deploy: 2405a11

.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: fee80ef0a1013f90939ae1a89d779839
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/clusttraj.rst.txt

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+clusttraj package
+=================
+
+Submodules
+----------
+
+clusttraj.classify module
+-------------------------
+
+.. automodule:: clusttraj.classify
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+clusttraj.distmat module
+------------------------
+
+.. automodule:: clusttraj.distmat
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+clusttraj.io module
+-------------------
+
+.. automodule:: clusttraj.io
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+clusttraj.main module
+---------------------
+
+.. automodule:: clusttraj.main
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+clusttraj.plot module
+---------------------
+
+.. automodule:: clusttraj.plot
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+clusttraj.utils module
+----------------------
+
+.. automodule:: clusttraj.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: clusttraj
+   :members:
+   :undoc-members:
+   :show-inheritance:

_sources/index.rst.txt

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+.. ClustTraj documentation master file, created by
+   sphinx-quickstart on Sat Sep 16 18:21:59 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to ClustTraj's documentation!
+=====================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   intro
+   install
+   clusttraj
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`

_sources/install.rst.txt

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+Installing ClustTraj
+====================
+
+Installing ``clusttraj`` is simple and can be achieved using ``pip``:
+
+.. code-block:: console
+
+    pip install clusttraj
+
+This will automatically install the package and its dependencies.
+
+We recommend performing the installation in an empty virtual environment.
+
+Dependencies
+************
+
+``clustttraj`` dependencies should be installed automatically by ``pip``.
+
+Currently, the following dependencies are installed:
+
+* `NumPy <http://www.numpy.org/>`_
+* `OpenBabel <http://openbabel.org/>`_
+* `RMSD <https://github.com/charnley/rmsd>`_
+* `QML <https://github.com/qmlcode/qml>`_
+* `SciPy <https://www.scipy.org/>`_
+* `scikit-learn <http://scikit-learn.org/stable/index.html>`_
+* `matplotlib <https://matplotlib.org/>`_
+
+Since the ``qml`` project development has been slow, we provide a fork repository in which
+we updated the package to be installable in modern enviroments with newer versions of 
+Python and libraries.
+This modified version can be downloaded and installed from `this link <https://github.com/hmcezar/qml>`_.
+
+Installation Problems
+*********************
+
+If you have problems installing ``clusttraj`` because installing ``qml`` fails, try installing 
+``qml`` yourself first.
+For Python 3.11, you might have to either disable setuptools distutils setting the environment 
+variable ``SETUPTOOLS_USE_DISTUTILS=stdlib`` before installing, or downgrading ``setuptools``
+to a version prior than 60.0.
+For example, you could install ``qml`` with:
+
+.. code-block:: console
+    
+    pip install "setuptools<60"
+    pip install "qml @ git+https://github.com/hmcezar/qml@develop"

_sources/intro.rst.txt

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+Introduction
+============
+
+``clusttraj`` is a Python package which aims to cluster similar configurations of molecular dynamics or Monte Carlo simulation trajectories.
+
+The optimal alignment between each snapshot is sought using reordering algorithms and optimal rotations.
+
+Any format supported by `openbabel <https://github.com/openbabel/openbabel>`_ is accepted as input or output, including the popular .xyz, .pdb and .xtc.
+
+Motivation
+**********
+
+The idea of ``clusttraj`` is to be an easy to use, and easy to extend platform for clustering trajectories.
+
+We also focus in providing options for the analysis of solute-solvent systems.
+
+Limitations
+***********
+
+``clusttraj`` is limited by the agglomerative clustering algorithms provided by `SciPy <https://www.scipy.org/>`_.
+
+However, there are many algorithms implemented for one to choose, as can be seen `here <https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html>`_.

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