From b43b2954e9cba79159e32903577030490c2d693a Mon Sep 17 00:00:00 2001
From: Tobias Schmidt <tobias.schmidt@unibas.ch>
Date: Fri, 15 Jun 2012 15:50:07 +0200
Subject: [PATCH] fix some typos in CopyResidue docu
---
modules/conop/doc/aminoacid.rst | 20 +++++++++++++-------
1 file changed, 13 insertions(+), 7 deletions(-)
diff --git a/modules/conop/doc/aminoacid.rst b/modules/conop/doc/aminoacid.rst
index fe42a4c63..975163172 100644
--- a/modules/conop/doc/aminoacid.rst
+++ b/modules/conop/doc/aminoacid.rst
@@ -69,7 +69,7 @@ Converter functions
Whether the set is empty, i.e. doesn't contain any amino acids.
-Maping functions
+Mapping functions
--------------------------------------------------------------------------------
The following functions help to convert one residue into another by reusing as
@@ -79,11 +79,16 @@ to standard amino acids.
.. function:: CopyResidue(src_res, dst_res, editor)
- Copies the atoms of ``src_res`` to ``dst_res`` using the residue names of
+ Copies the atoms of ``src_res`` to ``dst_res`` using the residue names
as guide to decide which of the atoms should be copied. If ``src_res`` and
``dst_res`` have the same name, or ``src_res`` is a modified version of
- ``dst_res``, CopyConserved will be called, otherwise CopyNonConserved will
- be called.
+ ``dst_res`` (i.e. have the same single letter code), CopyConserved will be
+ called, otherwise CopyNonConserved will be called.
+
+ :param src_res: The source residue
+ :type src_res: :class:`~mol.ResidueHandle`
+ :param dst_res: The destination residue
+ :type dst_res: :class:`~mol.ResidueHandle`
:returns: true if the residue could be copied, false if not.
@@ -93,13 +98,13 @@ to standard amino acids.
amino acid of ``src_res`` (or ``src_res`` itself) are identical to ``dst_res``.
If ``src_res`` and ``dst_res`` are identical, all heavy atoms are copied
- ``to dst_res``. If ``src_res`` is a modified version of ``dst_res`` and the
+ to ``dst_res``. If ``src_res`` is a modified version of ``dst_res`` and the
modification is a pure addition (e.g. the phosphate group of phosphoserine),
the modification is stripped off and all other heavy atoms are copied to
``dst_res``. If the modification is not a pure addition, only the backbone
heavy atoms are copied to ``dst_res``.
- Additionally, the selenium atom of MSE is converted to sulphur.
+ Additionally, the selenium atom of ``MSE`` is converted to sulphur.
:param src_res: The source residue
:type src_res: :class:`~mol.ResidueHandle`
@@ -111,7 +116,8 @@ to standard amino acids.
.. function:: CopyNonConserved(src_res, dst_res, editor)
- Copies the heavy backbone atoms of ``src_res`` to ``dst_res``.
+ Copies the heavy backbone atoms and Cbeta (except for ``GLY``) of ``src_res``
+ to ``dst_res``.
:param src_res: The source residue
:type src_res: :class:`~mol.ResidueHandle`
--
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