Figure 2. PyFREC performs automatic alignment of molecular fragments.
Example: (A) the photosensitizer m Tz-2I-BODIPY is split into: (B)
methyl-tetrazine (m Tz, EET acceptor) and (C) halogentated
bioorthogonal boron dipyrromethene (BODIPY-2I, EET
donor).4 Hydrogen atoms are not shown for clarity.
Output is generated for all atoms or a selected group of atoms used for
alignment of the molecular fragment. Another example involves the
alignment procedure performed on a bacteriochlorophyll molecule, where
the alignment has been performed on a rigid porphyrin moiety while the
flexible tail of the bacteriochlorophyll molecule was not
aligned.2
The order of atoms in the reference structure and in the molecular
fragment has to be the same. It is achieved by an automatic generation
of molecular fragments based on the reference structures with the
auxiliary script.