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Update README.rst
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charnley authored Jan 2, 2025
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Expand Up @@ -19,17 +19,19 @@ I want to know the minimal RMSD between two molecules

You have two molecules, A and B, and want to calculate the structural difference between them. If you just calculate the RMSD straight-forward, you might get too big a value, as seen below. You need to recenter and rotate the two molecules to get the true minimal RMSD. This is what this code does.

========== =========== ==========
No Changes Re-centered Rotated
---------- ----------- ----------
|begin| |translate| |rotate|
========== =========== ==========
RMSD 2.50 RMSD 1.07 RMSD 0.25
========== =========== ==========

.. |begin| image:: https://raw.githubusercontent.com/charnley/rmsd/master/img/plot_beginning.png
.. |translate| image:: https://raw.githubusercontent.com/charnley/rmsd/master/img/plot_translated.png
.. |rotate| image:: https://raw.githubusercontent.com/charnley/rmsd/master/img/plot_rotated.png

========== =========== ===========
No change Recentered Rotated
---------- ----------- -----------
RMSD = 2.2 RMSD = 0.8 RMSD = 0.2
========== =========== ===========
|fig1.1| |fig1.2| |fig1.3|
========== =========== ===========


.. |fig1.1| image:: https://raw.githubusercontent.com/charnley/rmsd/refs/heads/charnley/doc/notebooks/fig_rmsd_nothing.png
.. |fig1.2| image:: https://raw.githubusercontent.com/charnley/rmsd/refs/heads/charnley/doc/notebooks/fig_rmsd_recentered.png
.. |fig1.3| image:: https://raw.githubusercontent.com/charnley/rmsd/refs/heads/charnley/doc/notebooks/fig_rmsd_rotated.png


I do not know the order of the atoms
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