diff --git a/modules/conop/doc/conop.rst b/modules/conop/doc/conop.rst
index a7ebe2eaa24fd6cb3c6f2990e9ba939b77644544..6e8443558c8345033692c55e3d84c302d200b93d 100644
--- a/modules/conop/doc/conop.rst
+++ b/modules/conop/doc/conop.rst
@@ -63,7 +63,7 @@ be achieved with
conop.Conopology.Instance().RegisterBuilder(rbb,'rbb')
conop.Conopology.Instance().SetDefaultBuilder('rbb')
-All subsequent calls to :func:`io.LoadEntity` will make use of the
+All subsequent calls to :func:`ost.io.LoadEntity` will make use of the
RuleBasedBuilder instead of the heuristic builder. See
:ref:`here <mmcif-convert>` for more information on how to create the necessary
files to use the rule-based builder.
@@ -225,18 +225,20 @@ files to use the rule-based builder.
Connecting atoms
--------------------------------------------------------------------------------
-The high level interface is exposed by the Conopoloy singleton instance:
+A single function call to :func:`ConnectAll` is sufficient to assign residue and atoms properties as well as to connect atoms with bonds.
+
.. code-block:: python
-
- import conop
-
- cc=conop.Conopology.Instance()
-
+
+ # Suppose that BuildRawModel is a function that returns a protein structure
+ # with no atom properties assigned and no bonds formed.
ent=BuildRawModel(...)
- cc.ConnectAll(cc.GetBuilder(), ent)
+ print ent.bonds # will return an empty list
+ # Call ConnectAll() to assign properties/connect atoms
+ conop.ConnectAll(ent)
+ print ent.bonds # will print a list containing many bonds
-For fine grained control, the builder interface may be used directly.
+For fine grained control, the :class:`Builder` interface may be used directly.
.. _mmcif-convert:
diff --git a/modules/gfx/doc/gfx.rst b/modules/gfx/doc/gfx.rst
index 3535136fe6a633ce0abc783d60be0eef17887667..de9cf3ddbcf1170f9cfac59f7377ec284fdf3b5a 100644
--- a/modules/gfx/doc/gfx.rst
+++ b/modules/gfx/doc/gfx.rst
@@ -1,10 +1,13 @@
:mod:`~ost.gfx` - Realtime 3D Rendering
================================================================================
+For a introduction to the :mod:`~ost.gfx` module, please have a look at the :doc:`../intro-03`.
+
.. module:: ost.gfx
:synopsis: Realtime 3D Rendering
.. toctree::
:maxdepth: 2
+ scene
entity
\ No newline at end of file
diff --git a/modules/gfx/doc/scene.rst b/modules/gfx/doc/scene.rst
new file mode 100644
index 0000000000000000000000000000000000000000..27bf9b86b1a8aad58248cd98f642e319e02a4343
--- /dev/null
+++ b/modules/gfx/doc/scene.rst
@@ -0,0 +1,344 @@
+The Scene
+================================================================================
+
+.. currentmodule:: ost.gfx
+
+The scene is the central registry for graphical objects and manages rendering
+parameters. Among other parameters, it is used to setup the lighting, fog,
+background color and the position and viewing direction of the user. The scene
+is a singleton, meaning that there is only one scene available. The instance can
+be accessed via :func:`gfx.Scene`. Because the scene is so important and
+commonly used, the scene is also available as the `scene` variable in the
+interactive python shell as well as from scripts.
+
+Manipulating the Camera
+--------------------------------------------------------------------------------
+
+The users position and orientation in the scene is specified by the camera. The camera is represented by a center, a rotation and an offset from the center. These 3 attributes can be set independently. Manipulation of the camera is done by assigning a new :class:`~ost.mol.Transform` to the :attr:`Scene.transform` attribute.
+
+.. _camera-orbit:
+
+Orbiting around a Point
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The following code example will let the camera orbit around the center of the camera.
+
+.. code-block:: python
+
+ # tweakable parameters:
+ # - axis of rotation
+ # - angular step size. Making it bigger speeds up the rotation
+ # - number of frames
+ axis=geom.Vec3(0, 1, 0)
+ step_size=0.01
+ num_frames=100
+
+ angle=0.0
+ for i in range(num_frames):
+ angle+=step_size
+ if angle>math.pi*2:
+ angle-=math.pi*2
+ camera=scene.transform
+ rot=geom.AxisRotation(axis, angle)
+ camera.SetRot(rot)
+ camera.SetTrans(geom.Vec3(25.0, 0.0, -50))
+ scene.transform=camera
+ scene.Export('frame-%03d.png' % i, 500, 500)
+
+It is interesting to note that the offset from center (`trans`) is given in rotated coordinates. Transforming along z shifts the camera along the viewing direction. Setting x and y to non-zero causes the center of the camera not to be projected onto the center of the screen any longer. For example, setting the value `trans` to `geom.Vec3(50, 0, 0)` gives a viewing direction perpendicular to the vector from the camera position to the center.
+
+.. class:: Scene
+
+ .. attribute:: background
+
+ The background color of the scene. By default the background color is
+ transparent black.
+
+ :type: :class:`Color`
+
+ .. attribute:: center
+
+ The center of the scene. Read-write. Changing the center affects the
+ orientation of the camera, but not its position. To change the camera
+ position, use :attr:`transform`. Also available as
+ :meth:`GetCenter`/:meth:`SetCenter`.
+
+ See also :meth:`CenterOn`.
+
+ :type: :class:`~ost.geom.Vec3`
+
+ .. attribute:: transform
+
+ The camera transformation. Read-write. For an example usage see
+ :ref:`camera-orbit`. Also available as
+ :meth:`GetTransform`/:meth:`SetTransform`.
+
+ :type: :class:`~ost.mol.Transform`
+
+
+ .. attribute:: fov
+
+ The field of view angle (in degrees) in vertical direction. Read-write.
+ Also available as :meth:`GetFOV`/:meth:`SetFOV`.
+
+ :type: float.
+
+ .. method:: Add(obj[, replace_existing])
+
+ Add an object to the root node of the scene. This means that
+
+ * The object will be rendered on the screen.
+ * The object's bounding box affects the slabbing operations.
+
+ :param obj: The object to be added.
+ :type obj: :class:`GfxNode`
+ :param replace_existing: If true, existing objects of the same name are
+ silently replaced. If false (the default), trying to add an object with
+ an existing name will raise a RuntimeError.
+
+ :type replace_existing: bool
+
+
+ .. method:: AttachObserver(obs)
+
+ Attach a :class:`scene observer <SceneObserver>`. The new scene observer
+ will get notified when the scene's state changes or objects get updated.
+
+ :param obs:
+ :type obs: :class:`SceneObserver`
+
+
+ .. method:: AutoAutoslab(flag)
+
+ Enable/disable autoslabbing. If autoslabbing is enabled, the near and far
+ clipping planes will automatically be adjusted to contain all the objects in
+ the scene. This calculation is done before every redraw. Note that,
+ autoslabbing is not rotation invariant. See :meth:`AutoslabMax` for a
+ rotation-invariant version.
+
+ :param flag:
+ :type flag: bool
+
+
+ .. method:: Autoslab(fast[, force])
+
+ .. note::
+
+ This method looks stale. Remove it?
+
+ :param fast:
+ :type fast: bool
+ :param force:
+ :type force: bool
+
+ .. method:: AutoslabMax()
+
+ Adjust the near and far clipping planes in such a way that they contain the
+ bounding sphere of all the objects in the scene. In constrast to AutoSlab()
+ the near/far clipping planes calculated with :meth:`AutoslabMax` are
+ invariant to rotation.
+
+ .. method:: CenterOn(obj)
+
+ Center the camera on the center of the obj. This does not update offset and
+ rotation of the camera. However, since the offset and rotation are applied
+ after the centering, the position and viewing direction are affected by the
+ change of center.
+
+ :param obj: Object, or name of the object
+ :type obj: str, or :class:`GfxNode`
+
+
+ .. method:: Export(filename, width, height[, transparent])
+ Export(filename[, transparent])
+
+ Renders (exports) the scene into a PNG image.
+
+ :param filename: The output filename
+ :type filename: str
+ :param width: The width of the image. Defaults to the width of the
+ OpenGL window
+ :type width: int
+ :param height: The height of the image. Defaults to the height of the OpenGL
+ window.
+ :type height: int
+ :param transparent: If true, and the background color of the scene is
+ transparent, will produce a transparent image. If false, the alpha
+ component will be set to opaque.
+ :type transparent: bool
+
+ .. method:: ExportPov(filename[, working_dir])
+
+ Export the scene to POV-Ray format. The export will generate two files, one
+ containing a general description of the scene, including camera position and
+ materials and a second containing the geometric description of the objects.
+ The first file will be named `filename.pov`, the second `filename.inc`.
+
+ The files will be placed in working directory
+
+ .. note::
+
+ This method is highly experimental and does not work for more complex
+ objects. Stay tuned for updates.
+
+
+ :param filename: The base filename without file extension. `.pov` and `.inc`
+ will automatically be appended to te filename.
+ :type filename: str
+ :param working_dir: The working directory. Defaults to the current
+ directory.
+ :type working_dir: str
+
+
+ .. method:: GetFOV()
+
+ Get the field of view angle in the y direction (in degrees).
+ :rtype: float
+
+ .. method:: GetRTC()
+
+ .. note::
+
+ Looks stale. Remove it?
+
+ :rtype: :class:`Mat4`
+
+ .. method:: GetTransform()
+
+ See :attr:`transform`
+
+ .. method:: Remove(obj)
+
+ Remove the given object from the scene.
+
+ :param obj:
+ :type obj: :class:`GfxNode`
+
+ .. method:: RenderGL()
+
+ Renders the scene.
+
+ .. method:: RequestRedraw()
+
+ Request a redraw of the scene.
+
+
+ .. method:: Resize(width, height)
+
+ Resize the OpenGL context.
+
+ :param width: The new width
+ :type width: int
+ :param height: The new height
+ :type height: int
+
+ .. method:: SetBackground(color)
+
+ See :attr:`background`
+
+ :param color:
+ :type color: :class:`Color`
+
+ .. method:: SetBlur(arg2)
+
+ :param arg2:
+ :type arg2: int
+
+ .. method:: SetFOV(angle)
+
+ See :attr:`fov`.
+
+ :param angle:
+ :type angle: float
+
+ .. method:: SetFog(arg2)
+
+ :param arg2:
+ :type arg2: bool
+
+ .. method:: SetFogColor(arg2)
+
+ :param arg2:
+ :type arg2: :class:`Color`
+
+ .. method:: SetFogOffsets(arg2, arg3)
+
+ :param arg2:
+ :type arg2: float
+ :param arg3:
+ :type arg3: float
+
+ .. method:: SetLightDir(arg2)
+
+ :param arg2:
+ :type arg2: :class:`~ost.geom.Vec3`
+
+ .. method:: SetLightProp(arg2, arg3, arg4)
+
+ :param arg2:
+ :type arg2: :class:`Color`
+ :param arg3:
+ :type arg3: :class:`Color`
+ :param arg4:
+ :type arg4: :class:`Color`
+
+ .. method:: SetNearFar(near, far)
+
+ Manually sets the near and far clipping planes to the given values. Before
+ using this method, make sure :meth:`AutoAutoslab` is disabled.
+
+ :param near:
+ :type near: float
+ :param far:
+ :type far: float
+
+ .. method:: UnProject(point[, ignore_vp])
+
+ Apply the inverse of the current camera and perspective transformation. This
+ essentially gives the screen (or normalized view coordinates) of a point in
+ global coordinates. The inverse operations is available as :meth:`Project`.
+
+ :param point: The point in global coordinates.
+ :type point: :class:`~ost.geom.Vec3`
+ :param ignore_vp: If set to false (the default), also performs the viewport
+ transformation. Points inside the viewing frustum will have x and y
+ coordinates in the range [0, width)x[0, height]. If true, the returned
+ coordinates will be between [-1,1]x[-1,1].
+ :type ignore_vp: bool
+ :rtype: :class:`~ost.geom.Vec3`
+
+ .. method:: SetRTC(arg2)
+
+ :param arg2:
+ :type arg2: :class:`Mat4`
+
+ .. method:: SetShadow(arg2)
+
+ :param arg2:
+ :type arg2: bool
+
+ .. method:: SetShadowQuality(arg2)
+
+ :param arg2:
+ :type arg2: int
+
+ .. method:: SetStereoEye(arg2)
+
+ :param arg2:
+ :type arg2: int
+
+ .. method:: SetStereoInverted(arg2)
+
+ :param arg2:
+ :type arg2: bool
+
+ .. method:: SetTransform(new_transform)
+
+ See :attr:`transform`
+
+ .. method:: Stereo(mode)
+
+ :param mode:
+ :type mode: int
+
+
\ No newline at end of file
diff --git a/modules/gfx/pymod/export_scene.cc b/modules/gfx/pymod/export_scene.cc
index 9cae54473b3dc37cd301c55b1e54d643272fb308..e66235742552df1b54d131abc39285fe057e8210 100644
--- a/modules/gfx/pymod/export_scene.cc
+++ b/modules/gfx/pymod/export_scene.cc
@@ -91,6 +91,8 @@ void export_Scene()
.def("RenderGL", &Scene::RenderGL)
.def("Resize", &Scene::Resize)
.def("SetBackground", &Scene::SetBackground)
+ .add_property("transform", &Scene::GetTransform, &Scene::SetTransform)
+ .add_property("fov", &Scene::GetFOV, &Scene::SetFOV)
.add_property("center", &Scene::GetCenter, &Scene::SetCenter)
.add_property("near", &Scene::GetNear, &Scene::SetNear)
.add_property("far", &Scene::GetFar, &Scene::SetFar)
diff --git a/modules/mol/base/doc/query.rst b/modules/mol/base/doc/query.rst
index ff8ff21a41613745e62df35bb648edfb72763ff1..391156d7f8d7ae19ece74d2dd4748d028060526d 100644
--- a/modules/mol/base/doc/query.rst
+++ b/modules/mol/base/doc/query.rst
@@ -4,7 +4,7 @@ Queries
.. currentmodule:: ost.mol
OpenStructure includes a powerful query system that allows you to perform custom
-selections in a convenient way.
+selections on a molecular entity in a convenient way.
The Basics
@@ -175,11 +175,13 @@ The following properties may be used in predicates. The type is given for each p
Properties of Chains
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
**cname/chain** (str) :attr:`Chain name<ChainHandle.name>`
Properties of Residues
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
**rname** (str): :attr:`Residue name<ResidueHandle.name>`
**rnum** (int): :attr:`Residue number<ResidueHandle.number>`. Currently only the numeric part is honored.
@@ -198,12 +200,11 @@ index is the same for views and handles.
Properties of Atoms
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
**aname** (str): :attr:`Atom name<AtomHandle.name>`
**ele** (str): :attr:`Atom element<AtomHandle.element>`
-
-
**occ** (float): :attr:`Atom occupancy<AtomHandle.occupancy>`
**abfac** (float): :attr:`Atom B-factor<AtomHandle.b_factor>`