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updated adk_transitions docs
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orbeckst committed Oct 5, 2018
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2 changes: 1 addition & 1 deletion MDAnalysisData/descr/adk_transitions_FRODA.rst
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Expand Up @@ -13,7 +13,7 @@ Framework Rigidity Optimized Dynamics Algorithm (FRODA)
[Farrell2010]_. Each ensemble of independently generated paths
contains 200 trajectories in the CHARMM DCD format.

This data set contains the *FRODA* ensemble.
This data set contains the **FRODA** ensemble.

FRODA AdK with geometric targeting on a rigid decomposition (FRODA
server); closed (1AKE) to open (4AKE). Topology file: 1ake.pdb
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11 changes: 11 additions & 0 deletions docs/adk_transitions.rst
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Expand Up @@ -13,13 +13,24 @@ trajectories during which the close-to-open transiton of the enzyme
adenylate kinase [Seyler2014]_ is sampled using different
computational methods [Seyler2015]_.


.. currentmodule:: MDAnalysisData.adk_transitions

.. autosummary::

fetch_adk_transitions_DIMS
fetch_adk_transitions_FRODA

.. SeeAlso:: This set of trajectories was used in the `SPIDAL
Tutorial: MDAnalysis with Midas/radical.pilot`_ where the ensemble
of 400 DIMS+FRODA trajectories is analyzed with the *Path
Similarity Analysis* method [Seyler2015]_. Computations on such a
large(ish) dataset are sped up by parallelization at the task level
with `RADICAL-Pilot`_.

.. _`SPIDAL Tutorial: MDAnalysis with Midas/radical.pilot`:
https://www.mdanalysis.org/SPIDAL-MDAnalysis-Midas-tutorial/
.. _`RADICAL-Pilot`: https://radical-cybertools.github.io/



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