From 3d71eb91eb05f5d316a4612deb9466824c8133a8 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 14 Jun 2012 18:07:58 +0200
Subject: [PATCH] Polished documentation for AddAtom
---
modules/mol/base/doc/entity.rst | 28 ++++++++++++++--------------
1 file changed, 14 insertions(+), 14 deletions(-)
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 5418b813a..258475105 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -181,7 +181,7 @@ The Handle Classes
# select calpha atoms of peptides
calphas=ent.Select('aname=CA and peptide=true')
- # select atoms in a box of size 10, centered at the origin
+ # select atoms in a box of size 10, centred at the origin
in_box=ent.Select('x=-5:5 and y=-5:5 and z=-5:5')
:param query: The query to be executed. See :class:`Query` for details.
@@ -256,7 +256,7 @@ The Handle Classes
.. method:: FindWithin(pos, radius)
- Find all atoms in sphere of given radius centered at *pos*. To turn the
+ Find all atoms in sphere of given radius centred at *pos*. To turn the
returned list of atoms into an :class:`EntityView`, use
:func:`CreateViewFromAtomList`.
@@ -888,10 +888,10 @@ The View Classes
.. method:: AddResidue(residue_handle[, view_add_flags])
- Add residue to view. If the residue's chain is not already part of the view,
- it will be added. By default, only the residue is added, but not its atoms.
- This behaviour can be modified by passing in an appropriate combination of
- `view_add_flags`.
+ Add residue to view. If the residue's chain is not already part of the
+ view, it will be added. By default, only the residue is added, but not its
+ atoms. This behaviour can be modified by passing in an appropriate
+ combination of `view_add_flags`.
:param residue_handle:
:type residue_handle: ResidueHandle
@@ -904,12 +904,11 @@ The View Classes
Add the atom to view. The chain and residue of the atom are added to the
view if they haven't already been added.
-
:param atom_handle: The atom handle
- :type atom_handle: AtomHandle
+ :type atom_handle: :class:`AtomHandle`
:param view_add_flags: An ORed together combination of ViewAddFlags
- :type view_add_flags: int
- :rtype: class:`AtomView`
+ :type view_add_flags: :class:`int`
+ :rtype: :class:`AtomView`
.. method:: AddBond(bond_handle)
@@ -1226,12 +1225,12 @@ The View Classes
Add atom to the view. If the residue of the atom is not already part of the
view, it will be added. If the atom does not belong to chain, the result is
- undefined.
+ undefined. Foo
:param atom_handle: The atom to be added
:type atom_handle: :class:`AtomHandle`
:param view_add_flags: An ORed together combination of ViewAddFlags
- :type view_add_flags: int
+ :type view_add_flags: :class:`int`
:rtype: :class:`AtomView`
.. method:: AddResidue(residue_handle[, view_add_flags])
@@ -1478,11 +1477,12 @@ The View Classes
.. method:: AddAtom(atom_handle[, flags])
- Add atom to the view.
+ Add atom to the view.
+
:param atom_handle:
:type atom_handle: :class:`AtomHandle`
:param flags: An ORed together combination of ViewAddFlags.
- :type flags: int
+ :type flags: :class:`int`
:rtype: :class:`AtomView`
.. method:: GetCenterOfAtoms()
--
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