OpenStructure documentation

For Starters

Installation: install from binary | :doc:`install from source <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>` | :doc:`queries <mol/base/query>` | :doc:`algorithms <mol/alg/molalg>` | :doc:`mm <mol/mm/molmm>`

Trajectories: :doc:`basics <mol/base/traj>` | :ref:`analysis <traj-analysis>`

Input/Output: :ref:`loading and saving molecules <mol-io>`

Connectivity: :doc:`the conop module <conop/conop>` | :doc:`compound library <conop/compoundlib>`

Density Maps and Images

Overview: :doc:`images intro <intro-02>` | :doc:`img module <img/base/img>` | :doc:`img.alg module <img/alg/alg>`

Input/Output: :ref:`loading and saving density maps <img-io>`

Sequences and Alignments

Overview: :doc:`sequence module <seq/base/seq>` | :doc:`sequence algorithms <seq/alg/seqalg>`

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>`

Varia

Datasets: :doc:`tabular data <table>`

Supported File Formats: :doc:`structure formats<io/structure_formats>` | :doc:`sequence formats <io/sequence_formats>` | :doc:`sequence profile formats <io/sequence_profile_formats>` | :doc:`image formats <io/image_formats>`

Users: :doc:`Reporting a problem <users>`

lDDT: :doc:`lDDT command line executable and Python API<mol/alg/lddt>`

Molck: :doc:`Molecular Checker<mol/alg/molck>`

Actions: :doc:`OST Actions<actions>`

Extending OpenStructure

External Tools: :doc:`bindings <bindings/bindings>`

Howto: :doc:`write new modules <newmodule>` | :doc:`integrate third-party tools <external>` | :doc:`logging <base/logging>` | :doc:`instructions for developers <contributing>`