DEER-PREdict API Reference¶

DEER-PREdict has three main classes:

DEERpredict performs Double Electron-Electron Resonance predictions.
Functions: trajectoryAnalysis, run and save.
PREpredict performs Paramagnetic Relaxation Enhancement calculations.
Functions: trajectoryAnalysis, trajectoryAnalysisCbeta, run and save.
Operations is the base class containing attributes and methods inherited and used by the calculation classes.
Functions: precalculate_rotamer, rotamer_placement, lj_calculation, rotamerWeights, rotamerPREanalysis, calc_gamma_2, calc_gamma_2_Cbeta and calcTimeDomain.

New rotamer libraries should be defined in the DEERpredict.libraries.LIBRARIES dictionary.

RotamerLibrary class¶

DEERpredict.libraries.LIBRARIES: Loaded from DEERPREdict/lib/libraries.yml, rotamers libraries consist of a PDB file, a DCD files and a text file for the weights. These files are included in the DEERPREdict/lib folder.

DEERpredict.libraries.RotamerLibrary: Makes available the attributes top (rotamer topology), coord (rotamer coordinates) and weights (intrinsic probability of each rotamer).

Lennard-Jones parameters¶

DEERpredict.lennardjones: Lennard-Jones parameters of the CHARMM36 force field used to calculate the external energy contribution to the Boltzmann weight of each conformer.

DEERpredict.lennardjones.lj_parameters = {
    'C': {
        'vdw': 1.70,
        'p_q': 0,
        'p_Rmin2': 2.275,
        'eps': -0.020
    }, 
    ...
}