diff --git a/modules/doc/intro-02.rst b/modules/doc/intro-02.rst
index bfca96383d629ade80f7aecfb048d968b44444cc..95112b0bcc3accc7f5b883cd2e9730c9c1ee47e1 100644
--- a/modules/doc/intro-02.rst
+++ b/modules/doc/intro-02.rst
@@ -72,7 +72,7 @@ Isosurfaces are easy to create in OpenStructure:
The other way to visualize a 3-dimensional map is by showing one 2-dimensional
density slice at a time, allowing the user to move through the slices. In
-OpenStructure this is achieved using a DataViewer :doc:`gui/image-viewer`).
+OpenStructure this is achieved using a DataViewer).
A DataViewer showing the filtered map is created using the following command:
.. code-block:: python
diff --git a/modules/doc/newmodule.rst b/modules/doc/newmodule.rst
index a45283055f5a4e60af1f468b5846857d7c3c28c1..d821de02c707988b92138eae1426e70407e7bc53 100644
--- a/modules/doc/newmodule.rst
+++ b/modules/doc/newmodule.rst
@@ -14,7 +14,7 @@ for the platform-independent data like icons, images and examples.
OpenStructure uses `CMake <http://www.cmake.org>`_ to build the project. The
rules for the build-system are defined in `CMakeLists.txt` files. When running
-`CMake <http://cmake.org>`_, the files are compiled and copied into stage. The
+`cmake`, the files are compiled and copied into stage. The
real installation, if necessary, happens at a later stage. This is referred to
as staging of the files.
diff --git a/modules/geom/doc/vec.rst b/modules/geom/doc/vec.rst
index d3876bcb1f9b46049869a3be84e51bdef9ff7e23..bc88b3f2b0e020bdfa0b96480c561414e8f2fa7f 100644
--- a/modules/geom/doc/vec.rst
+++ b/modules/geom/doc/vec.rst
@@ -2,7 +2,6 @@ Vectors
================================================================================
.. currentmodule:: ost.geom
-
The :class:`Vec2`, :class:`Vec3`, :class:`Vec4` classes implement vectors in 2,
3 and four dimensions. They support basic arithmetic via overloaded operators.
Essentially, the following basic operations are available:
diff --git a/modules/gfx/doc/scene.rst b/modules/gfx/doc/scene.rst
index 27bf9b86b1a8aad58248cd98f642e319e02a4343..a31836aba84e028a379f012bb267d6398766c8b8 100644
--- a/modules/gfx/doc/scene.rst
+++ b/modules/gfx/doc/scene.rst
@@ -193,6 +193,7 @@ It is interesting to note that the offset from center (`trans`) is given in rota
.. method:: GetFOV()
Get the field of view angle in the y direction (in degrees).
+
:rtype: float
.. method:: GetRTC()
@@ -201,7 +202,7 @@ It is interesting to note that the offset from center (`trans`) is given in rota
Looks stale. Remove it?
- :rtype: :class:`Mat4`
+ :rtype: :class:`~ost.geom.Mat4`
.. method:: GetTransform()
@@ -310,7 +311,7 @@ It is interesting to note that the offset from center (`trans`) is given in rota
.. method:: SetRTC(arg2)
:param arg2:
- :type arg2: :class:`Mat4`
+ :type arg2: :class:`~ost.geom.Mat4`
.. method:: SetShadow(arg2)
diff --git a/modules/img/base/doc/img.rst b/modules/img/base/doc/img.rst
index efadb1a305323dd301e090d5b4347ddffaa0ad56..89670946546e1c6427206e0451abc0520933040e 100644
--- a/modules/img/base/doc/img.rst
+++ b/modules/img/base/doc/img.rst
@@ -1,6 +1,11 @@
:mod:`~ost.img` - Images and Density Maps
================================================================================
-
+
+.. toctree::
+ :hidden:
+
+ point-size-extent
+
.. module:: ost.img
:synopsis: Images and density maps
@@ -32,17 +37,17 @@ Creating and visualizing ImageHandles
As a first step, enter the following lines in the OpenStructure python console:
- .. code-block:: python
+.. code-block:: python
- im=img.CreateImage(img.Size(200,200))
+ im=img.CreateImage(img.Size(200,200))
This will create an empty, 2D image, with a height and width of 200 pixels,
whose origin (ie the pixel with the coordinates <0,0>) is in the top-left
corner.
- .. code-block:: python
+.. code-block:: python
- v=gui.CreateDataViewer(im)
+ v=gui.CreateDataViewer(im)
A viewer window will pop up (see below), showing a white frame on a black
background. The inner area of the white frame is the image, which is empty.
@@ -53,21 +58,21 @@ Reading and writing into an image
Data can be read and written from and into an image using the following
commands:
- .. code-block:: python
-
- # writes the real value 23.4 into pixel 10,10
- im.SetReal(img.Point(10,10),23.4)
- # reads the value in pixel 10,10
- val=im.GetReal(img.Point(10,10))
+.. code-block:: python
+
+ # writes the real value 23.4 into pixel 10,10
+ im.SetReal(img.Point(10,10),23.4)
+ # reads the value in pixel 10,10
+ val=im.GetReal(img.Point(10,10))
The complex equivalents are also available
- .. code-block:: python
-
- # writes the complex value value 2+3j into pixel 10,10
- im.SetComplex(img.Point(10,10),2+3j)
- # reads the value in pixel 10,10
- val=im.GetComplex(img.Point(10,10))
+.. code-block:: python
+
+ # writes the complex value value 2+3j into pixel 10,10
+ im.SetComplex(img.Point(10,10),2+3j)
+ # reads the value in pixel 10,10
+ val=im.GetComplex(img.Point(10,10))
The image knows in which domain it is, and will adjust the type of data being
written accordingly. For example, if one writes a complex value in a
@@ -79,180 +84,114 @@ converted to complex by setting the imaginary part to 0.
Image properties
-----------------
-Every 2D or 3D image in OpenStructure has some basic properties, which are discussed in detail in the next paragraphs.
-
-Point
-^^^^^^^^
-
-.. class:: Point(x=0, y=0, z=0)
-
- This class represents an image pixel. It is defined using three integer
- numbers, corresponding to the pixel’s indexes along the weight and depth
- dimensions respectively.
-
-
-Size
-^^^^^^^^
-
-.. class:: Size(width, height, depth)
- Size(width, height)
-
- This property describes the size of an image. It is defined using three
- integer numbers: When depth is not specified, the size is assumed to refer to
- a 2D image two-dimensional (depth=1).
-
- The :class:`Size` class can be passed to the :func:`CreateImage` function to
- define the size of the image being created.
-
- .. code-block:: python
-
- # uses the size class to create an image
- s=img.Size(40,20,30)
- i=img.CreateImage(s)
- # uses a temporary instance of the Size class
- i=img.CreateImage(img.Size(40,20,30))
-
-Extent
-^^^^^^^^
-
-.. class:: Extent(first_point, last_point)
- Extent(first_point, size)
- Extent(size, center_point)
-
- This property describes the extent of an image in pixels. The image extent is
- a rectangle in 2d and a cuboid in 3d, and can be defined in a number of ways:
- giving the first and the last point of the extent, specifying the first point
- and the size of the extent, or listing the size of the extent and its central
- point.
-
-
- Some examples:
+.. _data-domain:
- .. code-block:: python
+The data domain
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- # defines a rectangular extent that goes from pixel (2,4) to pixel (5,10)
- s=img.Extent(img.Point(2,4),img.Point(5,10))
- # defines the same extent using its first point and its size
- s=img.Extent(img.Point(2,4),img.Size(4,7))
- # again the same extent using its size and central pixel
- s=img.Extent(img.Size(4,7),img.Point(3,7))
+The data domain of an image specifies wether the image contains data in the
+spatial or frequency domain. A :obj:`HALF_FREQUENCY` domain also exists,
+representing centrosymmetric frequency data (such as the data coming from the
+Fourier transform of an image from the real spatial domain)
- The :class:`Extent` class can be passed to the :func:`CreateImage` function to
- create an image with a specific extent.
+.. data:: SPATIAL
- .. code-block:: python
+ Real-valued spatial images
- # uses the Extent class to create an image
- e=img.Extent(img.Point(2,4),img.Size(4,7))
- i=img.CreateImage(e)
- # uses a temporary instance of the Extent class
- i=img.CreateImage(img.Extent(img.Point(2,4),img.Size(4,7)))
+.. data:: COMPLEX_SPATIAL
- Given an :class:`Extent`, is it possible to recover its full size, and also
- the length of each of its dimensions separately.
+ Complex-valued spatial images, i.e. resulting from a Fourier transform of
+ the :obj:`FREQUENCY` domain.
+
+.. data:: FREQUENCY
+
+ Complex frequeny domain.
+
+.. data:: HALF_FREQUENCY
- Examples:
+ Centrosymmetric frequency images
+
- .. code-block:: python
- # gets the size of an extent (e is a 3D extent)
- s=e.GetSize()
- # gets the three dimensions separately
- w=e.GetWidth()
- h=e.GetHeight()
- d=e.GetDepth()
+.. _spatial-origin:
- When one needs to visit all the image pixels belonging to an :class:`Extent`
- in sequence, one can use an :class:`ExtentIterator`:
+The spatial origin
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
- .. code-block:: python
+The spatial origin of an image is the first pixel of its extent. Specifically,
+this is the top left pixel for 2D images and the top-front-left corner for 3D
+images.
- # defines an iterator over an extent e
- ei=ExtentIterator(e)
- # visits all the pixels in the extent and
- # prints out their values
- for pixel in ei:
- print i.GetReal(pixel)
+.. _absolute-origin:
-.. _data-type:
+The absolute origin
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-DataType
-^^^^^^^^
+The absolute origin of an image describes the coordinates, in the absolute
+reference system used by OpenStructure, of the pixel in with all indexes equal
+to 0. Please note that the pixel does not necessarily need to belong to the
+extent of the image.
- The DataType of an image represents the nature of the data it contains. An image can contain 'REAL' or :obj:`COMPLEX` values.
+.. _pixel-sampling:
-.. _data-domain:
+Pixel sampling
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-DataDomain
-^^^^^^^^^^
- The data domain of an image specifies wether the image contains data in the
- spatial or frequency domain. A :obj:`HALF_FREQUENCY` domain also exists,
- representing centrosymmetric frequency data (such as the data coming from the
- Fourier transform of an image from the real spatial domain)
+The pixel sampling property of an image describes the size of its pixels. For
+the same image, the size of pixels in the :obj:`SPATIAL` and in the
+:obj:`FREQUENCY` :ref:`data-domain` are obviously interdependent.
+OpenStructure takes care of the transformation and allows access to both pixel
+sampling irrespective of the current image domain.
- .. data:: SPATIAL
+The ImageHandle class
+--------------------------------------------------------------------------------
- Real-valued spatial images
+The public interface of the ImageHandle class provides many ways to manipulate
+image properties. What follows is a brief description of the most important
+methods and attributes of the ImageHandle class.
- .. data:: COMPLEX_SPATIAL
+.. class:: ImageHandle
- Complex-valued spatial images, i.e. resulting from a Fourier transform of
- the :obj:`FREQUENCY` domain.
+ .. attribute:: size
+
+ The size of the image. Read-only.
- .. data:: FREQUENCY
+ :type: :class:`Size`
- Complex frequeny domain.
+ .. attribute:: extent
+
+ The extent of the image. Read-only.
- .. data:: HALF_FREQUENCY
+ :type: :class:`Extent`
- Centrosymmetric frequency images
+ .. attribute:: type
+
+ The DataType of an image represents the nature of the data it contains. An
+ image can contain :obj`REAL` or :obj:`COMPLEX` values.
+
+ .. attribute:: absolute_origin
+
+ The absolute origin of an image describes the coordinates, in the absolute
+ reference system used by OpenStructure, of the pixel in with all indexes
+ equal to 0. Please note that the pixel does not necessarily need to belong
+ to the extent of the image. Read-write.
+
+ :type: :class:`~ost.geom.Vec3`
+ .. attribute:: spatial_origin
+
+ The spatial origin of an image is the first pixel of its extent.
+ Specifically, this is the top left pixel for 2D images and the
+ top-front-left corner for 3Dimages.
+
+ :type: :class:`Point`
-.. _spatial-origin:
-
-SpatialOrigin
-^^^^^^^^^^^^^^
-
-Type: :class:`Point`
-
- The spatial origin of an image is the first pixel of its extent. Specifically,
- this is the top left pixel for 2D images and the top-front-left corner for 3D
- images.
-
-.. _absolute-origin:
-
-AbsoluteOrigin
-^^^^^^^^^^^^^^^^
-
-Type: :class:`~ost.geom.Vec3`
-
- The absolute origin of an image describes the coordinates, in the absolute
- reference system used by OpenStructure, of the pixel in with all indexes equal
- to 0. Please note that the pixel does not necessarily need to belong to the
- extent of the image.
-
-.. _pixel-sampling:
-
-PixelSampling
-^^^^^^^^^^^^^^^^^
-
-Type: :class:`~ost.geom.Vec3`
-
- The pixel sampling property of an image describes the size of its pixels. For
- the same image, the size of pixels in the :obj:`SPATIAL` and in the
- :obj:`FREQUENCY` :ref:`data-domain` are obviously interdependent.
- OpenStructure takes care of the transformation and allows access to both pixel
- sampling irrespective of the current image domain.
-
-ImageHandle
------------
-
-The public interface of the ImageHandle class provides many ways to manipulate image properties. What follows is a brief description of the most important methods of the
-ImageHandle class.
-
-.. class:: ImageHandle
+ .. attribute:: domain
+
+ The current domain of the image. See :ref:`data-domain`. Read-only.
+
.. method:: Apply(algorithm)
@@ -300,10 +239,10 @@ ImageHandle class.
Creates and returns a new image that contains a copy of a portion of the
original image. The extracted image keeps the same :ref:`data-type` of the
original image, but extractions from images in the 'FREQEUNCY' or
- 'HALF FREQUENCY' domains result in :obj:`COMPLEX ` :obj:`SPATIAL` images. This
- transformation is necessary, since the there is no guarantee that the
- extracted :obj:`FREQUENCY` sub-image is centered around the origin and hence
- back-transformable to :obj:`SPATIAL`.
+ 'HALF FREQUENCY' domains result in :obj:`COMPLEX ` :obj:`SPATIAL` images.
+ This transformation is necessary, since the there is no guarantee that the
+ extracted :obj:`FREQUENCY` sub-image is centered around the origin and
+ hence back-transformable to :obj:`SPATIAL`.
:param extent: Portion of the image to extract
:type extent: :class:`Extent`
@@ -326,8 +265,9 @@ ImageHandle class.
.. method:: GetComplex(pixel)
- Returns the complex value of the specified image pixel. If the image holds data of the 'REAL' :ref:`data-type`, the method return s complex value with the pixel content
- as real part and a null imaginary part.
+ Returns the complex value of the specified image pixel. If the image holds
+ data of the 'REAL' :ref:`data-type`, the method return s complex value with
+ the pixel content as real part and a null imaginary part.
:param pixel: Image pixel
:type pixel: :class:`Point`
@@ -335,16 +275,12 @@ ImageHandle class.
.. method:: GetDomain()
- Returns the :ref:`data-domain` of an image (:obj:`SPATIAL`,
- :obj:`FREQUENCY`or :obj:`HALF_FREQUENCY`)
-
- :rtype: DataDomain ???????????
+ See :attr:`domain`
.. method:: GetExtent()
- Returns the :class:`Extent` of an image.
+ See :attr:`extent`
- :rtype: :class:`Extent`
.. method:: GetFrequencySampling()
@@ -372,9 +308,9 @@ ImageHandle class.
Returns the interpolated value of the virtual pixel corresponding to the
specified fractional indexes. This is computed by using bilinear
interpolation (trilinear for 3D images). If the image holds data of the
- :obj:`COMPLEX ` :ref:`data-type`, the method computes the interpolated value as a
- weighted vector sum of the values of the surrounding pixels, then returns
- the amplitude of the interpolated value.
+ :obj:`COMPLEX ` :ref:`data-type`, the method computes the interpolated
+ value as a weighted vector sum of the values of the surrounding pixels,
+ then returns the amplitude of the interpolated value.
:param frac_pixel: Fractional pixel indexes
:type frac_pixel: :class:`~ost.geom.Vec3`
@@ -390,8 +326,8 @@ ImageHandle class.
.. method:: GetReal(pixel)
Returns the value of the specified image pixel. If the image holds data of
- the :obj:`COMPLEX ` :ref:`data-type`, the method return the amplitude of the
- pixel content.
+ the :obj:`COMPLEX ` :ref:`data-type`, the method return the amplitude of
+ the pixel content.
:param pixel: Image pixel
:type pixel: :class:`Point`
diff --git a/modules/img/base/doc/point-size-extent.rst b/modules/img/base/doc/point-size-extent.rst
new file mode 100644
index 0000000000000000000000000000000000000000..af2731adb21d7ffae75bb859d78f16835b392965
--- /dev/null
+++ b/modules/img/base/doc/point-size-extent.rst
@@ -0,0 +1,143 @@
+Point, Size, Extent
+================================================================================
+
+.. currentmodule:: ost.img
+
+
+This document describes some of the classes used in the :mod`~ost.img` module to describe image properties such as size, pixel coordinates and extents.
+
+
+Point
+--------------------------------------------------------------------------------
+
+.. class:: Point(x=0, y=0, z=0)
+ Point(vec)
+ Point(size)
+ Point(point)
+
+ :param x: integral x coordinate
+ :type x: int
+ :param y: integral y coordinate
+ :type y: int
+ :param z: integral z coordinate
+ :type z: int
+ :param vec: The vectors coordinates will be rounded to the next
+ integral value. In case of a :class:`~ost.geom.Vec4`, the coordinates will
+ be divided by the homogenous coordinate.
+ :type vec: :class:`~ost.geom.Vec3`, :class:`~ost.geom.Vec4`
+ :param point:
+ :type point: Initialize from point
+
+ This class represents an image pixel. It is defined using three integer
+ numbers, corresponding to the pixel’s indexes along the width, height and
+ depth dimensions respectively.
+
+ .. method:: __getitem__(index)
+
+ Read-write access to the coordinates.
+
+ ..code-block:: python
+
+ p=img.Point(1,2,3)
+ print p
+ p[1]=5
+
+ .. method:: ToVec3()
+
+ Converts the point to a :class:`~ost.geom.Vec3`
+
+ .. method:: ToVec2()
+
+ Converts the point to a :class:`~ost.geom.Vec2`. The z coordinate of the
+ point is ommitted.
+
+ .. method:: ToVec4()
+
+ Converts the point to a :class:`~ost.geom.Vec4`, with the homogenous
+ coordinate set to 1.
+
+
+
+
+Size
+--------------------------------------------------------------------------------
+
+.. class:: Size(width, height, depth)
+ Size(width, height)
+
+ This property describes the size of an image. It is defined using three
+ integer numbers: When depth is not specified, the size is assumed to refer to
+ a 2D image two-dimensional (depth=1).
+
+ The :class:`Size` class can be passed to the :func:`CreateImage` function to
+ define the size of the image being created.
+
+ .. code-block:: python
+
+ # uses the size class to create an image
+ s=img.Size(40,20,30)
+ i=img.CreateImage(s)
+ # uses a temporary instance of the Size class
+ i=img.CreateImage(img.Size(40,20,30))
+
+Extent
+--------------------------------------------------------------------------------
+
+.. class:: Extent(first_point, last_point)
+ Extent(first_point, size)
+ Extent(size, center_point)
+
+ This class describes the extent of an image in pixels. The image extent is
+ a rectangle in 2d and a cuboid in 3d, and can be defined in a number of ways:
+ giving the first and the last point of the extent, specifying the first point
+ and the size of the extent, or listing the size of the extent and its central
+ point.
+
+
+ **Some examples:**
+
+ .. code-block:: python
+
+ # defines a rectangular extent that goes from pixel (2,4) to pixel (5,10)
+ s=img.Extent(img.Point(2,4),img.Point(5,10))
+ # defines the same extent using its first point and its size
+ s=img.Extent(img.Point(2,4),img.Size(4,7))
+ # again the same extent using its size and central pixel
+ s=img.Extent(img.Size(4,7),img.Point(3,7))
+
+ The :class:`Extent` class can be passed to the :func:`CreateImage` function to
+ create an image with a specific extent.
+
+ .. code-block:: python
+
+ # uses the Extent class to create an image
+ e=img.Extent(img.Point(2,4),img.Size(4,7))
+ i=img.CreateImage(e)
+ # uses a temporary instance of the Extent class
+ i=img.CreateImage(img.Extent(img.Point(2,4),img.Size(4,7)))
+
+ Given an :class:`Extent`, is it possible to recover its full size, and also
+ the length of each of its dimensions separately.
+
+ **Examples:**
+
+ .. code-block:: python
+
+ # gets the size of an extent (e is a 3D extent)
+ s=e.GetSize()
+ # gets the three dimensions separately
+ w=e.GetWidth()
+ h=e.GetHeight()
+ d=e.GetDepth()
+
+ When one needs to visit all the image pixels belonging to an :class:`Extent`
+ in sequence, one can use an :class:`ExtentIterator`:
+
+ .. code-block:: python
+
+ # defines an iterator over an extent e
+ ei=ExtentIterator(e)
+ # visits all the pixels in the extent and
+ # prints out their values
+ for pixel in ei:
+ print i.GetReal(pixel)
\ No newline at end of file
diff --git a/modules/img/base/pymod/export_data.cc b/modules/img/base/pymod/export_data.cc
index 390be6ffce6ccd6d0f56528b9477c266b54a6e46..b9f2cf3c18946b88461fff4d939452db33dad876 100644
--- a/modules/img/base/pymod/export_data.cc
+++ b/modules/img/base/pymod/export_data.cc
@@ -61,6 +61,7 @@ void export_Data()
class_<ConstData, boost::noncopyable>("ConstData", no_init )
.def("GetType",&ConstData::GetType)
+ .add_property("type", &ConstData::GetType)
.def("GetDomain",&ConstData::GetDomain)
.def("GetExtent",&ConstData::GetExtent)
.def("GetReal",&ConstData::GetReal)
diff --git a/modules/index.rst b/modules/index.rst
index a9d779a20a79ba0afc6e6e26b6d9293426a68258..5a2146becb744215ea2f48e77050414577107dce 100644
--- a/modules/index.rst
+++ b/modules/index.rst
@@ -2,47 +2,92 @@ OpenStructure documentation
================================================================================
.. toctree::
+ :hidden:
:maxdepth: 1
-Introduction
---------------------------------------------------------------------------------
-
-.. toctree::
- :maxdepth: 2
-
install
intro
-
-
-Modules
---------------------------------------------------------------------------------
-
-.. toctree::
- :maxdepth: 1
-
base/generic
base/base
geom/geom
-
mol/base/mol
conop/conop
-
img/base/img
img/alg/alg
-
seq/base/seq
-
io/io
-
gfx/gfx
gui/gui
+ newmodule
+ external
+
+For Starters
+--------------------------------------------------------------------------------
+
+**Installation**: :doc:`install`
+
+**Tutorial Style**: :doc:`introduction <intro>` | :doc:`molecules intro <intro-01>` | :doc:`images intro <intro-02>` | :doc:`graphics intro <intro-03>`
+
+
+
+
+Molecules
+--------------------------------------------------------------------------------
+
+**Overview**: :doc:`molecules intro <intro-01>` | :doc:`mol overview <mol/base/mol>` | :doc:`graphical entity<gfx/entity>` | :doc:`entity <mol/base/entity>`
+
+**Input/Output**: :ref:`loading and saving molecules <mol-io>`
+
+**Connectivity**: :doc:`the conop module <conop/conop>`
+
+
+
+
+Images
+--------------------------------------------------------------------------------
+
+**Overview**: :doc:`images intro <intro-02>` | :doc:`img module <img/base/img>` | :doc:`img.alg module <img/alg/alg>`
+
+
+
+
+Sequences and Alignments
+--------------------------------------------------------------------------------
+
+**Overview**: :doc:`sequence module <seq/base/seq>`
+
+**Input/Output**: :ref:`loading and saving sequences <seq-io>`
+
+
+
+
+Graphics
+--------------------------------------------------------------------------------
+
+**Overview** :doc:`graphics intro <intro-03>`
+
+**Main Classes**: :doc:`the scene <gfx/scene>` | :doc:`graphical entity <gfx/entity>`
+
+
+
+
+Graphical User Interface
+--------------------------------------------------------------------------------
+
+**Overview**: :doc:`module overview <gui/gui>` | :doc:`organization <gui/layout>` :doc:`tools <gui/tools>`
+
+**Widgets**: :doc:`python shell <gui/python_shell>` | :doc:`sequence viewer <gui/sequence_viewer>`
+
+
+
Extending OpenStructure
--------------------------------------------------------------------------------
-.. toctree::
- :maxdepth: 1
-
- newmodule
- external
+**Howto:** :doc:`write new modules <newmodule>` | :doc:`integrate third-party tools <external>`
+
+
+
+
+
\ No newline at end of file
diff --git a/modules/io/doc/io.rst b/modules/io/doc/io.rst
index e9bf3a29cdeaaf701e011a92b96afc2a789c245f..b2037b3addfce4c660774d6177e33c261db729a6 100644
--- a/modules/io/doc/io.rst
+++ b/modules/io/doc/io.rst
@@ -1,6 +1,11 @@
:mod:`~ost.io` - Input and Output of Sequences, Structures and Maps
================================================================================
+.. toctree::
+ :hidden:
+
+ formats
+
.. module:: ost.io
:synopsis: Input and output of sequences, alignments, structures, images and density maps.
@@ -12,6 +17,8 @@ such as PDB, SDF and CHARMM trajectory files are available. Sequence and
alignment file formats such as FASTA and CLUSTALW are supported as well as
various image data (e.g. png, dm3) and density map files (e.g. CCP4, MRC).
+.. _mol-io:
+
Molecular Structures
--------------------------------------------------------------------------------
@@ -103,12 +110,16 @@ file:
.. autofunction:: ost.io.SavePDB
-
+
+
+.. _seq-io:
+
Sequences and Alignments
--------------------------------------------------------------------------------
Loading sequence or alignment files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
.. function:: LoadSequence(filename, format='auto')
Load sequence data from disk. If format is set to 'auto', the function guesses