From cb8db7594618558dd177646a38d6e52f2ef30e5e Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Wed, 7 Jul 2010 10:10:31 +0000
Subject: [PATCH] update docs
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2538 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/base/doc/generic.rst | 6 ++++
modules/doc/intro-03.rst | 4 +--
modules/gfx/doc/entity.rst | 15 +++++++++
modules/mol/base/doc/entity.rst | 60 ++++++++++++++++++++++-----------
4 files changed, 63 insertions(+), 22 deletions(-)
diff --git a/modules/base/doc/generic.rst b/modules/base/doc/generic.rst
index 03ed133b5..e24ca06b9 100644
--- a/modules/base/doc/generic.rst
+++ b/modules/base/doc/generic.rst
@@ -159,4 +159,10 @@ API documentation
.. method:: SetBoolProp(key, value)
Set bool property, overriding a property with the same name
+
+ .. method:: RemoveProp(key)
+
+ Removes the property with given key, regardless of its type. If the property
+ does not exist, the method has no effect.
+
diff --git a/modules/doc/intro-03.rst b/modules/doc/intro-03.rst
index 5a6fc08aa..c2d6713d7 100644
--- a/modules/doc/intro-03.rst
+++ b/modules/doc/intro-03.rst
@@ -23,7 +23,7 @@ of data.
The last command is not mandatory, but very convenient to center the camera on the object.
-The :class:`~ost.gfx.Scene`
+The Scene
--------------------------------------------------------------------------------
@@ -57,7 +57,7 @@ manipulated:
The last command assigns a uniform red coloring to all atoms.
-The :class:`Graphical Entity <ost.gfx.Entity>`
+The Graphical Entity
--------------------------------------------------------------------------------
Now let's look at the graphical entity in more detail. The graphical entity is
diff --git a/modules/gfx/doc/entity.rst b/modules/gfx/doc/entity.rst
index a3bf16719..4ebe5f7d8 100644
--- a/modules/gfx/doc/entity.rst
+++ b/modules/gfx/doc/entity.rst
@@ -100,11 +100,26 @@ Render Options
Defaults to off.
:type: bool
+
+
+
**bond_order_distance**
The distance between the lines depicting higher order bonds.
+
+Loading and Displaying an Entity
+--------------------------------------------------------------------------------
+
+This code examples shows how to load a structure and display it on the screen. It also shows how to programmatically combine different render modes in one graphical entity.
+
+.. literalinclude:: /../../examples/demos/load_and_display.py
+
+
+Entity API Reference
+--------------------------------------------------------------------------------
+
.. class:: Entity(name, entity)
Entity(name, render_mode, entity)
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 8aa95e6a8..0280c9a23 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -65,7 +65,13 @@ The Handle Classes
This property is read-only. Also available as :meth:`GetAtomList`
:type: A list of :class:`atom handles<AtomHandle>`
-
+
+ .. attribute:: bounds
+
+ Axis-aligned bounding box of the entity. Read-only
+
+ :type: :class:`ost.geom.AlignedCuboid`
+
.. attribute:: mass
The total mass of the entity in Dalton. Also available as :meth:`GetMass`.
@@ -322,7 +328,13 @@ The Handle Classes
This property is read-only. Also available as :meth:`GetAtomList`
:type: A list of :class:`atom handles<AtomHandle>`
-
+
+ .. attribute:: bounds
+
+ Axis-aligned bounding box of the chain. Read-only
+
+ :type: :class:`ost.geom.AlignedCuboid`
+
.. attribute:: mass
The total mass of this chain in Dalton. Also available as :meth:`GetMass`
@@ -425,6 +437,12 @@ The Handle Classes
:type: str
+ .. attribute:: bounds
+
+ Axis-aligned bounding box of the residue. Read-only.
+
+ :type: :class:`ost.geom.AlignedCuboid`
+
.. attribute:: mass
The total mass of this residue in Dalton. Also available as :meth:`GetMass`.
@@ -774,6 +792,12 @@ The View Classes
:type: A list of :class:`AtomViews <AtomView>`
+ .. attribute:: bounds
+
+ Axis-aligned bounding box of the entity view. Read-only.
+
+ :type: :class:`ost.geom.AlignedCuboid`
+
.. attribute:: handle
The underlying :class:`handle <EntityHandle>` of the entity view. Also
@@ -906,7 +930,7 @@ The View Classes
:param residue: Residue handle
:type residue: ResidueHandle
- :returns: The residue view pointing the the handle, or an invalid handle if the residue is not part of the view
+ :returns: The residue view pointing the the handle, or an invalid handle if the residue is not part of the view
:rtype: class:`ResidueView`
.. method:: FindAtom(chain_name, res_num, atom_name)
@@ -1101,7 +1125,13 @@ The View Classes
This property is read-only. Also available as :meth:`GetAtomList`
:type: A list of :class:`atom handles<AtomHandle>`
-
+
+ .. attribute:: bounds
+
+ Axis-aligned bounding box of the chain. Read-only
+
+ :type: :class:`ost.geom.AlignedCuboid`
+
.. attribute:: mass
The total mass of this chain in Dalton. Also available as :meth:`GetMass`
@@ -1258,14 +1288,6 @@ The View Classes
:type flags: int
:rtype: :class:`EntityView`
- .. method:: Apply(visitor)
-
- Apply entity visitor to view. In Python, you usually don't have to use this
- method.
-
- :param visitor: The visitor
- :type visitor: :class:`EntityVisitor`
-
.. class:: ResidueView
.. attribute:: name
@@ -1302,6 +1324,12 @@ The View Classes
:type: str
+ .. attribute:: bounds
+
+ Axis-aligned bounding box of the residue view. Read-only
+
+ :type: :class:`ost.geom.AlignedCuboid`
+
.. attribute:: mass
The total mass of this residue in Dalton. Also available as :meth:`GetMass`.
@@ -1400,14 +1428,6 @@ The View Classes
.. method:: GetAtomList()
See :attr:`atoms`
-
- .. method:: Apply(visitor)
-
- Apply entity visitor to the residue. In Python, you don't have to use this
- method. Is is mainly used in C++.
-
- :param visitor:
- :type visitor: :class:`EntityVisitor`
.. method:: Select(query[, flags])
--
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