tools

February 25^th, 2026

Package containing miscellaneous useful scripts:

• QuickPlotAbs: quickly plot absorption spectra from ASCII files
• plotter_TDDFT: plot TDDFT data
• molgeom
  • molgeom: retrieve geometrical properties of molecules, e.g., obtain, distances, angles, and dihedral angles
  • reorient: perform rotational operations on geometries of molecules
• SpectraFitter: fit Gaussian shapes to experimental spectra to obtain smooth curves useful for further processing
  • Inspired by this recent publication: N. Larina and V. Khodorkovsky, Analyzing experimental UV–vis spectra of conjugated molecules in solution: Pekarian function fit, New J. Chem., 2025, 49, 3937–3945, https://doi.org/10.1039/D4NJ05537C
• PSS_Calculator: retrieve absorption spectrum of metastable isomer from stable and PSS spectrum together with ratio at PSS
• Epsilonator:
  • calculate molar absorptivity spectrum (e.g., of Stable isomer) including uncertainties using data from multiple measurements
  • calculate molar absorptivity spectrum including uncertainties of Metastable isomer using absorption spectrum and ratio at PSS.
• Averaging: obtain average of values that include uncertainties

Installation

Anaconda Powershell Prompt

conda create -n toolbox
conda activate toolbox
conda install git pip
git clone https://github.com/CrespiLab/toolbox
cd toolbox
pip install -e .

User Instructions

Make sure to activate the environment.

conda activate toolbox

QuickPlotAbs

quickplotabs 'Path\to\folder\containing\ASCII\files\' (--wavelength 'wavelength') (--legend)

plotter_TDDFT

TBA

SpectraFitter

To start the program, use the command:

spectrafitter

PSS_Calculator

To start the program, use the command:

psscalc

Epsilonator

TBA

Averaging

To start the program, use the command:

average