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mhmohona committed Oct 13, 2024
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#. **Diffusion maps** are a non-linear dimensionality reduction technique that embeds the coordinates of each frame onto a lower-dimensional space, such that the distance between each frame in the lower-dimensional space represents their "diffusion distance", or similarity. It integrates local information about the similarity of each point to its neighours, into a global geometry of the intrinsic manifold. This means that this technique is not suitable for trajectories where the transitions between conformational states is not well-sampled (e.g. replica exchange simulations), as the regions may become disconnected and a meaningful global geometry cannot be approximated. Unlike PCA, there is no explicit mapping between the components of the lower-dimensional space and the original atomic coordinates; no physical interpretation of the eigenvectors is immediately available.

For computing similarity, see the tutorials in :ref:`trajectory-similarity-analysis`.
For computing similarity, see the tutorials in :ref:`_trajectory-similarity-overview`.

.. toctree::
:maxdepth: 1
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.. -*- coding: utf-8 -*-
.. _trajectory-similarity-analysis:
.. _trajectory-similarity-overview:

======================
Trajectory similarity
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