diff --git a/CMakeLists.txt b/CMakeLists.txt
index 48f8616d20d08033970629fd83dde0e9765443b3..cfbf4a364cc0b393ef7a416da19e12339d22a1a9 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -240,3 +240,10 @@ message(STATUS
" Optimize (-DOPTIMIZE) : ${_OPT}\n"
" Double Precision (-DUSE_DOUBLE_PRECISION) : ${_DOUBLE_PREC}\n"
" Compound Lib (-DCOMPOUND_LIB) : ${_COMP_LIB}")
+
+# doc target to create HTML documentation
+set(SPHINX sphinx-build)
+set(SPHINX_OPTIONS -c doc/conf -b html -d doc/html/doctrees)
+add_custom_target(doc COMMAND
+ ${SPHINX} ${SPHINX_OPTIONS} modules doc/html
+ VERBATIM)
\ No newline at end of file
diff --git a/doc/conf/conf.py b/doc/conf/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..d7a1455a17fa44609c07625ed99d33de930ce6f1
--- /dev/null
+++ b/doc/conf/conf.py
@@ -0,0 +1,196 @@
+# -*- coding: utf-8 -*-
+#
+# OpenStructure documentation build configuration file, created by
+# sphinx-quickstart on Sat Apr 3 13:01:52 2010.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.append(os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest',
+ 'sphinx.ext.coverage', 'sphinx.ext.pngmath',
+ 'sphinx.ext.ifconfig']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'OpenStructure'
+copyright = u'2010, OpenStructure authors'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '1.0'
+# The full version, including alpha/beta/rc tags.
+release = '1.0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of documents that shouldn't be included in the build.
+#unused_docs = []
+
+# List of directories, relative to source directory, that shouldn't be searched
+# for source files.
+exclude_trees = []
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. Major themes that come with
+# Sphinx are currently 'default' and 'sphinxdoc'.
+html_theme = 'sphinxdoc'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents. If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_use_modindex = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'openstructure-doc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+ ('index', 'OpenStructure.tex', u'OpenStructure Documentation',
+ u'OpenStructure authors', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_use_modindex = True
diff --git a/modules/conop/doc/conop.rst b/modules/conop/doc/conop.rst
new file mode 100644
index 0000000000000000000000000000000000000000..fb65ee1ad4e33a27ecf0ba0b9e50851531b8be72
--- /dev/null
+++ b/modules/conop/doc/conop.rst
@@ -0,0 +1,255 @@
+:mod:`conop` -- Connectivity and Topology of Molecules
+================================================================================
+
+.. module:: conop
+ :synopsis: The conop modules implement different strategies to derive
+ connectivity information of molecules.
+
+The main task of the conop module is to connect atoms with bonds. While the
+bond class is also part of the base module, the conop module deals with setting
+up the correct bonds between atoms.
+
+Motivation
+--------------------------------------------------------------------------------
+Traditionally the connectivity between atoms has not been reliably described in
+a PDB file. Different programs adopted various ways of finding out if two atoms
+are connected. One way chosen is to rely on proper naming of the atoms. For
+example, the backbone atoms of the standard amino acids are named as N, CA, C
+and O and if atoms with these name appear in the same residue they are shown
+connected. Another way is to apply additional heuristics to find out if a
+peptide bond between two consecutive residues is formed. Breaks in the backbone
+are indicated, e.g., by introducing a discontinuity in the numbering of the residue.
+
+Loader heuristics are great if you are the one that implemented them but are
+problematic if you are just the user of a software that has them. As time goes
+on, these heuristics become buried in thousands of lines of code and they are
+often hard yet impossible to trace back.
+
+Different clients of the framework have different requirements. A visualisation
+software wants to read in a PDB files as is without making any changes. A
+script in an automated pipeline, however, does want to either strictly reject
+files that are incomplete or fill-in missing structural features. All these
+aspects are implemented in the conop module, separated from the loading of the
+PDB file, giving clients a fine grained control over the loading process.
+
+The Builder interface
+--------------------------------------------------------------------------------
+
+The conop module defines a :class:`Builder` interface, to run connectivity
+algorithms, that is to connect the atoms with bonds and perform basic clean up
+of errorneous structures. The clients of the conop module can specify how the
+Builder should treat unknown amino acids, missing atoms and chemically
+infeasible bonds.
+
+The exact behaviour for a builder is implementation-specific. So far, two
+classes implement the Builder interface: A heuristic and a rule-based builder. The builders mainly differ in the source of their connectivity information. The
+HeuristicBuilder uses a hard-coded heuristic connectivity table for the 20
+standard amino acids as well as nucleotides.For other compounds such as ligands
+the HeuristicBuilder runs a distance-based connectivity algorithm that connects
+two atoms if they are closer than a certain threshold. The RuleBasedBuilder
+uses a connectivity library containing all molecular components present in the
+PDB files on PDB.org. The library can easily be extended with custom
+connectivity information, if required. By default the heuristic builder is used,
+however the builder may be switched by setting the !RuleBasedBuilder as the
+default. To do so, one has first to create a new instance of a RuleBasedBuilder
+and register it in the builder registry of the conop module. In Python, this can
+be achieved with
+
+.. code-block:: python
+
+ from ost import conop
+ compound_lib=conop.CompoundLib.Load('...')
+ rbb=conop.RuleBasedBuilder(compound_lib)
+ conop.Conopology.Instance().RegisterBuilder(rbb,'rbb')
+ conop.Conopology.Instance().SetDefaultBuilder('rbb')
+
+All subsequent calls to :func:`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.
+
+
+.. class:: Builder
+
+ .. method:: CompleteAtoms(residue)
+
+ add any missing atoms to the residue based on its key, with coordinates set
+ to zero.
+
+ :param residue: must be a valid residue
+ :type residue: mol.ResidueHandle
+
+ .. method:: CheckResidueCompleteness(residue)
+
+ verify that the given residue has all atoms it is supposed to have based on
+ its key.
+
+ :param residue: must be a valid residue
+ :type residue: mol.ResidueHandle
+
+ .. method:: IsResidueComplete(residue)
+
+ Check whether the residue has all atoms it is supposed to have. Hydrogen
+ atoms are not required for a residue to be complete.
+
+ :param residue: must be a valid residue
+ :type residue: mol.ResidueHandle
+
+ .. method:: IdentifyResidue(residue)
+
+ attempt to identify the residue based on its atoms, and return a suggestion
+ for the proper residue key.
+
+ :param residue: must be a valid residue
+ :type residue: mol.ResidueHandle
+
+ .. method:: ConnectAtomsOfResidue(residue)
+
+ Connects atoms of residue based on residue and atom name. This method does
+ not establish inter-residue bonds. To connect atoms that belong to
+ different residues, use :meth:`ConnectResidueToPrev`, or
+ :meth:`ConnectResidueToNext`.
+
+ :param residue: must be a valid residue
+ :type residue: mol.ResidueHandle
+
+ .. method:: ConnectResidueToPrev(residue, prev)
+
+ Connect atoms of residue to previous. The order of the parameters is
+ important. In case of a polypeptide chain, the residues are thought to be
+ ordered from N- to C- terminus.
+
+ :param residue: must be a valid residue
+ :type residue: mol.ResidueHandle
+ :param prev: valid or invalid residue
+ :type prev: mol.ResidueHandle
+
+
+ .. method:: DoesPeptideBondExist(n, c)
+
+ Check if peptide bond should be formed between the `n` and `c` atom. This
+ method is called by ConnectResidueWithNext() after making sure that
+ both residues participating in the peptide bond are peptide linking
+ components.
+
+ By default, :meth:`IsBondFeasible` is used to check whether the two atoms
+ form a peptide bond.
+
+ :param n: backbone nitrogen atom (IUPAC name `N`). Must be valid.
+ :type n: mol.AtomHandle
+ :param c: backbone C-atom (IUPAC name `C`). Must be valid.
+ :type c: mol.AtomHandle
+
+ .. method:: IsBondFeasible(atom_a, atom_b)
+
+ Overloadable hook to check if bond between to atoms is feasible. The
+ default implementation uses a distance-based check to check if the
+ two atoms should be connected. The atoms are connected if they are in
+ the range of 0.8 to 1.2 times their van-der-WAALS radius.
+
+ :param atom_a: a valid atom
+ :type atom_b: mol.AtomHandle
+ :param atom_a: a valid atom
+ :type atom_b: mol.AtomHandle
+
+ .. method:: GuessAtomElement(atom_name, hetatm)
+
+ guess element of atom based on name and hetatm flag
+
+ :param atom_name: IUPAC atom name, e.g. `CA`, `CB` or `N`.
+ :type atom_name: string
+ :param hetatm: Whether the atom is a hetatm or not
+ :type hetatm: bool
+
+ .. method:: AssignBackboneTorsionsToResidue(residue)
+
+ For :meth:`peptide-linking residues <mol.ResidueHandle.IsPeptideLinking>`,
+ residues, assigns phi, psi and omega torsions to amino acid.
+
+ :param residue: must be a valid residue
+ :type residue: mol.ResidueHandle
+
+
+.. class:: RuleBasedBuilder
+
+ The :class:`RuleBasedBuilder` implements the :class:`Builder` interface.
+ Refer to its documentation for a basic description of the methods.
+
+ .. method:: CheckResidueCompleteness(residue)
+
+ By using the description of the chemical compound, the completeness of
+ the residue is verified. The method distinguishes between required atoms
+ and atoms that are optional, like `OXT` that is only present, if not
+ peptide bond is formed. Whenever an unknown atom is encountered,
+ :meth:`OnUnknownAtom` is invoked. Subclasses of the
+ :class:`RuleBasedBuilder` may implement some additional logic to deal with
+ unknown atom. Likewise, whenever a required atom is missing,
+ :meth:`OnMissingAtom` is invoked. Hydrogen atoms are not considered as
+ required by default.
+
+ :param residue: must be a valid residue
+ :type residue: mol.ResidueHandle
+
+ .. method:: IdentifyResidue(residue)
+
+ Looks-up the residue in the database of chemical compounds and returns
+ the name of the residue or "UNK" if the residue has not been found in the
+ library.
+
+ :param residue: must be a valid residue
+ :type residue: mol.ResidueHandle
+
+
+ .. method:: OnUnknownAtom(atom)
+
+ Invoked whenever an unkknown atom has been encountered during a residue
+ completeness check.
+
+ The default implementation guesses the atom properties based on the name
+ and returns false, meaning that it should be treated as an unknown atom.
+
+ Custom implementations of this method may delete the atom, or modify it.
+
+ :param atom: the unknown atom
+ :type atom: mol.AtomHandle
+
+ .. method:: OnMissingAtom(atom)
+
+ Invoked whenever an atom is missing. It is up to the overloaded method
+ to deal with the missing atom, either by ignoring it or by inserting a
+ dummy atom.
+
+ :param atom: The missing atom's name
+ :type atom: string
+
+Connecting atoms
+--------------------------------------------------------------------------------
+
+The high level interface is exposed by the Conopoloy singleton instance:
+
+.. code-block:: python
+
+ import conop
+
+ cc=conop.Conopology.Instance()
+
+ ent=BuildRawModel(...)
+ cc.ConnectAll(cc.GetBuilder(), ent)
+
+For fine grained control, the builder interface may be used directly.
+
+
+.. _mmcif-convert:
+
+Convert MM CIF dictionary
+--------------------------------------------------------------------------------
+
+The CompoundLib may be created from a MM CIF dictionary. The latest dictionary
+can be found on the `wwPDB site <http://www.wwpdb.org/ccd.html>`_.
+
+After downloading the file in MM CIF use the :program:`chemdict_tool` to convert
+the MM CIF dictionary into our internal format.
+
+.. code-block:: bash
+
+ chemdict_tool create <components.cif> <compounds.chemlib>
diff --git a/modules/geom/doc/geom.rst b/modules/geom/doc/geom.rst
new file mode 100644
index 0000000000000000000000000000000000000000..27accb014bd6291c9c96b861ecc4e4fb232c48da
--- /dev/null
+++ b/modules/geom/doc/geom.rst
@@ -0,0 +1,15 @@
+:mod:`geom` -- vectors, matrices and geometrical objects
+================================================================================
+
+.. module:: geom
+ :synopsis: Functions and classes for vectors, matrices and geometrical
+ objects in 2, 3 and four dimensions
+
+The geom modules contains functions and classes for vectors, matrices and other geometrical objects in 2, 3 and four dimensions.
+
+
+.. toctree::
+
+ vec
+
+
\ No newline at end of file
diff --git a/modules/geom/doc/vec.rst b/modules/geom/doc/vec.rst
new file mode 100644
index 0000000000000000000000000000000000000000..b3da8088bc8748bdede06b340ecb3e0222db4555
--- /dev/null
+++ b/modules/geom/doc/vec.rst
@@ -0,0 +1,187 @@
+Vectors
+================================================================================
+.. currentmodule:: 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:
+
+ * adding and subtracting two vectors
+ * negation
+ * multiplying and dividing by scalar value
+
+This is shown in the following example:
+
+.. code-block:: python
+
+ vec_a=geom.Vec2(1, 0)
+ vec_b=geom.Vec2(0, 1)
+ print vec_a, vec_b
+ print vec_a+vec_b
+ print vec_a*3-vec_b
+
+The standard vector operations are implemented as :ref:`free standing functions <vector-functions>`:
+
+
+.. code-block:: python
+
+ vec_a=geom.Vec3(1, 0, 0)
+ vec_b=geom.Vec3(0, 1, 0)
+
+ print geom.Dot(vec_a, vec_b)
+ print geom.Cross(vec_a, vec_b)
+
+ print geom.Normalize(geom.Vec3(1, 1, 0))
+
+ print geom.Length(geom.Vec3(1, 1, 1))
+
+
+Vector Classes
+--------------------------------------------------------------------------------
+.. class:: Vec2([x=0.0, y=0.0, z=0.0])
+ Vec2(vec)
+
+ Real-valued vector in 2 dimensions.
+
+ :param x: x coordinate
+ :type x: float or int
+ :param y: y coordinate
+ :type y: float or int
+ :param vec: the coordinates are set to the coordinates of vec. If vec is a
+ :class:`Vec2`, the coordinates are copied directly, If vec is a
+ :class:`Vec3`, the x and y coordinates are set to the
+ coordinates of vec and z is silently swallowed. If vec is of
+ type :class:`Vec4`, x and y are divided by the homogenous
+ coordinate w, raising a DivideByZeroException when w is zero.
+ :type vec: Vec2, Vec3 or Vec4
+
+ .. attribute:: x
+
+ The x-coordinate of the vector.
+
+ :type: float
+
+ .. attribute:: y
+
+ The y-coordinate of the vector.
+.. class:: Vec3([x=0.0, y=0.0, z=0.0])
+ Vec3(vec)
+
+ Real-valued vector in 3 dimensions.
+
+ :param x: x coordinate
+ :param y: y coordinate
+ :param z: z coordinate
+ :param vec: the coordinates are set to the coordinates of vec. If vec is a
+ :class:`Vec3`, the coordinates are copied directly, If vec is a
+ :class:`Vec2`, the x and y coordinates are set to the
+ coordinates of vec and z is initialized to zero. If vec is of
+ type :class:`Vec4`, x, y and z are divided by homogenous
+ coordinate w, raising a DivideByZeroException when w is zero.
+ :type vec: Vec2, Vec3 or Vec4
+
+ .. attribute:: x
+
+ The x-coordinate of the vector.
+
+ :type: float or int
+
+ .. attribute:: y
+
+ The y-coordinate of the vector.
+
+ :type: float or int
+
+ .. attribute:: z
+
+ The z-coordinate of the vector.
+
+ :type: float or int
+
+.. class:: Vec4([x=0.0, y=0.0, z=0.0, w=1.0])
+ Vec4(vec)
+
+ Real-valued vector in 4 dimensions.
+
+ :param x: x coordinate
+ :type x: float or int
+ :param y: y coordinate
+ :type y: float or int
+ :param z: z coordinate
+ :type z: float or int
+ :param w: w (homogenous) coordinate
+ :type w: float or int
+ :param vec: the coordinates are set to the coordinates of vec. If vec is a
+ :class:`Vec4`, the coordinates are copied directly, If vec is a
+ :class:`Vec2`, the x and y coordinates are set to the
+ coordinates of vec and z and w are initialized to 0 and 1,
+ respectively. If vec is of type :class:`Vec4`, x, y and z are
+ divided by homogenous coordinate w, raising a
+ DivideByZeroException when w is zero.
+
+ .. attribute:: x
+
+ The x-coordinate of the vector.
+
+ :type: float or int
+
+ .. attribute:: y
+
+ The y-coordinate of the vector.
+
+ :type: float or int
+
+ .. attribute:: z
+
+ The z-coordinate of the vector.
+
+ :type: float or int
+
+ .. attribute:: w
+
+ The homogenous coordinate.
+
+ :type: float or int
+
+
+.. _vector-functions:
+
+Functions Operating on Vectors
+--------------------------------------------------------------------------------
+
+.. function:: Cross(vec_a, vec_b)
+
+ Cross product of `vec_a` and `vec_b`
+
+ :type vec_a: Vec3
+ :type vec_b: Vec3
+
+.. function:: Dot(vec_a, vec_b)
+
+ Dot (scalar) product of `vec_a` and `vec_b`
+
+ :param vec_a: first vector
+ :type vec_a: Vec3
+ :param vec_b: second vector
+ :type vec_b: Vec3
+
+.. function:: Length(vec)
+
+ Length of vector
+
+ :param vec:
+ :type vec: Vec2, Vec3 or Vec4
+
+.. function:: Length2(vec)
+
+ Returns the squared length of `vec`
+
+ :param vec:
+ :type vec: Vec2, Vec3 or Vec4
+
+.. function:: Normalize(vec)
+
+ Returns a normalized version of `vec`
+
+ :param vec: Vector to be normalized
+ :type vec: Vec2, Vec3 or Vec4
+
diff --git a/modules/index.rst b/modules/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..52dcde170b022e7824aa2cedd23d3a5c3c65332d
--- /dev/null
+++ b/modules/index.rst
@@ -0,0 +1,8 @@
+OpenStructure documentation
+================================================================================
+
+.. toctree::
+
+ geom/doc/geom
+ conop/doc/conop
+ mol/base/doc/mol
\ No newline at end of file
diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst
new file mode 100644
index 0000000000000000000000000000000000000000..aaed57b35ea03c395926d4cf745c2483c80cf6a7
--- /dev/null
+++ b/modules/mol/base/doc/editors.rst
@@ -0,0 +1,151 @@
+Editors
+================================================================================
+
+.. currentmodule:: mol
+
+The structure, topology and connectivity of entities is edited via editors. This
+includes operations such as changing atom positions, connecting atoms with bonds
+as well as adding and removing chains, residues and atoms.
+
+Edit Modes
+--------------------------------------------------------------------------------
+
+Editors support two modes: An unbuffered edit mode and a buffered edit mode. In
+the unbuffered edit mode, dependent information such as the spatial organizer
+and the internal coordinate system (in case of the XCSEditor) are updated after
+every change. In buffered edit mode, the updates are delayed until one of the
+following happens:
+
+ * The last editor goes out of scope.
+ * :meth:`XCSEditor.UpdateICS` or :meth:`ICSEditor.UpdateXCS` is called
+ explicitly.
+
+
+The editors follow the RIAA (resource allocation is initialisation) principle:
+Whenever an editor is requested an internal reference counter is incremented. In
+the destructor, this reference count is decremented. When the count drops to
+zero, the dependent infomation is updated.
+
+In Python, one can not rely on the destructors being called. It is adviced to
+always put a call to :meth:`XCSEditor.UpdateICS` or
+:meth:`ICSEditor.UpdateXCS` when the editing is finished. Alternatively, starting from Python version 2.6, one can use the
+`with <http://docs.python.org/reference/compound_stmts.html#with>`_ statement
+to make sure the destructor are called and the dependent information is updated.
+
+
+Basic Editing Operations
+--------------------------------------------------------------------------------
+
+The basic functionality of editors is implemented in the EditorBase class.
+
+.. class:: EditorBase
+
+ Inherited by :class:`XCSEditor`, :class:`ICSEditor`.
+
+ .. method:: InsertChain(chain_name)
+
+ Add new chain to the entity
+
+ :param chain_name: The chain's name. In the scope of an entity, chain names
+ are unique. If a chain of the same already exists an
+ IntegrityError is raised.
+ :type chain_name: string
+ :returns: :class:`ChainHandle`
+
+ .. method:: AppendResidue(chain, residue_name, [res_num])
+
+ Append residue to the end of the chain. If res_num is not given, the
+ residue number will be set to the residue number of the last added residue
+ plus one. The insertion code is the same.
+
+ :param chain: Must be a valid chain
+ :type chain: :class:`ChainHandle`
+ :param residue_name: 3-letter-code of the residue, e.g. ``GLY``.
+ :type residue_name: string
+ :returns: :class:`ResidueHandle`
+
+ .. method:: InsertAtom(residue, atom_name, pos, [prop=mol.AtomProp()])
+
+ Insert new atom and add it to residue. For atoms with alternative atom
+ locations use :meth:`InsertAltAtom`.
+
+ :param residue: is the parent residue and must be valid
+ :type residue: :class:`ResidueHandle`
+ :param atom_name: is the atom name. While free to choose a name, it is
+ adviced to properly name the atoms according to IUPAC
+ rules as several algorithms as well as most
+ :class:`builders <conop.Builder>` in the :mod:`conop`
+ module rely on proper naming.
+ :type atom_name: string
+ :param pos: is the position of the atom in global coordinates
+ :type pos: :class:`geom.Vec3`
+ :param prop: are the atom's properties such as element, van der Waals
+ radius charge and so on. The default set of atom
+ properties is rather meaningless.
+ :type prop: class:`AtomProp`
+ :returns: :class:`AtomHandle`
+
+Editor for the External Coordinate System
+--------------------------------------------------------------------------------
+
+The XCSEditor defines the interface for manipulating the external coordinate
+system. The external coordinate system directly operates on atom positions in
+euclidian space.
+
+.. class:: XCSEditor
+
+ Inherits :class:`EditorBase`
+
+ .. method:: ApplyTransform(transform)
+
+ Apply a transformation the entity transform. The entity transform is a
+ global transformation applied to all atoms.
+
+ :param transform: The transformation to be applied
+ :type transform: :class:`geom.Mat4`
+
+ .. method:: SetTransform(transform)
+
+ Set the entity transformation. See also :meth:`ApplyTransform`
+
+ :param transform: The transformation to be applied
+ :type transform: :class:`geom.Mat4`
+
+ .. method:: SetAtomPos(atom, pos)
+
+ Set the (transformed) position of atom. This method will also update the
+ original position of the atom by applying the inverse of the entity
+ transform.
+
+ :param atom: must be a valid atom handle
+ :type atom: :class:`mol.AtomHandle`
+ :param pos: The new position
+ :type pos: :class:`geom.Vec3`
+
+ .. method:: SetOriginalAtomPos(atom, pos)
+
+ Set the origininal (untransformed) position of the atom. This method will
+ also update the transformed position by applying the entity transform to
+ the original pos.
+
+ :param atom: must be a valid atom handle
+ :type atom: :class:`mol.AtomHandle`
+ :param pos: The new untransformed position
+ :type pos: :class:`geom.Vec3`
+
+Editor for the Internal Coordinate System
+--------------------------------------------------------------------------------
+The :class:`ICSEditor` is used to manipulate the internal coordinate system that
+is defined by bond lengths and angles. By default the internal coordinate system
+is not calculates. However, upon requesting an :class:`ICSEditor` for the first
+time, the internal coordinate system is initialized. This involves the build-up
+of a directed-graph for the bond network as well as calculating the internal
+coordinate matrices.
+
+The use :class:`XCSEditor` and :class:`ICSEditor` are mutually exclusive. This
+means that whenever a :class:`XCSEditor` has pending changes, the results of
+using an :class:`ICSEditor` is undefined and vice versa.
+
+.. class:: ICSEditor
+
+ Inherits :class:`EditorBase`
diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
new file mode 100644
index 0000000000000000000000000000000000000000..75e5c6fdea49ec877259a013762b3126c82c6e92
--- /dev/null
+++ b/modules/mol/base/doc/entity.rst
@@ -0,0 +1,332 @@
+The Molecular Entity
+================================================================================
+
+.. currentmodule:: mol
+
+This document describes the :class:`EntityHandle` and related classes.
+
+
+.. function:: CreateEntity()
+
+ 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, create a new editor.
+
+ :returns: The newly created :class:`EntityHandle`
+
+.. class:: EntityHandle
+
+ The entity class represents a molecular structure. Such a structure is in
+ general made up of one or more linear chains of residues, which in turn are
+ formed by one or more atoms.
+
+ The interface of entities is tailored to biological macromolecules, but this
+ does not prevent it to be used for molecules in general: An entity also
+ represent a ligand or a collection of water molecules - hence the rather
+ generic name.
+
+ .. method:: FindChain(chain_name)
+
+ Get chain by name. See also :meth:`GetChainList`
+
+ :param chain_name: Chain identifier, e.g. "A"
+ :type chain_name: string
+ :returns: A valid :class:`ChainHandle`, if the entity contains a
+ chain with the given name, an invalid
+ :class:`ChainHandle` otherwise.
+
+ .. method:: GetChainList()
+
+ Get list of all chains of this entity. To access a single chain, use
+ :meth:`FindChain`.
+
+ :returns: A list of :class:`ChainHandles<ChainHandle>`
+
+ .. method:: FindResidue(chain_name, res_num)
+
+ Get residue by chain name and residue number. See also
+ :meth:`GetResidueList`
+
+ :param chain_name: Chain identifier, e.g. "A"
+ :type chain_name: string
+ :param res_num: residue number
+ :type res_num: mol.ResNum
+
+ :returns: A valid :class:`ResidueHandle` if the chain exists and
+ the chain contains a residue of the given residue
+ number, an invalid :class:`ResidueHandle` otherwise.
+
+ .. method:: GetResidueList()
+
+ Get list of all residues of this entity. To access a single residue, use
+ :meth:`FindResidue`.
+
+ :returns: A list of :class:`ResidueHandles<ResidueHandle>`
+
+ .. method:: FindAtom(chain_name, res_num, atom_name)
+
+ Get atom by chain name, residue number and atom name. See also
+ :meth:`GetAtomList`
+
+ :param chain_name: Chain identifier, e.g. "A"
+ :type chain_name: string
+ :param res_num: residue number
+ :type res_num: mol.ResNum
+ :param atom_name: atom name, e.g. CA
+ :type atom_name: string
+
+ :returns: A valid :class:`AtomHandle` if an atom matching the
+ parameters could be found, an invalid
+ :class:`AtomHandle` otherwise
+
+ .. method:: GetAtomList()
+
+ Get list of all atoms of this entity. To access a single atom, use
+ :meth:`FindAtom`
+
+ :returns: A list of :class:`AtomHandles<AtomHandle>`
+
+ .. method:: RequestXCSEditor([edit_mode=mol.EditMode.BUFFERED_EDIT])
+
+ Request :class:`XCSEditor` for editing the external coordinate system. This
+ call will fail when there are pending changes of the internal coordinate
+ system.
+
+ :param edit_mode: Must be EditMode.BUFFERED_EDIT or
+ EditMode.UNBUFFERED_EDIT. For more details, see the
+ editor documentation.
+ :type edit_mode: mol.EditMode
+
+ :returns: :class:`XCSEditor`
+ .. method:: RequestICSEditor([edit_mode=mol.EditMode.BUFFERED_EDIT])
+
+ Request :class:`ICSEditor` for editing the internal coordinate system, such
+ as torsions, bond lengths and angle between two bonds. This call will fail
+ when there are pending changes of the external coordinate system.
+
+ :param edit_mode: Must be EditMode.BUFFERED_EDIT or
+ EditMode.UNBUFFERED_EDIT. For more details, see the
+ editor documentation.
+ :type edit_mode: mol.EditMode
+
+ :returns: :class:`ICSEditor`
+
+ .. method:: Select(query, flags)
+
+ Perform a selection on the entity. The result of the selection is an
+ :class:`EntityView` which contains usually only a subset of chains,
+ residues, atoms and bonds of the original entity.
+
+ :param query: The query to be executed. See :class:`Query` for details.
+ :type query: string or :class:`Query`
+ :param flags: An ORed combination of :class:`QueryFlags`.
+ :type flags: int
+ :returns: An :class:`entity view <EntityView>`.
+ :raises: :class:`QueryError` when the query could not be executed due
+ to syntactic errors.
+
+ .. method:: CreateFullView()
+
+ Creates an entity view containing all chains, residues, atoms and bonds of
+ this entity.
+
+ .. code-block:: python
+
+ # these two lines are identical
+ full=ent.Select('')
+ full=ent.CreateFullView()
+
+ :returns: :class:`EntityView`
+
+ .. method:: CreateEmptyView()
+
+ Creates an entity view pointing to this entity, but otherwise empty. This
+ method is usually the starting point for manual entity view creation, e.g.
+
+ .. code-block:: python
+
+ view=ent.CreateEmtpyView()
+ for atom in ent.atoms:
+ if ComplicatedPredicate(atom):
+ view.AddAtom(atom)
+
+ :returns: :class:`EntityView`
+
+ .. method:: Copy()
+
+ Creates a deep copy of the entity.
+
+ :returns: A new :class:`EntityHandle` that is an exact copy of this entity.
+
+ .. note::
+
+ alternative atom positions are not handled yet.
+
+ .. method:: GetCenterOfAtoms()
+
+ Get center of atoms, that is the average atom position of the entity. Use
+ :meth:`GetCenterOfMass` to calculate the mass-weighted center of the entity.
+
+ :returns: :class:`geom.Vec3`
+
+ .. method:: GetCenterOfMass()
+
+ Calculates the center of mass of the entity. Use :meth:`GetCenterOfAtoms`
+ to calculate the non-mass-weighted center of the entity.
+
+ :returns: :class:`geom.Vec3`
+
+ .. method:: GetGeometricCenter()
+
+ Calculates the mid-point of the axis aligned bounding box of the entity.
+
+ :returns: :class:`geom.Vec3`
+
+ .. method:: GetMass()
+
+ Calculates the total mass of the entity by summing up the masses of all
+ atoms.
+
+ :returns: The mass in Dalton
+
+ .. method:: Apply(visitor)
+
+ Apply EntityVisitor to the entity. In Python, you shouldn't bother using
+ this function. EntityVisitory are mainly used in C++ to implement
+ algorithms that operate are able to operate on EntityViews or
+ EntityHandles.
+
+ .. method:: FindWithin(pos, radius)
+
+ Find all atoms in sphere of given radius centered at *pos*. To turn the
+ returned list of atoms into an :class:`EntityView`, use
+ :func:`CreateViewFromAtomList`.
+
+ :param pos: Center of sphere
+ :type pos: :class:`geom.Vec3`
+ :param radius: The radius of the sphere
+ :type radius: float
+
+ :returns: A list of :class:`AtomHandles<AtomHandle>`
+
+.. class:: ChainHandle
+
+ .. method:: FindResidue(res_num)
+
+ Get residue by residue number. See also :meth:`GetResidueList`
+
+ :param res_num: residue number
+ :type res_num: mol.ResNum
+
+ :returns: A valid :class:`ResidueHandle` if the chain contains
+ a residue with matching residue number, an invalid
+ :class:`ResidueHandle` otherwise.
+
+ .. method:: GetResidueList()
+
+ Get list of all residues of this chain. For peptide chains, the residues
+ are usually ordered from N- to C-terminus.To access a single residue, use
+ :meth:`FindResidue`.
+
+ :returns: A list of :class:`ResidueHandles<ResidueHandle>`
+
+ .. method:: FindAtom(res_num, atom_name)
+
+ Get atom by residue number and atom name. See also :meth:`GetAtomList`
+
+ :param res_num: residue number
+ :type res_num: mol.ResNum
+ :param atom_name: atom name, e.g. CA
+ :type atom_name: string
+
+ :returns: A valid :class:`AtomHandle` if an atom matching the
+ parameters could be found, an invalid
+ :class:`AtomHandle` otherwise
+
+ .. method:: GetAtomList()
+
+ Get list of all atoms of this chain. To access a single atom, use
+ :meth:`FindAtom`
+
+ :returns: A list of :class:`AtomHandles<AtomHandle>`
+
+.. class:: ResidueHandle
+
+ .. method:: FindAtom(atom_name)
+
+ Get atom by atom name. See also :meth:`GetAtomList`
+
+ :param atom_name: atom name, e.g. CA
+ :type atom_name: string
+
+ :returns: A valid :class:`AtomHandle` if an atom with the given
+ name could be found, an invalid :class:`AtomHandle`
+ otherwise
+
+ .. method:: GetAtomList()
+
+ Get list of all atoms of this residue. To access a single atom, use
+ :meth:`FindAtom`.
+
+.. class:: AtomHandle
+
+.. class:: EntityView
+
+ Represents a subpart of an :class:`EntityHandle`.
+
+Functions
+--------------------------------------------------------------------------------
+
+
+Boolean Operators
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. function:: Intersection(view_a, view_b)
+
+ Calculates and returns the intersection of `view_a` and `view_b`. `view_a`
+ and `view_b` must be views of the same entity.
+
+ :param view_a: first view
+ :type view_a: EntityView
+ :param view_b: second view
+ :type view_b: EntityView
+
+.. function:: Difference(view_a, view_b)
+
+ Calculates and returns the difference between `view_a` and `view_b`. `view_a`
+ and `view_b` must be views of the same entity.The returned view will
+ contain atoms, residues, chains and bonds that are in `view_a` and not in
+ `view_b`.
+
+ :param view_a: first view
+ :type view_a: EntityView
+ :param view_b: second view
+ :type view_b: EntityView
+
+.. function:: Union(view_a, view_b)
+
+ Calculates and returns the union of `view_a` and `view_b`. `view_a`
+ and `view_b` must be views of the same entity.The returned view will contain
+ all atoms, residues, chains and bonds that are either in `view_a`, `view_b`
+ or part of both views.
+
+ :param view_a: first view
+ :type view_a: EntityView
+ :param view_b: second view
+ :type view_b: EntityView
+
+
+Other Entity-Related Functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. function:: CreateViewFromAtomList(atom_list)
+
+ Returns a view made up of the atoms in *atom_list*. All atoms are required to
+ be atoms of the same entity. Duplicate atoms are only added to the view once.
+
+ :param atom_list: the atoms
+ :type atom_list: :class:`AtomHandleList` or :class:`AtomViewList`
+ :raises: :class:`IntegrityError` if atoms of different entities are
+ encountered
+
+ :returns: :class:`EntityView`
\ No newline at end of file
diff --git a/modules/mol/base/doc/query.rst b/modules/mol/base/doc/query.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8b5d26c3257e6f4a40d9b52c6fda73711c477733
--- /dev/null
+++ b/modules/mol/base/doc/query.rst
@@ -0,0 +1,124 @@
+Queries
+================================================================================
+
+.. class:: Query
+
+ Blabla
+
+It is often convenient to highlight or focus certain parts of the structure.
+OpenStructure includes a powerful query system that allows you to perform custom
+selections in a convenient way.
+
+Please refer to the tutorial on the query language for an introduction.
+
+The query language reference
+--------------------------------------------------------------------------------
+
+The query consists of one or more predicates combined with boolean
+operators. A predicate takes the form *prop op value*. Operators are
+one of `` =, !=, >, >=, <=`` and ``<``. A predicate has the following form:
+*PROPERTY - OPERATOR - ARGUMENT*.
+
+The following properties may be used in predicates. The supported type of the
+value is given for each property.
+
+ * ``rname`` residue name. type: string
+ * ``rnum`` residue number. currently only numeric part is honored.
+ type: int
+ * ``rtype`` residue type as given by the DSSP code, i.e. H for helix, E
+ for extended. type: string
+ * ``aname`` atom name. type: string
+ * ``ele`` element of atom. type: string
+ * ``cname`` chain name. type: string
+ * ``occ`` occupancy, between 0 and 1. type: float
+ * ``abfac`` B (temperature) factor of atom. type: float
+ * ``rbfac`` average B (temperature) factor of residue. type: float.
+ Note that this does not work for views as expected. When running a
+ second selection statement on a view, all atoms of the residue handle
+ and not the view are considered in the calculation
+ * ``ishetatm`` whether the atom is a hetorogenous atom. type: bool or int
+ (0 for false, 1 for true)
+ * ``peptide`` whether the residue is peptide linking. type: bool or int
+ (0 for false, 1 for true)
+ * ``x`` X coordinate of atom. type: float
+ * ``y`` Y coordinate of atom. type: float
+ * ``z`` Z coordinate of atom. type: float
+ * ``rindex`` index of residue in chain. This index is the same for views
+ and handles
+ * For :ref:`generic properties in queries <genprop-in-queries>` see below.
+
+Distance-based selections within a given atom position are supported by
+the within statement. To select atoms within 5 Angstrom of the point
+``{1, 2, 3}``, one would write:
+
+``5 <> {1,2,3}``
+
+Negation of this expression is possible with the not operator, i.e.
+
+``not 5 <> {1,2,3}``
+will select atoms that are further than five Angstrom apart from ``{1, 2 , 3}``
+
+Abbreviations
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Two abbreviations exist for convenience:
+
+Instead of writing
+
+``aname=CA or aname=C or aname=O or aname=N``,
+
+one can write
+
+``aname=CA,N,C,O``.
+
+For integral value ranges, one can use the colon syntax: instead of
+
+``rnum>=10 and rnum<=20``
+
+one can write
+
+``rnum=10:20``
+
+.. _genprop-in-queries:
+
+Generic Properties in Queries
+--------------------------------------------------------------------------------
+
+The query language can also be used for numeric generic properties (i.e.
+float and int), 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.
+
+.. code-block:: python
+
+ # set generic properties for atom, residue, chain
+ atom_handle.SetGenericFloatProperty("testpropatom", 5.2)
+ resid_handle.SetGenericFloatProperty("testpropres", 1.1)
+ chain_handle.SetGenericIntProperty("testpropchain", 10)
+
+ # query statements
+ sel_a=e.Select("gatestpropatom<=10.0")
+ sel_r=e.Select("grtestpropres=1.0")
+ sel_c=e.Select("gctestpropchain>5")
+
+Since generic properties do not need to be defined for all parts of an entity
+(e.g. it could be specified for one single :class:`AtomHandle`), the query
+statement will throw an error unless you specify a default value in the query
+statement which can be done using a ':' character:
+
+.. code-block:: python
+
+ # if one or more atoms have no generic properties
+
+ sel=e.Select("gatestprop=5")
+ # this will throw an error
+
+ # you can specify a default value:
+ sel=e.Select("gatestprop:1.0=5")
+ # this will run through smoothly and use 1.0 as
+ # the default value for all atoms that do not
+ # have the generic property 'testprop'
+
+Using this method, you will be warned if a generic property is not set for all
+atoms, residues or chains unless you specify a default value. So, be careful
+when you do.