From 5f58882cb82da706a718b5a80ba700e291e0952f Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 4 Mar 2015 16:22:29 +0100
Subject: [PATCH] Fixing Sphinx syntax glitches
---
modules/io/doc/mmcif.rst | 3 +--
modules/mol/alg/pymod/superpose.py | 20 ++++++++++++++------
2 files changed, 15 insertions(+), 8 deletions(-)
diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index b8b91c3c8..8082ec1c3 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -955,8 +955,7 @@ of the annotation available.
Retrieve database_pdb_rev.date_original.
- :returns: database_pdb_rev.date_original as :class:`str` in format
- 'yyyy-mm-dd'
+ :returns: database_pdb_rev.date_original as :class:`str` in format 'yyyy-mm-dd'
.. method:: AddRevision(int num, String date, String status)
diff --git a/modules/mol/alg/pymod/superpose.py b/modules/mol/alg/pymod/superpose.py
index 55afedf60..9af62d7fa 100644
--- a/modules/mol/alg/pymod/superpose.py
+++ b/modules/mol/alg/pymod/superpose.py
@@ -298,24 +298,32 @@ def Superpose(ent_a, ent_b, match='number', atoms='all', iterative=False, max_it
:param ent_a: The model entity
:type ent_a: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
+
:param ent_b: The reference entity
:type ent_b: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
+
:param match: Method to gather residues/ atoms
:type match: :class:`str`
+
:param atoms: The subset of atoms to be used in the superposition
:type atoms: :class:`str`, :class:`list`, :class:`set`
+
:param max_iterations: They number of iterations that will be run during
- iterative superposition
+ iterative superposition
:type max_iterations: :class:`int`
- :param distance_threshold: The distance threshold between which two atoms that
- will be used in the next superposition iteration
+
+ :param distance_threshold: The distance threshold between which two atoms
+ that will be used in the next superposition
+ iteration
+ :type distance_threshold: :class:`float`
+
:returns: An instance of :class:`SuperpositionResult`, containing members
- * ``rmsd`` - RMSD of the superposed entities
+ * ``rmsd`` - RMSD of the superposed entities
- * ``view1`` - First :class:`~ost.mol.EntityView` used
+ * ``view1`` - First :class:`~ost.mol.EntityView` used
- * ``view2`` - Second :class:`~ost.mol.EntityView` used
+ * ``view2`` - Second :class:`~ost.mol.EntityView` used
"""
not_supported="Superpose called with unsupported matching request."
## create views to superpose
--
GitLab