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    "**Table of contents**<a id='toc0_'></a>    \n",
    "- [How to add a new fluorophore or new photophysical transitions](#toc1_)    \n",
    "  - [Adding a fluorophore](#toc1_1_)    \n",
    "  - [Adding a single state transition](#toc1_2_)    \n",
    "  - [Adding an ET transition](#toc1_3_)    \n",
    "  - [*Spectra](#toc1_4_)    \n",
    "  - [**Constants](#toc1_5_)    \n",
    "\n",
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    "# <a id='toc1_'></a>[How to add a new fluorophore or new photophysical transitions](#toc0_)"
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    "## <a id='toc1_1_'></a>[Adding a fluorophore](#toc0_)\n",
    "1. Create a new instance of FluorophoreData in fluodata.py\n",
    "2. Overwrite the known constants**\n",
    "3. Create a Fluorophore instance with a name matching the variable in fluodata.py\n",
    "4. 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)."
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    "## <a id='toc1_2_'></a>[Adding a single state transition](#toc0_)\n",
    "1. Check if the involved photophysical states are present in transitions.py SingleState, if not, add them\n",
    "2. Add the transition as a transition.py - TransitionType\n",
    "3. 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."
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    "## <a id='toc1_3_'></a>[Adding an ET transition](#toc0_)\n",
    "1. Check if the involved photophysical states are present in transitions.py SingleState and if the PairedState exists, if not, add them\n",
    "2. Add the transition as a transition.py - TransitionType\n",
    "3. 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(). "
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    "## <a id='toc1_4_'></a>[*Spectra](#toc0_)\n",
    "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]."
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    "## <a id='toc1_5_'></a>[**Constants](#toc0_)\n",
    "If a cross section is provided, it should correspond to the excitation wavelength used. Energy transfers refer to absorption spectra, not individual cross sections."
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