From eba625d441a126b28eb62020e41be380a10a4496 Mon Sep 17 00:00:00 2001 From: "Jimmy C. Kromann" Date: Fri, 3 Jan 2025 17:16:01 +0100 Subject: [PATCH] Update README.rst --- README.rst | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/README.rst b/README.rst index f3129e9..152e4cc 100644 --- a/README.rst +++ b/README.rst @@ -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 @@ -156,7 +156,7 @@ Submit issues or pull requests on GitHub. 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, @@ -173,27 +173,26 @@ http://github.com/charnley/rmsd, * - **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