From a1a739a12d5dd12883b6180e0778baadff6cc535 Mon Sep 17 00:00:00 2001 From: "Jimmy C. Kromann" Date: Sun, 5 Jan 2025 12:08:05 +0100 Subject: [PATCH] Update README.rst --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index b30bdb5..ba15ebe 100644 --- a/README.rst +++ b/README.rst @@ -50,7 +50,7 @@ I do not know the order of the atoms Atom reordering methods can be used in cases where the atoms in the two molecules are not in the same order (**Figure 2.a**). These algorithms find the optimal mapping of atoms between the two structures to minimize RMSD. -Each method has limitations because finding the best atom mapping depends on properly aligning structures. This is usually done by comparing atom-pair distances. Using the _Hungarian cost minimization for atom distance works well if the molecules are aligned. If not, you use the molecular inertia eigenvectors (**Figure 2.b**), to rotate such the eigenvectors are aligned. +Each method has limitations because finding the best atom mapping depends on properly aligning structures. This is usually done by comparing atom-pair distances. Using the Hungarian_ cost minimization for atom distance works well if the molecules are aligned. If not, you use the molecular inertia eigenvectors (**Figure 2.b**), to rotate such the eigenvectors are aligned. Or, use atomic descriptors (**Figure 2.c**), independent of the coordinate system, to reorder the atoms. Note that all reordering methods have limitations and drawbacks, and the actual order might not be found.