paramagpy.fit

Functions

ensemble_average(dataArray)	Calculate the ensemble average for the calculated values in the column ‘cal’ of the argument <dataArray> over models of the PDB file.
extract_atom_data(data[, csa, separateModels])	Extract values required for PCS/PRE calculations
extract_ccr_data(data[, separateModels])	Extract values required for CCR calculations
extract_rdc_data(data[, separateModels])	Extract values required for RDC calculations
fit_error_bootstrap(fittingFunction, …)	Perform uncertainty analysis sourcing noise from fractioning the experimental data.
fit_error_models(fittingFunction, **kwargs)	Perform uncertainty analysis sourcing noise from cooridinates as defined by models of the PDB structure.
fit_error_monte_carlo(fittingFunction, …)	Perform uncertainty analysis sourcing noise from experimental uncertainties This function takes a fitting routine <fittingFunction> and repeats it for the specified iterations in a Monte-Carlo approach.
gridsearch_fit_atom_from_pcs(metals, dataArrays)	Calculate likely regions for an atom on a grid using an experimental PCS value and multiple delta-chi-tensors.
gridsearch_fit_atom_restrain_distance(…)	Given two RMSD density maps, this function will compare all points pairwise and return only those within the bounds of a given distance cutoff and within a certain number of points that are that are sorted by RMSD value.
gridsearch_fit_atom_restrain_distance_cutoff(…)	Given two RMSD density maps, this function will compare all points pairwise and return only those within the bounds of a given distance cutoff and within a given RMSD cutoff.
metal_standard_deviation(metals, params)	Calculate the standard deviation in parameters <params> for a list of metal objects <metals>.
nlr_fit_metal_from_ccr(initMetals, dataArrays)	Fit Chi tensor to CCR values using non-linear regression.
nlr_fit_metal_from_pcs(initMetals, dataArrays)	Fit deltaChi tensor to PCS values using non-linear regression.
nlr_fit_metal_from_pre(initMetals, …[, …])	Fit Chi tensor to PRE values using non-linear regression.
pcs_gradient_orthogonality_cross(metals, …)	An experimental metric for calculating the likelihood of a particular nuclear position being well localised from multiple tensors.
pcs_gradient_orthogonality_dot(metals, position)	An experimental metric for calculating the likelihood of a particular nuclear position being well localised from multiple tensors.
qfactor(dataArray[, ensembleAverage, …])	Calculate the Q-factor to judge tensor fit quality
sphere_grid(origin, radius, points)	Make a grid of cartesian points within a sphere
svd_calc_metal_from_pcs(pos, pcs, idx, errors)	Solve PCS equation by single value decomposition.
svd_calc_metal_from_pcs_offset(pos, pcs, …)	Solve PCS equation by single value decomposition with offset.
svd_calc_metal_from_rdc(vec, …)	Solve RDC equation by single value decomposition.
svd_fit_metal_from_rdc(initMetals, dataArrays)	Fit deltaChi tensor to RDC values using Single Value Decomposition.
svd_gridsearch_fit_metal_from_pcs(…[, …])	Fit deltaChi tensor to PCS values using Single Value Decomposition over a grid of points in a sphere.

Classes

DensityMap(origin, size, density)

A class to help with calculations on a grid.