`
     :raises: :class:`NoSymmetryError` when no symmetry can be found;
              :class:`NoIsomorphicSymmetryError` in case of isomorphic
-             subgraph but *substructure_match* is False.
+             subgraph but *substructure_match* is False;
              :class:`TooManySymmetriesError` when more than `max_symmetries`
-             isomorphisms are found.
+             isomorphisms are found; :class:`DisconnectedGraphError` if
+             graph for *model_ligand*/*target_ligand* is disconnected.
     """
 
     # Get the Graphs of the ligands
@@ -1153,3 +1154,8 @@ class DisconnectedGraphError(Exception):
     """ Exception raised when the ligand graph is disconnected.
     """
     pass
+
+# specify public interface
+__all__ = ('LigandScorer', 'ComputeSymmetries', 'NoSymmetryError',
+           'NoIsomorphicSymmetryError', 'TooManySymmetriesError',
+           'DisconnectedGraphError')

modules/mol/alg/pymod/ligand_scoring_lddtpli.py

@@ -944,3 +944,6 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
             self.__chain_mapping_mdl = \
             self._chain_mapper.GetChemMapping(self.model)
         return self.__chain_mapping_mdl
+
+# specify public interface
+__all__ = ('LDDTPLIScorer',)

modules/mol/alg/pymod/ligand_scoring_scrmsd.py

@@ -442,3 +442,6 @@ def _SCRMSD_symmetries(symmetries, model_ligand, target_ligand,
             best_rmsd = rmsd
 
     return best_rmsd
+
+# specify public interface
+__all__ = ('SCRMSDScorer', 'SCRMSD')

modules/mol/alg/tests/CMakeLists.txt

@@ -20,8 +20,7 @@ if (COMPOUND_LIB)
   list(APPEND OST_MOL_ALG_UNIT_TESTS test_qsscoring.py
                                      test_nonstandard.py
                                      test_chain_mapping.py
-                                     test_ligand_scoring.py
-                                     test_ligand_scoring_fancy.py)
+                                     test_ligand_scoring.py)
 endif()
 
 ost_unittest(MODULE mol_alg SOURCES "${OST_MOL_ALG_UNIT_TESTS}" LINK ost_io)