OpenStructure documentation
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.. toctree::
  :hidden:
  :maxdepth: 1
  
  install
  intro
  users
  base/generic
  base/base
  geom/geom
  mol/base/mol
  mol/alg/molalg
  mol/mm/molmm
  conop/conop
  img/base/img
  img/alg/alg
  seq/base/seq
  seq/alg/seqalg
  db/db

  bindings/bindings

  io/io
  gfx/gfx
  gui/gui
  newmodule
  external
  contributing
  table
  mol/alg/lddt
  mol/alg/molck
  actions

For Starters
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**Installation**: :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
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**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
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**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
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**Overview**: :doc:`sequence module <seq/base/seq>` | :doc:`sequence algorithms <seq/alg/seqalg>`

**Input/Output**: :ref:`loading and saving sequences <seq-io>`




Graphics
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**Overview**: :doc:`graphics intro <intro-03>`

**Main Classes**: :doc:`the scene <gfx/scene>` | :doc:`graphical entity <gfx/entity>`




Graphical User Interface
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**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
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**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>`

**Database**: :doc:`Efficiently store structural data<db/db>`

Extending OpenStructure
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**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>`
