From a537c66ec3d031217ffb98272bd93cb9d3fd137e Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Mon, 28 Aug 2017 14:16:00 +0200
Subject: [PATCH] Doc cleanup/update
---
doc/buildsystem.rst | 2 +-
doc/dev_setup.rst | 2 +-
loop/doc/mm_system_creation.rst | 2 +-
loop/doc/structure_db.rst | 5 --
modelling/doc/pipeline.rst | 59 ++++++++++++----------
modelling/doc/sidechain_reconstruction.rst | 2 +-
6 files changed, 36 insertions(+), 36 deletions(-)
diff --git a/doc/buildsystem.rst b/doc/buildsystem.rst
index eab8bc91..4bb19268 100644
--- a/doc/buildsystem.rst
+++ b/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
diff --git a/doc/dev_setup.rst b/doc/dev_setup.rst
index 86b447a3..ea7f1c86 100644
--- a/doc/dev_setup.rst
+++ b/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
diff --git a/loop/doc/mm_system_creation.rst b/loop/doc/mm_system_creation.rst
index 817c4c55..fbfd1738 100644
--- a/loop/doc/mm_system_creation.rst
+++ b/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`
diff --git a/loop/doc/structure_db.rst b/loop/doc/structure_db.rst
index 7ee297af..33c307ef 100644
--- a/loop/doc/structure_db.rst
+++ b/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.
diff --git a/modelling/doc/pipeline.rst b/modelling/doc/pipeline.rst
index 71c5ba32..db7dc9d5 100644
--- a/modelling/doc/pipeline.rst
+++ b/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**
diff --git a/modelling/doc/sidechain_reconstruction.rst b/modelling/doc/sidechain_reconstruction.rst
index 32ff794c..52e4b1c7 100644
--- a/modelling/doc/sidechain_reconstruction.rst
+++ b/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
--
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