Doc cleanup/update

doc/buildsystem.rst

@@ -149,7 +149,7 @@ safely delete the whole source folder.
 .. _python: https://www.python.org/
 .. _boost: http://www.boost.org/
 .. _eigen3: http://eigen.tuxfamily.org/index.php?title=Main_Page
-.. _openmm: https://simtk.org/home/openmm
+.. _openmm: http://openmm.org
 
 ..  LocalWords:  cmake makefiles CMakeLists txt DOCTEST LINKCHECK conf html
 ..  LocalWords:  doctest linkcheck qmean DQMEAN eigen CMakeCache

doc/dev_setup.rst

@@ -221,4 +221,4 @@ modules from there, use the binaries from :file:`stage/bin`, etc..
 
 
 .. |pylint| replace:: Pylint
-.. _pylint: http://www.pylint.org
+.. _pylint: https://www.pylint.org

loop/doc/mm_system_creation.rst

@@ -92,7 +92,7 @@ Create MM systems for loops
     :type loop_length:  :class:`int`
     :param is_n_ter: For each *res_indices[i]*, *is_n_ter[i]* defines whether
                      that residue is N-terminal.
-    :type is_n_ter:  :class:`list` :class:`bool`
+    :type is_n_ter:  :class:`list` of :class:`bool`
     :param is_c_ter: For each *res_indices[i]*, *is_c_ter[i]* defines whether
                      that residue is C-terminal.
     :type is_c_ter:  :class:`list` of :class:`bool`

loop/doc/structure_db.rst

@@ -868,11 +868,6 @@ The PsipredPrediction class
     :returns:           Number of elements in container
 
 
-.. class:: PsipredPredictionList
-
-  Represents a list of :class:`PsipredPrediction` objects
-
-
 
 .. [soding2005] Söding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.
 .. [sanner1996] Sanner M, Olson AJ, Spehner JC (1996). Reduced Surface: an Efficient Way to Compute Molecular Surfaces. Biopolymers 38 (3): 305-320.

modelling/doc/pipeline.rst

@@ -38,10 +38,10 @@ Build Raw Modelling Handle
   .. attribute:: model
 
     The resulting model. This includes one chain per target chain (in the same
-    order as the sequences in `seqres`) and (if they were included) a chain
-    named '_' for ligands. You can therefore access `model.chains` items and
-    `seqres` items with the same indexing and the optional ligand chain follows
-    afterwards.
+    order as the sequences in :attr:`seqres`) and (if they were included) a
+    chain named '_' for ligands. You can therefore access `model.chains` items
+    and :attr:`seqres` items with the same indexing and the optional ligand
+    chain follows afterwards.
 
     :type: :class:`~ost.mol.EntityHandle`
 
@@ -57,26 +57,30 @@ Build Raw Modelling Handle
   .. attribute:: seqres
 
     List of sequences with one :class:`~ost.seq.SequenceHandle` for each chain 
-    of target protein.
+    of the target protein.
 
     :type: :class:`~ost.seq.SequenceList`
 
   .. attribute:: profiles
 
     List of profiles with one :class:`ost.seq.ProfileHandle` for each chain of
-    target protein. Please note, that this attribute won't be set by simply
-    calling :func:`BuildFromRawModel`. You have to fill it manually or even
-    better by the convenient function :func:`SetSequenceProfiles`, 
-    to ensure consistency with the seqres.
+    the target protein (same order as in :attr:`seqres`). Please note, that this
+    attribute won't be set by simply calling :func:`BuildFromRawModel`. You have
+    to fill it manually or even better by the convenient function
+    :func:`SetSequenceProfiles`,  to ensure consistency with the seqres.
+
+    :type: :class:`list` of :class:`ost.seq.ProfileHandle`
 
   .. attribute:: psipred_predictions
 
-    List of predictions with one :class:`promod3.loop.PsipredPrediction` for 
-    each chain of target protein. 
-    Please note, that this attribute won't be set by simply
-    calling :func:`BuildFromRawModel`. You have to fill it manually or even
-    better by the convenient function :func:`SetPsipredPredictions`, 
-    to ensure consistency with the seqres.
+    List of predictions with one :class:`promod3.loop.PsipredPrediction` for
+    each chain of the target protein (same order as in :attr:`seqres`). Please
+    note, that this attribute won't be set by simply calling
+    :func:`BuildFromRawModel`. You have to fill it manually or even better by
+    the convenient function :func:`SetPsipredPredictions`,  to ensure
+    consistency with the seqres.
+
+    :type: :class:`list` of :class:`~promod3.loop.PsipredPrediction`
 
   .. attribute:: backbone_scorer_env
 
@@ -353,14 +357,14 @@ Modelling Steps
 
 .. function:: SetSequenceProfiles(mhandle, profiles)
 
-  Sets the given sequence profiles and ensures consistency with the seqres 
-  of **mhandle**
+  Sets the :attr:`sequence profiles <ModellingHandle.profiles>` of **mhandle**
+  while ensuring consistency with the :attr:`~ModellingHandle.seqres`.
 
-  :param mhandle:       Will have the profiles attached afterwards
-  :param profiles:      The sequence profiles to attach
+  :param mhandle:  Will have the profiles attached afterwards
+  :param profiles: The sequence profiles to attach
 
-  :type mhandle:        :class:`ModellingHandle`
-  :type profiles:       :class:`ost.seq.ProfileHandleList`
+  :type mhandle:   :class:`ModellingHandle`
+  :type profiles:  :class:`list` of :class:`ost.seq.ProfileHandle`
 
   :raises: :class:`ValueError` when the given **profiles** are not consistent
            with seqres in **mhandle**
@@ -368,14 +372,15 @@ Modelling Steps
 
 .. function:: SetPsipredPredictions(mhandle, predictions)
 
-  Sets the given predictions and ensures consistency with the seqres 
-  of **mhandle**
+  Sets the :attr:`predictions <ModellingHandle.psipred_predictions>` of
+  **mhandle** while ensuring consistency with the
+  :attr:`~ModellingHandle.seqres`.
 
-  :param mhandle:       Will have the predictions attached afterwards
-  :param predictions:   The predictions to attach
+  :param mhandle:     Will have the predictions attached afterwards
+  :param predictions: The predictions to attach
 
-  :type mhandle:        :class:`ModellingHandle`
-  :type predictions:    :class:`promod3.loop.PsipredPredictionList`
+  :type mhandle:      :class:`ModellingHandle`
+  :type predictions:  :class:`list` of :class:`~promod3.loop.PsipredPrediction`
 
   :raises: :class:`ValueError` when the given **predictions** are not consistent
            with seqres in **mhandle**

modelling/doc/sidechain_reconstruction.rst

@@ -96,7 +96,7 @@ SidechainReconstructor Class
 
 
   .. method:: Reconstruct(start_resnum, num_residues, chain_idx=0)
-  .. method:: Reconstruct(start_resnum_list, num_residues_list, chain_idx_list)
+              Reconstruct(start_resnum_list, num_residues_list, chain_idx_list)
 
     Reconstruct sidechains for one or several loops (extracted from environment). 
     All residues in the loop(s) are expected to contain valid CB positions