How to add a new fluorophore or new photophysical transitions¶
Adding a fluorophore¶
Create a new instance of FluorophoreData in fluodata.py
Overwrite the known constants**
Create a Fluorophore instance with a name matching the variable in fluodata.py
Provide datafiles containing absorption and emission spectra* in a folder in fluorophore_spectra and keep the naming convention (e.g., absorption of S0 should be named absorption_S0.csv). The name of the folder should be provided as a str in fluo_data.py (data_files=str).
Adding a single state transition¶
Check if the involved photophysical states are present in transitions.py SingleState, if not, add them
Add the transition as a transition.py - TransitionType
For automatic read-in, add the rate constant to fluo_data.py (to base class with value 0 and to class instance with true value). Add the transition to transitions.py - derive_transitions(). If the rate depends on other factors, add appropriate constants to fluo_data.py**, look for an appropriate function in formulas.py and if not available, add it. Call the function in derive_transitions() to get the rate constant.
Adding an ET transition¶
Check if the involved photophysical states are present in transitions.py SingleState and if the PairedState exists, if not, add them
Add the transition as a transition.py - TransitionType
For automatic read-in, provide absorption spectra* of the acceptor state and emission spectra* for the donor state. Add the transition to transitions.py - derive_energy_transfer_transitions().
*Spectra¶
The absorption spectra should contain absolute extinction coefficient values for each wavelength (nm) [200, 201, …, 1000]. The emission spectrum should contain relative values where 1 corresponds to maximum emission, for each wavelength (nm) [200, 201, …, 1000].
**Constants¶
If a cross section is provided, it should correspond to the excitation wavelength used. Energy transfers refer to absorption spectra, not individual cross sections.