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.