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‎doc/source/api/diffpy.structure.example_package.rst‎

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.. _example_package documentation:
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|title|
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=======
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.. |title| replace:: diffpy.structure.example_package package
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.. automodule:: diffpy.structure.example_package
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:members:
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:undoc-members:
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:show-inheritance:
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|foo|
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-----
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.. |foo| replace:: diffpy.structure.example_package.foo module
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.. automodule:: diffpy.structure.example_package.foo
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:members:
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:undoc-members:
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:show-inheritance:
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|bar|
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-----
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.. |bar| replace:: diffpy.structure.example_package.bar module
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.. automodule:: diffpy.structure.example_package.foo
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:members:
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:undoc-members:
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:show-inheritance:

‎doc/source/api/diffpy.structure.rst‎

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:tocdepth: -1
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diffpy.structure package
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========================
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|title|
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=======
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.. |title| replace:: diffpy.structure package
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.. automodule:: diffpy.structure
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:members:
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-----------
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.. toctree::
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:titlesonly:
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diffpy.structure.parsers
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diffpy.structure.expansion
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diffpy.structure.apps
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diffpy.structure.example_package
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Submodules
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----------
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diffpy.structure.spacegroups module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.structure.spacegroups
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.structure._legacy_importer module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.structure._legacy_importer
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.structure.structureerrors module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.structure.structureerrors
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.structure.spacegroupmod module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.structure.spacegroupmod
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.structure.utils module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.structure.utils
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.structure.lattice module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.structure.lattice
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.structure.structure module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.structure.structure
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.structure.mmlibspacegroups module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.structure.mmlibspacegroups
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:members:
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:undoc-members:
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:show-inheritance:
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diffpy.structure.symmetryutilities module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.structure.symmetryutilities
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:members:
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:undoc-members:
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diffpy.structure.atom module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.structure.atom
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diffpy.structure.pdffitstructure module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. automodule:: diffpy.structure.pdffitstructure
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:members:
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:undoc-members:
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:show-inheritance:
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|module|
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--------
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diffpy.structure.sgtbxspacegroups module
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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.. |module| replace:: diffpy.structure.example_submodule module
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.. automodule:: diffpy.structure.sgtbxspacegroups
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.. automodule:: diffpy.structure.example_submodule
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:undoc-members:
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:show-inheritance:

‎doc/source/conf.py‎

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from importlib.metadata import version
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from pathlib import Path
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autodoc_mock_imports = ["importlib.metadata"]
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use Path().resolve() to make it absolute, like shown here.
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"m2r",
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]
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autodoc_member_order = "groupwise"
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ["_templates"]
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# Display all warnings for missing links.
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nitpicky = True
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nitpick_ignore = [
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("py:class", "array_like"),
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("py:class", "Parser"),
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("py:class", "CifFile"),
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]
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# -- Options for HTML output ----------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# Example configuration for intersphinx: refer to the Python standard library.
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# intersphinx_mapping = {'http://docs.python.org/': None}
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intersphinx_mapping = {
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"python": ("https://docs.python.org/3", None),
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"numpy": ("https://numpy.org/doc/stable/", None),
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}

‎doc/source/index.rst‎

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.. |title| replace:: diffpy.structure documentation
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diffpy.structure - Crystal structure container and parsers for structure formats.
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diffpy.structure - Crystal structure container and parsers for structure formats..
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| Software version |release|.
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| Last updated |today|.
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The diffpy.structure package provides objects for storing atomic
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coordinates, displacement parameters and other crystal structure data.
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diffpy.structure supports import and export of structure data in several
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structure formats such as CIF, PDB, xyz. It provides conversion
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between fractional and absolute Cartesian coordinates, functions for
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symmetry expansion from asymmetric unit and generation of symmetry
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constraints for atom positions and displacement parameters. diffpy.structure
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includes definitions of all space groups in over 500 symmetry settings.
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=======
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Authors
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=======
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diffpy.structure is developed by members of the Billinge Group at
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Columbia University and at Brookhaven National Laboratory including
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Pavol Juhás, Christopher L. Farrow, Xiaohao Yang, Simon J.L. Billinge.
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diffpy.structure is developed by Billinge Group
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and its community contributors.
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For a detailed list of contributors see
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https://github.com/diffpy/diffpy.structure/graphs/contributors.
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Acknowledgments
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===============
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Space group codes in *spacegroupmod.py* and *mmlibspacegroups.py*
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originate from the pymmlib project, http://pymmlib.sourceforge.net.
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Less common settings of space groups were generating using the
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Computational Crystallography Toolbox,
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http://cctbx.sourceforge.net.
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.. index:: citation, reference
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Reference
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=========
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If you use this program for a scientific research that leads
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to publication, we ask that you acknowledge use of the program
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by citing the following paper in your publication:
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P. Juhás, C. L. Farrow, X. Yang, K. R. Knox and S. J. L. Billinge,
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`Complex modeling: a strategy and software program for combining
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multiple information sources to solve ill posed structure and
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nanostructure inverse problems
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<http://dx.doi.org/10.1107/S2053273315014473>`__,
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*Acta Crystallogr. A* **71**, 562-568 (2015).
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============
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Installation
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============
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=================
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Table of contents
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=================
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.. toctree::
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:titlesonly:
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