doc: refactor mol.alg submodules

ost.mol.alg submodules are now documented in separate pages. This should
make it clearer what to import.

modules/mol/alg/doc/chain_mapping.rst

+:mod:`chain_mapping <ost.mol.alg.chain_mapping>` -- Chain Mapping
+--------------------------------------------------------------------------------
+
+.. automodule:: ost.mol.alg.chain_mapping
+   :members:
+   :member-order: bysource
+   :synopsis: Chain mapping in assemblies

modules/mol/alg/doc/contact_score.rst

+:mod:`contact_score <ost.mol.alg.contact_score>` -- Contact based scores
+--------------------------------------------------------------------------------
+
+.. automodule:: ost.mol.alg.contact_score
+   :members:
+   :member-order: bysource
+   :synopsis: Contact based scores

modules/mol/alg/doc/dockq.rst

+:mod:`dockq <ost.mol.alg.dockq>` -- DockQ implementation
+--------------------------------------------------------------------------------
+
+.. module:: ost.mol.alg.dockq
+  :synopsis: DockQ implementation
+
+.. autofunction:: ost.mol.alg.dockq.DockQ

modules/mol/alg/doc/helix_kinks.rst

+:mod:`helix_kinks <ost.mol.alg.helix_kinks>` -- Algorithms to calculate Helix Kinks
+---------------------------------------------------------------------------------------------------------------
+
+.. automodule:: ost.mol.alg.helix_kinks
+   :synopsis: Algorithms to calculate Helix Kinks
+   :members:
\ No newline at end of file

modules/mol/alg/doc/ligand_scoring.rst

+:mod:`ligand_scoring <ost.mol.alg.ligand_scoring>` -- Ligand scoring functions
+-----------------------------------------------------------------------------------
+
+.. module:: ost.mol.alg.ligand_scoring
+   :synopsis: 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 with lDDT-PLI
+
+.. automodule:: ost.mol.alg.ligand_scoring_scrmsd
+   :members:
+   :member-order: bysource
+   :synopsis: Scoring of ligands with Symmetry-corrected RMSD
\ No newline at end of file

modules/mol/alg/doc/molalg.rst

@@ -4,6 +4,21 @@
 .. module:: ost.mol.alg
    :synopsis: Algorithms operating on molecular structures
 
+Submodules
+--------------------------------------------------------------------------------
+
+* :doc:`chain_mapping`
+* :doc:`contact_score`
+* :doc:`dockq`
+* :doc:`helix_kinks`
+* :doc:`ligand_scoring`
+* :doc:`qsscore`
+* :doc:`scoring`
+* :doc:`stereochemistry`
+* :doc:`structure_analysis`
+* :doc:`trajectory_analysis`
+
+
 Local Distance Test scores (lDDT, DRMSD)
 --------------------------------------------------------------------------------
 
@@ -83,106 +98,6 @@ Local Distance Test scores (lDDT, DRMSD)
     :rtype:  :class:`str`
 
 
-:mod:`stereochemistry <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
-   :synopsis: Stereochemistry checks
-
-.. currentmodule:: ost.mol.alg
-
-
-:mod:`scoring <ost.mol.alg.scoring>` -- Specialized scoring functions
---------------------------------------------------------------------------------
-
-.. autoclass:: ost.mol.alg.scoring.lDDTBSScorer
-   :members:
-
-.. autoclass:: ost.mol.alg.scoring.Scorer
-   :members:
-   :member-order: bysource
-
-.. currentmodule:: ost.mol.alg
-
-
-: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_scrmsd
-   :members:
-   :member-order: bysource
-   :synopsis: Scoring of ligands
-
-
-:mod:`chain_mapping <ost.mol.alg.chain_mapping>` -- Chain Mapping
---------------------------------------------------------------------------------
-
-.. automodule:: ost.mol.alg.chain_mapping
-   :members:
-   :member-order: bysource
-   :synopsis: Chain mapping in assemblies
-
-.. currentmodule:: ost.mol.alg
-
-
-:mod:`qsscore <ost.mol.alg.qsscore>` -- New QS score implementation
---------------------------------------------------------------------------------
-
-.. note::
-
-  This is a new implementation of QS Score, introduced in OpenStructure 2.4 and
-  tightly integrated with the chain mapping algorithms.
-  The :doc:`previous qsscoring code <qsscoring_deprecated>` that comes with
-  `Bertoni et al. <https://www.nature.com/articles/s41598-017-09654-8>`_ is
-  considered deprecated.
-
-.. automodule:: ost.mol.alg.qsscore
-   :members:
-   :member-order: bysource
-   :synopsis: QS Score implementation
-
-.. currentmodule:: ost.mol.alg
-
-
-:mod:`DockQ <ost.mol.alg.dockq>` -- DockQ implementation
---------------------------------------------------------------------------------
-
-.. autofunction:: ost.mol.alg.dockq.DockQ
-
-.. currentmodule:: ost.mol.alg
-
-
-:mod:`Contact Scores <ost.mol.alg.contact_scores>` -- Contact based scores
---------------------------------------------------------------------------------
-
-.. automodule:: ost.mol.alg.contact_score
-   :members:
-   :member-order: bysource
-   :synopsis: Contact Scores
-
-.. currentmodule:: ost.mol.alg
-
-
 GDT - Global Distance Test
 --------------------------
 
@@ -1153,26 +1068,7 @@ used to skip frames in the analysis.
   :param view_ring2: Second group of atoms
   :type view_ring2: :class:`~ost.mol.EntityView`.
   :param stride: Size of the increment of the frame's index between two 
-     consecutive frames analyzed.  
-
-
-:mod:`helix_kinks <ost.mol.alg.helix_kinks>` -- Algorithms to calculate Helix Kinks
----------------------------------------------------------------------------------------------------------------
-
-.. automodule:: ost.mol.alg.helix_kinks
-   :members:
-
-:mod:`trajectory_analysis <ost.mol.alg.trajectory_analysis>` -- DRMSD, pairwise distances and more
----------------------------------------------------------------------------------------------------------------
-
-.. automodule:: ost.mol.alg.trajectory_analysis
-   :members:
-
-:mod:`structure_analysis <ost.mol.alg.structure_analysis>` -- Functions to analyze structures
----------------------------------------------------------------------------------------------------------------
-
-.. automodule:: ost.mol.alg.structure_analysis
-   :members:
+     consecutive frames analyzed.
 
 
 .. _mapping-functions:
@@ -1180,8 +1076,6 @@ used to skip frames in the analysis.
 Mapping functions
 --------------------------------------------------------------------------------
 
-.. currentmodule:: ost.mol.alg
-
 The following functions help to convert one residue into another by reusing as
 much as possible from the present atoms. They are mainly meant to map from
 standard amino acid to other standard amino acids or from modified amino acids

modules/mol/alg/doc/qsscore.rst

+:mod:`qsscore <ost.mol.alg.qsscore>` -- New QS score implementation
+--------------------------------------------------------------------------------
+
+.. note::
+
+  This is a new implementation of QS Score, introduced in OpenStructure 2.4 and
+  tightly integrated with the chain mapping algorithms.
+  The :doc:`previous qsscoring code <qsscoring_deprecated>` that comes with
+  `Bertoni et al. <https://www.nature.com/articles/s41598-017-09654-8>`_ is
+  considered deprecated.
+
+.. automodule:: ost.mol.alg.qsscore
+   :members:
+   :member-order: bysource
+   :synopsis: New QS score implementation

modules/mol/alg/doc/scoring.rst

+:mod:`scoring <ost.mol.alg.scoring>` -- Specialized scoring functions
+--------------------------------------------------------------------------------
+
+.. module:: ost.mol.alg.scoring
+   :synopsis: Specialized scoring functions
+
+.. autoclass:: ost.mol.alg.scoring.lDDTBSScorer
+   :members:
+
+.. autoclass:: ost.mol.alg.scoring.Scorer
+   :members:
+   :member-order: bysource

modules/mol/alg/doc/stereochemistry.rst

+:mod:`stereochemistry <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
+   :synopsis: Stereochemistry checks

modules/mol/alg/doc/structure_analysis.rst

+:mod:`structure_analysis <ost.mol.alg.structure_analysis>` -- Functions to analyze structures
+---------------------------------------------------------------------------------------------------------------
+
+.. automodule:: ost.mol.alg.structure_analysis
+   :synopsis: Functions to analyze structures
+   :members:
\ No newline at end of file

modules/mol/alg/doc/trajectory_analysis.rst

+:mod:`trajectory_analysis <ost.mol.alg.trajectory_analysis>` -- DRMSD, pairwise distances and more
+---------------------------------------------------------------------------------------------------------------
+
+.. automodule:: ost.mol.alg.trajectory_analysis
+   :synopsis: DRMSD, pairwise distances and more
+   :members:
\ No newline at end of file

modules/mol/base/doc/mol.rst

@@ -14,3 +14,14 @@ The mol module implements data structures to work with molecular datasets. At it
   query
   surface
   traj
+  ../alg/molalg
+  ../alg/chain_mapping
+  ../alg/contact_score
+  ../alg/dockq
+  ../alg/helix_kinks
+  ../alg/ligand_scoring
+  ../alg/qsscore
+  ../alg/scoring
+  ../alg/stereochemistry
+  ../alg/structure_analysis
+  ../alg/trajectory_analysis
\ No newline at end of file