more work on documentation

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2359 5a81b35b-ba03-0410-adc8-b2c5c5119f08

doc/conf/conf.py

@@ -88,7 +88,7 @@ exclude_trees = []
 pygments_style = 'sphinx'
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+modindex_common_prefix = ['ost.']
 
 
 # -- Options for HTML output ---------------------------------------------------

modules/base/doc/generic.rst

@@ -82,12 +82,12 @@ to access a property of a different data type, e.g.:
 Use of Generic Properties in Queries
 --------------------------------------------------------------------------------
 
-The :doc:`query` can also be used for numeric generic properties (i.e. bool, 
+The :doc:`../mol/base/query` can also be used for numeric generic properties (i.e. bool, 
 int, float), but the syntax is slightly different. To access any generic 
 properties, it needs to be specified that they are generic and at which level 
 they are defined. Therefore, all generic properties start with a 'g', followed 
 by an 'a', 'r' or 'c' for atom, residue or chain level respectively. For more 
-details see :doc:`query`. 
+details see :doc:`../mol/base/query`. 
 
 
 API documentation

modules/conop/doc/conop.rst

-:mod:`conop` -- Connectivity and Topology of Molecules
+:mod:`~ost.conop` -- Connectivity and Topology of Molecules
 ================================================================================
 
-.. module:: conop
+.. module:: ost.conop
    :synopsis: The conop modules implement different strategies to derive
                connectivity information of molecules.
 

modules/doc/newmodule.rst

@@ -114,7 +114,7 @@ the module shared library, a `CMakeLists.txt` file needs to be written for the
   
 
 The line containing the `DEPENDS_ON` directive lists all the modules on which
-the new module depends (in this case :mod:`mol` and :mod:`mol.alg`).  The 
+the new module depends (in this case :mod:`mol` and :mod:`ost.mol.alg`).  The 
 `module` macro will take care of staging the headers, in this case into 
 `ost/mod` and compiling, linking and staging of a library with the  name 
 `libost_mod.so` (`libost_gmod.dylib` on MacOS X).
@@ -243,7 +243,7 @@ Here is finally the build script skeleton that needs to be put into
   
 In the last line the call to the 'target\_link\_libraries' function contains the 
 names of the modules on which the 'mod' unit test code depends (in this case, 
-the :mod:`mol` and :mod:`mol.alg` modules), in addition to the `mod` module 
+the :mod:`mol` and :mod:`ost.mol.alg` modules), in addition to the `mod` module 
 itself.
 
 The Python Wrapper

modules/geom/doc/geom.rst

-:mod:`ost.geom` -- vectors, matrices and geometrical objects
+:mod:`~ost.geom` -- vectors, matrices and geometrical objects
 ================================================================================
 
 .. module:: ost.geom

modules/img/alg/doc/alg.rst

-:mod:`img.alg` - Image Processing Algorithms
+:mod:`~ost.img.alg` - Image Processing Algorithms
 ================================================================================
 
-
+.. module:: ost.img.alg
+  :synopsis: Image processing algorithms
+  
 Usage of Image Algorithms
 --------------------------------------------------------------------------------
 
 Image algorithms are objects. To execute them, the algorithms are applied to an 
-image by passing it to the :meth:`img.ImageHandle.Apply` or 
-:meth:`img.ImageHandle.ApplyIP` method:
+image by passing it to the :meth:`ost.img.ImageHandle.Apply` or 
+:meth:`ost.img.ImageHandle.ApplyIP` method:
 
 .. code-block:: python
   

modules/img/base/doc/img.rst

-:mod:`img` Images and Density Maps
+:mod:`~ost.img` Images and Density Maps
 ================================================================================
   
-.. module:: mol
-   :synopsis: Images and Density Maps
+.. module:: ost.img
+   :synopsis: Images and density maps
               
 Introduction : The ImageHandle
 --------------------------------------------------------------------------------

modules/index.rst

@@ -11,7 +11,7 @@ Introduction
   :maxdepth: 2
 
   intro
-  install.rst
+  install
   
 Modules
 --------------------------------------------------------------------------------
@@ -27,6 +27,7 @@ Modules
   mol/base/mol
   seq/base/seq
   base/base
+  io/io
 
 Extending OpenStructure
 --------------------------------------------------------------------------------

modules/io/doc/io.rst

+:mod:`~ost.io` - Input and Output of Sequences, Structures and Maps
+================================================================================
+
+.. module:: ost.io
+  :synopsis: Input and output of sequences, structures and density maps
+
+The io module deals with input and output of :class:`entities 
+<ost.mol.EntityHandle>`, :class:`alignments <ost.seq.AlignmentHandle>`, and
+:class:`images <ost.img.ImageHandle>`. Importers for common file formats such 
+as PDB, SDF, FASTA, CLUSTAL W, DX and CHARMM trajectory files are available. 
+
+Molecular Structures
+--------------------------------------------------------------------------------
+
+Loading Molecular Structures
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The :mod:`~ost.io` modules offers several ways to load molecular structures 
+depending on your requirements. The most general way is offered by 
+:func:`~ost.io.LoadEntity`, which will automatically detect the file format based 
+on the file extension.
+
+.. function:: LoadEntity(filename, format='auto')
+
+  Load entity from disk. If format is set to 'auto', the function guesses the 
+  filetype based on the extension of the file. Files ending in '.pdb', '.ent', 
+  '.ent.gz', '.pdb.gz' will automatically be loaded as PDB files, for example. 
+  For files without or exotic extensions, the format can be set explicitly as 
+  the second parameter. 
+  
+  .. code-block:: python
+
+    # recognizes SDF file by file extension
+    ent=io.LoadEntity('file.sdf')
+
+    # In this case, there is no file extensions, so you have to say it's a 
+    # SDF file explicitly
+    ent=io.LoadEntity('file', 'sdf')
+
+  For a list of file formats supported by :func:`LoadEntity`, see :doc:`formats`.
+  
+  :raises: :exc:`~ost.io.IOUnknownFormatException` if the format string supplied 
+      is not recognized or the file format can not be detected based on the 
+      file extension
+      
+      :exc:`~ost.io.IOException` if the import fails due to an erroneous or 
+      inexistent file
+
+Some of the formats have a dedicated function that allows you to tweak many 
+parameters that affect the import. PDB files can be loaded with 
+:func:`~ost.io.LoadPDB`. It offers a tighter control over the exact loading 
+behaviour.
+
+.. autofunction:: ost.io.LoadPDB
+
+
+Saving Molecular Structures
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Saving a complete entity or a view is a matter of calling 
+:func:`~ost.io.SaveEntity`.
+
+.. code-block:: python
+  
+  ent=io.LoadEntity('protein.pdb')
+  # save full entity
+  io.SaveEntity(ent, 'full.pdb')
+  # only save C-alpha atoms
+  io.SaveEntity(ent.Select('aname=CA and peptide=true'), 'calpha.pdb')
+  
+:func:`~ost.io.SavePDB` provides a simple way to save several entities into one 
+file:
+
+
+.. code-block:: python
+  
+  ent=io.LoadEntity('protein.pdb')
+  # Save complete entity
+  io.SavePDB(ent, 'full.pdb')
+  # Save chain A and chain B separately
+  io.SavePDB([ent.Select('cname=A'), ent.Select('cname=B')], 'split.pdb')
+
+
+.. function:: SaveEntity(ent, filename, format='auto')
+  
+  Save entity to disk. If format is set to 'auto', the function guesses the 
+  filetype based on the file extension, otherwise the supplied format is checked 
+  against the available export plugins.
+  
+  :param ent: The entity to be saved
+  :type  ent: :class:`~ost.mol.EntityHandle` or :class:`~ost.mol.EntityView`
+  :param filename: The filename
+  :type  filename: string
+  :param format: Name of the format
+  :type  format: string
+  
+  :raises: :exc:`~ost.io.IOUnknownFormatException` if the format string supplied 
+      is not recognized or the file format can not be detected based on the 
+      file extension
+      
+.. autofunction:: ost.io.SavePDB
+
+  
\ No newline at end of file

modules/io/pymod/__init__.py

@@ -17,29 +17,35 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #------------------------------------------------------------------------------
 from _io import *
-from ost import mol,conop
+from ost import mol, conop
 
 def LoadPDB(filename, restrict_chains="", no_hetatms=False,
             fault_tolerant=False, load_multi=False,
             join_spread_atom_records=False, calpha_only=False):
   """
-  Load PDB file from disk.
+  Load PDB file from disk and returns one or more entities. Several options 
+  allow to customize the exact behaviour of the PDB import.
 
-  If restrict_chains is not an empty string, only chains listed in the
-  string will be imported.
+  :param restrict_chains: If not an empty string, only chains listed in the
+     string will be imported.
 
-  If fault_tolerant is set to true, the import will succeed, even if the
-  PDB contains faulty records. The faulty records will be ignored in that
-  case.
+  :param fault_tolerant: If True, the import will succeed, even if the
+     PDB contains faulty records. The faulty records will be ignored and import 
+     continues as if the records haven't been present.
 
-  If not_hetatms is set to True, HETATM records will be ignored
+  :param no_hetatms: If set to True, HETATM records will be ignored
 
-  If load_multi is set to true, a list of entities will be returned instead
-  of only the first.
+  :param load_multi: If set to True, a list of entities will be returned instead
+     of only the first. This is useful when dealing with multi-PDB files.
 
-  If join_spread_atom_records is set to true, atom records belonging to the
-  same residue are joined, even if they do not appear sequentially in the PDB
-  file.
+  :param join_spread_atom_records: If set to true, atom records belonging to the
+     same residue are joined, even if they do not appear sequentially in the PDB
+     file.
+  :rtype: :class:`~ost.mol.EntityHandle` or a list thereof if `load_multi` is 
+      True.
+      
+  :raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous or 
+      inexistent file
   """
   conop_inst=conop.Conopology.Instance()
   builder=conop_inst.GetBuilder("DEFAULT")
@@ -78,7 +84,13 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=False,
 
 def SavePDB(models, filename):
   """
-  Save entity or list of entities to disk
+  Save entity or list of entities to disk. If a list of entities is supplied the 
+  PDB file will be saved as a multi PDB file. Each of the entities is wrapped 
+  into a MODEL/ENDMDL pair.
+  
+  :param models: The entity or list of entities (handles or views) to be saved
+  :param filename: The filename
+  :type  filename: string
   """
   if not getattr(models, '__len__', None):
     models=[models]

modules/mol/base/doc/editors.rst

 Editors
 ================================================================================
 
-.. currentmodule:: mol
+.. currentmodule:: ost.mol
 
 The structure, topology and connectivity of entities is edited via editors. This 
 includes operations such as changing atom positions, connecting atoms with bonds 
@@ -118,7 +118,7 @@ euclidian space.
      transform.
      
      :param atom: must be a valid atom handle
-     :type  atom: :class:`mol.AtomHandle`
+     :type  atom: :class:`ost.mol.AtomHandle`
      :param pos: The new position
      :type  pos: :class:`geom.Vec3`
      
@@ -129,7 +129,7 @@ euclidian space.
      the original pos.
      
      :param atom: must be a valid atom handle
-     :type  atom: :class:`mol.AtomHandle`
+     :type  atom: :class:`ost.mol.AtomHandle`
      :param pos: The new untransformed position
      :type  pos: :class:`geom.Vec3`
   

modules/mol/base/doc/entity.rst

 The Molecular Entity
 ================================================================================
 
-.. currentmodule:: mol
+.. currentmodule:: ost.mol
 
 This document describes the :class:`EntityHandle` and related classes.
 
@@ -10,7 +10,7 @@ This document describes the :class:`EntityHandle` and related classes.
 
    Creates a new entity. The created entity is empty, that is, it does not
    contain any atoms, residues, chains, bonds or torsions. To populate the
-   entity, use an :ref:`editor`.
+   entity, use an :doc:`editors`.
    
    :returns: The newly created :class:`EntityHandle`
    

modules/mol/base/doc/mol.rst

-:mod:`mol` -- Molecular structures and surfaces
+:mod:`~ost.mol` -- Molecular structures and surfaces
 ================================================================================
 
-.. module:: mol
+.. module:: ost.mol
    :synopsis: Contains classes and functions to deal with molecular structures
               and surfaces
 

modules/seq/base/doc/seq.rst

-:mod:`seq` -- Sequences and Alignments
+:mod:`~ost.seq` -- Sequences and Alignments
 ================================================================================
 
-.. module:: seq
+.. module:: ost.seq
    :synopsis: Contains classes and functions to deal with sequences and 
               alignments