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charnley authored Jan 3, 2025
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Expand Up @@ -103,7 +103,7 @@ Usage examples

Use ``calculate_rmsd --help`` to see all the features. Usage is pretty straight
forward, call ``calculate_rmsd`` with two structures in either ``.xyz`` or
``.pdb``. In this example Ethane has the exact same structure, but is
``.pdb``. In this example, Ethane has the same structure but is
translated in space, so the RMSD should be zero.

.. code-block:: bash
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Citation
========

Please cite this project when using it for scientific publications. And cite the relevant methods implemnted.
Please cite this project when using it for scientific publications. And cite the relevant methods implemented.

**Implementation**:
Calculate Root-mean-square deviation (RMSD) of Two Molecules Using Rotation, GitHub,
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* - **Kabsch**
- ``--rotation-method kabsch`` (Default)
- Wolfgang Kabsch (1976),
A solution for the best rotation to relate two sets of vectors,
Acta Crystallographica, A32:922-923

http://dx.doi.org/10.1107/S0567739476001873

* - **Quaternion**
- ``--rotation-method quaternion``
- Michael W. Walker and Lejun Shao and Richard A. Volz (1991),
Estimating 3-D location parameters using dual number quaternions, CVGIP: Image Understanding, 54:358-367,
- Walker, Shao & Volz (1991),
CVGIP: Image Understanding, 54:358-367,

http://dx.doi.org/10.1016/1049-9660(91)90036-o

* - **Distance Hungarian Assignment**
- ``--reorder-method inertia-hungarian`` (Default)
- David F. Crouse (2016). On implementing 2D rectangular assignment algorithms. (Vol. 52, Issue 4, pp. 1679–1696). Institute of Electrical and Electronics Engineers (IEEE).
- Crouse (2016). Vol. 52, Issue 4, pp. 1679–1696, IEEE.

http://dx.doi.org/10.1109/TAES.2016.140952

* - **FCHL19**
- ``--reorder-method qml``
- Christensen et al, FCHL revisited: Faster and more accurate quantum machine learning, J. Chem. Phys. 152, 044107 (2020)
- Christensen et al (2020), J. Chem. Phys. 152, 044107

https://doi.org/10.1063/1.5126701

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