fixed bug on line 283 where lines_read is not getting updated if ignore_hydrogens is set
fixed bug on line 283 where lines_read is not getting updated if ignore_hydrogens is set

Added two new flags to add (-a, --add-idx) or remove (-r, --remove-idx) specific atoms by their index from the supplied structures files before calculation.

Added extra output of the rotated structure_A for all the atoms if only a subset has been used due to -n, -a or -r flags.

charnley/rmsd