Лаборатория изучения механизмов органических реакций

align

Usage: align [-first] file1.xyz file2.xyz > aligned_file.xyz

Align structures each to other.
cat *.xyz | align > aligned_file.xyz
Dependencies: perl

*.xyz - concatenated xyz-files, usually from IRC.
These files should have consistent numbering of atoms.
Each structure is aligned to previous one or 
(with option -first) to the first one.
Step between aligned structures (in sqrt(amu)*angstrem) is added 
to aligned_file.xyz.