The definition includes: name and identification “serial” number of the fragment (numbers based on the residue ID numbers from the PDB file), and a list of atoms from the PDB file that belong to the fragment. This enables the most flexible way to split any PDB file into several fragments by selecting specific atoms from each residue included into the simulation.
The section provides information about vibrational modes coupled to the electronic excited state. The section contains: the vibrational mode number and its wavenumber, electron-vibrational coupling, and the vibrational decay rate. These properties of electronic excited states can be obtained from quantum chemical calculations or empirically. Thus, PyFREC provides a flexible way of integrating computed and experimental data into a single simulation.