**isomers**to align:

This site is a web implementation of ArbAlign which uses the Kuhn-Munkres or Hungarian algorithm to optimally align two arbitrarily ordered isomers. Given two isomers A and B whose Cartesian coordinates are given in XYZ format, it will optimally align B on A to minimize the Kabsch root-mean-square deviation (RMSD) between structure A and B after

- a Kuhn-Munkres assignment/reordering (quick)
- a Kuhn-Munkres assignment/reordering factoring in axes swaps and reflections (~48x slower)

### Cartesian Coordinates:

The user needs to provide the Cartesian coordinates (XYZ) of the two structures to be aligned. One can use OpenBabel to convert molecular coordinates from virtually any format to Cartesian (XYZ). The only limitation here is that the size of the coordinate file not exceed 20kb to ensure timely alignment.

### Options: Aligning by atom label, type or connectivity:

- The most general case is to match the atoms of the same label. For example, sulfuric acid’s atom labels would be S, O, O, O, O, H, and H.
- The atom type can include other information including bonding and local environments as defined in the Tripos SYBYL Mol2 file format implemented in OpenBabel. For example, sulfuric acid’s atom types would be S.O2, O.2, O.2, O.3, O.3, H, and H, where S.O2, O.2 and O.3 are defined as sulphone sulfur, sp2 oxygen and sp3 oxygen, respectively.
- The atoms can also include connectivity information based on the multilevel neighborhoods of atoms (MNA) file format implemented in OpenBabel. In the current case, we only consider the connectivity to the nearest neighbor (level 1). Accordingly, sulfuric acid’s connectivity types are S-SOOOO, O-OS, O-OS, O-OHS, O-OHS, H-HO, and H-HO.

One can select which alignment option to use. By default, atoms are aligned by label.

### Options: Including or Excluding Hydrogens:

One can select the 'Exclude Hydrogens' radio button to align the heavy atoms only. By default, all atoms are aligned.

### Options: Considering Axes Swaps and Reflections:

- Because the definition of positive and negative axes directions are somewhat arbitrary, performing reflections may be necessary for optimal alignment.
- Because the order of a, b, and c axes can be somewhat arbitrary, axes swaps may be necessary to obtain the best alignment.

- Swaps correspond to the switching of (x,y,z) axis to ([x,y,z], [x,y,z], [x,y,z]). There are six such possible swaps.
- Reflections take (x,y,z) coordinates to (±x, ±y, ±z). There are eight possible reflections.

There are forty-eight combinations of swaps and reflections to consider. Some of these combinations are redundant, but we perform all of them for the sake of simplicity.

By default, all swaps and reflections are performed. One can select the 'Ignore Swaps and Reflections' radio button otherwise.

Berhane Temelso, Joel M. Mabey, Toshiro Kubota, Nana Appiah-padi, George C. Shields. *J. Chem. Info. Model.*. 2017, 57 (5), 1045–1054