Would it be possible to include an option to apply rot + trans matrix to original PDB as oppose to the cleaned PDB?

[noahharrison64]

This would be useful if you are trying to align structures which contain cofactors, such as ligands.

[noahharrison64]

I actually just decided to implement a relatively naive version of this myself. The code only works when supplying PDB files as input:
Checks for align_cofactors arg,
if True then
define input_dir (where the PDB files are stored)
Add input_dir arg to write_superposed_pdbs and subfunctions:
Transform original PDBs pulled from input_dir as oppose to cleaned_pdbs.

Have tested and code appears to function correctly both when align_cofactors is True and when it is False.
Forked here