From e9a0192f86efddfb8a33f3f2cfe8cc9eb0564cce Mon Sep 17 00:00:00 2001 From: Xavier Robin <xavalias-github@xavier.robin.name> Date: Thu, 27 Jun 2024 15:44:06 +0200 Subject: [PATCH] doc: refactor seq.alg submodules --- modules/index.rst | 14 +++++++++++-- modules/mol/alg/doc/stereochemistry.rst | 2 +- modules/seq/alg/doc/aaindex.rst | 22 +++++++++++++++++++ modules/seq/alg/doc/renumber.rst | 7 +++++++ modules/seq/alg/doc/seqalg.rst | 28 ++++++------------------- 5 files changed, 48 insertions(+), 25 deletions(-) create mode 100644 modules/seq/alg/doc/aaindex.rst create mode 100644 modules/seq/alg/doc/renumber.rst diff --git a/modules/index.rst b/modules/index.rst index 9727d322b..e307b9702 100644 --- a/modules/index.rst +++ b/modules/index.rst @@ -13,16 +13,26 @@ OpenStructure documentation geom/geom mol/base/mol mol/alg/molalg + mol/alg/chain_mapping + mol/alg/contact_score + mol/alg/dockq + mol/alg/helix_kinks + mol/alg/ligand_scoring + mol/alg/qsscore + mol/alg/scoring + mol/alg/stereochemistry + mol/alg/structure_analysis + mol/alg/trajectory_analysis mol/mm/molmm conop/conop img/base/img img/alg/alg seq/base/seq seq/alg/seqalg + seq/alg/renumber + seq/alg/aaindex db/db - bindings/bindings - io/io gfx/gfx gui/gui diff --git a/modules/mol/alg/doc/stereochemistry.rst b/modules/mol/alg/doc/stereochemistry.rst index 6c9ccee87..0ed0dd38f 100644 --- a/modules/mol/alg/doc/stereochemistry.rst +++ b/modules/mol/alg/doc/stereochemistry.rst @@ -1,5 +1,5 @@ :mod:`mol.alg.stereochemistry <ost.mol.alg.stereochemistry>` -- Stereochemistry Checks --------------------------------------------------------------------------------- +-------------------------------------------------------------------------------------- .. warning:: diff --git a/modules/seq/alg/doc/aaindex.rst b/modules/seq/alg/doc/aaindex.rst new file mode 100644 index 000000000..cb8754814 --- /dev/null +++ b/modules/seq/alg/doc/aaindex.rst @@ -0,0 +1,22 @@ +:mod:`seq.alg.aaindex <ost.seq.alg.aaindex>` -- AAIndex annotations +-------------------------------------------------------------------------------- + +.. module:: ost.seq.alg.aaindex + :synopsis: AAIndex annotations + +.. autoclass:: ost.seq.alg.aaindex.AAIndex + :members: + :special-members: __getitem__ + +The annotations/scores can either refer to single amino acids or represent +pairwise values. The two types are: + +.. autoclass:: ost.seq.alg.aaindex.AnnoType + :members: + :undoc-members: + +The actual data of an entry in the aaindex database is stored in a +:class:`aaindex.AAIndexData` object: + +.. autoclass:: ost.seq.alg.aaindex.AAIndexData + :members: diff --git a/modules/seq/alg/doc/renumber.rst b/modules/seq/alg/doc/renumber.rst new file mode 100644 index 000000000..ff1618839 --- /dev/null +++ b/modules/seq/alg/doc/renumber.rst @@ -0,0 +1,7 @@ +:mod:`seq.alg.renumber <ost.seq.alg.renumber>` -- Renumber entities +-------------------------------------------------------------------- + +.. module:: ost.seq.alg.renumber + :synopsis: Renumber entities + +.. autofunction:: ost.seq.alg.renumber.Renumber diff --git a/modules/seq/alg/doc/seqalg.rst b/modules/seq/alg/doc/seqalg.rst index a293192f7..98e0568c6 100644 --- a/modules/seq/alg/doc/seqalg.rst +++ b/modules/seq/alg/doc/seqalg.rst @@ -4,6 +4,12 @@ .. module:: ost.seq.alg :synopsis: Algorithms for sequences +Submodules +-------------------------------------------------------------------------------- + +* :doc:`aaindex – AAIndex annotations <aaindex>` +* :doc:`renumber – Renumber entities <renumber>` + Algorithms for Alignments -------------------------------------------------------------------------------- @@ -123,8 +129,6 @@ Algorithms for Alignments :returns: List of column entropies -.. autofunction:: ost.seq.alg.renumber.Renumber - .. function:: SequenceIdentity(aln, ref_mode=seq.alg.RefMode.ALIGNMENT, seq_a=0, seq_b=1) Calculates the sequence identity between two sequences at index seq_a and seq_b in @@ -1035,23 +1039,3 @@ etc.) to be set, which is the case if you load a file in hhm format. :raises: Exception if profile doesn't have HMM information assigned - -AAIndex annotations -------------------- - -.. autoclass:: ost.seq.alg.aaindex.AAIndex - :members: - :special-members: __getitem__ - -The annotations/scores can either refer to single amino acids or represent -pairwise values. The two types are: - -.. autoclass:: ost.seq.alg.aaindex.AnnoType - :members: - :undoc-members: - -The actual data of an entry in the aaindex database is stored in a -:class:`aaindex.AAIndexData` object: - -.. autoclass:: ost.seq.alg.aaindex.AAIndexData - :members: -- GitLab