Rotate a group of atoms in a XYZ coordinate file for computational chemistry rotate.pl: This script rotates atoms in an XYZ coordinate file. All atoms are 0-indexed.
usage: rotate.pl -theta|-t -rotated|-r -output|-o -input|-i -atom2|-a2 -atom1|-a1
required named arguments: -theta, -t THETA the angle that the atom should be rotated
-rotated, -r ROTATED a comma-delimited list of atoms that need to be rotated
-output, -o OUTPUT output file
-input, -i INPUT the source file to be read
-atom2, -a2 ATOM2 the 2nd atom defining the axis of rotation
-atom1, -a1 ATOM1 the 1st atom defining the axis of rotation
Example: perl rotate.pl -i ethane.xyz -a1 2 -a2 0 -o ethane.rotated.x.xyz -rotated 1,3,4 -th 60
requires Data::Printer, Getopt::ArgParse, and Devel::Confess