DENSS.denss

DENSS.denss#

B2u(B)#: Calculate atomic displacement, u, from B-factor

exception NumbaDeprecationWarning(msg, loc=None, highlighting=True)#

Bases: NumbaWarning, DeprecationWarning

Warning category for use of a deprecated feature.

exception NumbaPendingDeprecationWarning(msg, loc=None, highlighting=True)#

Bases: NumbaWarning, PendingDeprecationWarning

Warning category for use of a feature that is pending deprecation.

P2Rg(r, P)#

class PDB(filename=None, natoms=None, ignore_waters=True, chain=None)#

Bases: object

Load pdb file.

add_ImplicitH()#

calculate_distance_matrix(return_squareform=False)#

calculate_unique_volume(n=16, use_b=False, atomidx=None)#: Generate volumes and radii for each atom of a pdb by accounting for overlapping sphere volumes, i.e., each radius is set to the value that yields a volume of a sphere equal to the corrected volume of the sphere after subtracting spherical caps from bonded atoms.

generate_pdb_from_defaults(natoms)#

lookup_unique_volume()#

read_cif(filename, ignore_waters=True)#

Read a CIF file and load atom information.

Parameters:

filename – Path to the CIF file
chain_id – Optional chain ID to filter atoms (default: None, read all chains)
ignore_waters – Whether to ignore water molecules (default: True)

read_pdb(filename, ignore_waters=True, chain=None)#

remove_atomalt()#

remove_atoms_from_object(idx)#

remove_by_atomname(atomname)#

remove_by_atomnum(atomnum)#

remove_by_atomtype(atomtype)#

remove_by_chain(chain)#

remove_by_resname(resname)#

remove_by_resnum(resnum)#

remove_waters()#

write(filename)#: Write PDB file format using pdb object as input.

class PDB2MRC(pdb, ignore_waters=True, explicitH=True, modifiable_atom_types=None, center_coords=True, radii_sf=None, recalculate_atomic_volumes=False, exvol_type='gaussian', use_b=False, global_B=None, resolution=None, voxel=None, side=None, nsamples=None, rho0=None, shell_contrast=None, shell_mrcfile=None, shell_type='water', Icalc_interpolation=True, fit_scale=True, fit_offset=False, data_filename=None, data_units='a', n1=None, n2=None, qmin=None, qmax=None, nq=None, penalty_weight=1.0, penalty_weights=[1.0, 0.01], fit_rho0=True, fit_shell=True, fit_all=True, min_method='Nelder-Mead', min_opts='{"adaptive": True}', fast=False, use_sasrec_during_fitting=False, ignore_warnings=False, quiet=False, run_all_on_init=False, logger=None)#

Bases: object

calc_F_with_modified_params(params, full_qr=False)#: Calculates structure factor sum from set of parameters with optimized performance

calc_I_with_modified_params(params)#: Calculates intensity profile for optimization of parameters

calc_chi2()#

calc_penalty(params)#: Calculates a penalty using quadratic loss function for parameters dependent on a target value for each parameter.

calc_rho_with_modified_params(params)#: Calculates electron density map for protein in solution. Includes the excluded volume and hydration shell calculations.

calc_score_with_modified_params(params)#

calculate_average_radii()#

calculate_excluded_volume(quiet=False)#

calculate_excluded_volume_in_A3()#: Calculate the excluded volume of the particle in angstroms cubed.

calculate_global_B()#

calculate_hydration_shell()#

calculate_invacuo_density()#

calculate_structure_factors()#

initialize_penalties(penalty_weight=None)#: Initialize penalty weights more efficiently by avoiding redundant calculations

load_data(filename=None, Iq_exp=None, units=None)#

make_grids()#

minimize_parameters(fit_radii=False)#

run_all()#: Run all necessary steps to generate density maps, structure factors, and scattering profile using current settings.

save_Iq_calc(prefix=None, qmax=None, nq=None, qc=None, use_sasrec=True)#: Save the calculated Iq curve to a .dat file.

save_fit(prefix=None)#: Save the combined experimental and calculated Iq curve to a .fit file.

scale_radii(radii_sf=None)#: Scale all the modifiable atom type radii in the pdb

set_radii(atom_types, radii)#: For each atom type in atom_types, set its value to corresponding radius in radii.

class PDB2SAS(pdb, q=None, numba=True)#

Bases: object

Calculate the scattering of an object from a set of 3D coordinates using the Debye formula.

pdb - a saxstats PDB file object. q - q values to use for calculations (optional).

calc_I(numba=True)#

calc_debye(natoms_limit=1000)#: Calculate the scattering of an object from a set of 3D coordinates using the Debye formula.

calc_form_factors(B=0.0)#

Calculate the scattering of an object from a set of 3D coordinates using the Debye formula.

B - B-factors (i.e. Debye-Waller/temperature factors) of atoms (default=0.0)

class Sasrec(Iq, D, qc=None, r=None, nr=None, alpha=0.0, ne=2, extrapolate=True)#

Bases: object

Bt(q=None)#

Ct()#: Return the values of C, a m x n variance-covariance matrix

Ct2()#: Return the values of C, a m x n variance-covariance matrix while smoothing P(r)

Et()#: Calculate En function, for use in ravg calculation

Ft()#: Calculate Fn function, for use in Rg calculation

Gmn()#: Return the mxn matrix of coefficients for the integral of (2nd deriv of P(r))**2 used for smoothing

I0errf()#: Calculate error on I0 from Shannon intensities from inverse C variance-covariance matrix

Icerrt()#: Return the standard errors on I_c(q).

Ish2I0()#: Calculate I0 from Shannon intensities

Ish2Iq()#: Calculate I(q) from intensities at Shannon points.

Ish2P()#: Calculate P(r) from intensities at Shannon points.

Ish2Q()#: Calculate Porod Invariant Q from Shannon intensities

Ish2Qr()#: Calculate Rambo Invariant Qr (Vc^2/Rg) from Shannon intensities

Ish2Vc()#: Calculate Volume of Correlation from Shannon intensities

Ish2Vp()#: Calculate Porod Volume from Shannon intensities

Ish2avgr()#: Calculate average vector length r from Shannon intensities

Ish2lc()#: Calculate length of correlation from Shannon intensities

Ish2mwVc(RNA=False)#: Calculate molecular weight via the Volume of Correlation from Shannon intensities

Ish2mwVp()#: Calculate molecular weight via Porod Volume from Shannon intensities

Ish2rg()#: Calculate Rg from Shannon intensities

Perrt()#: Return the standard errors on P(r).

Qerrf()#: Calculate error on Q from Shannon intensities from inverse C variance-covariance matrix

St()#

Vcerrf()#: Calculate error on Vc from Shannon intensities from inverse C variance-covariance matrix

Vperrf()#: Calculate error on Vp from Shannon intensities from inverse C variance-covariance matrix

Yt()#: Return the values of Y, an m-length vector.

avgrerrf()#: Calculate error on Rg from Shannon intensities from inverse C variance-covariance matrix

calc_chi2()#

create_lowq()#: Create a calculated q range for Sasrec for low q out to q=0. Just the q values, not any extrapolation of intensities.

estimate_Vp_etal()#

Estimate Porod volume using modified method based on oversmoothing.

Oversmooth the P(r) curve with a high alpha. This helps to remove shape scattering that distorts Porod assumptions.

extrapolate()#: Extrapolate to high q values

gamma0()#: Calculate gamma at r=0. gamma is P(r)/4*pi*r^2

lcerrf()#: Calculate error on lc from Shannon intensities from inverse C variance-covariance matrix

mwVcerrf()#

mwVperrf()#: Calculate error on mwVp from Shannon intensities from inverse C variance-covariance matrix

optimize_alpha(gui=False)#: Scan alpha values to find optimal alpha

rgerrf()#: Calculate error on Rg from Shannon intensities from inverse C variance-covariance matrix

rgerrfold()#: Calculate error on Rg from Shannon intensities from inverse C variance-covariance matrix

shannon_channels(D, qmax=0.5, qmin=0.0)#: Return the number of Shannon channels given a q range and maximum particle dimension

update()#

abs2(x)#

abs2_fast(x, out=None)#

align(refrho, movrho, coarse=True, abort_event=None)#: Align second electron density map to the first.

align2xyz(rho, return_transform=False)#: Align rho such that principal axes align with XYZ axes.

align_multiple(refrho, rhos, cores=1, abort_event=None, single_proc=False)#: Align multiple (or a single) maps to the reference.

average_pairs(rhos, cores=1, abort_event=None, single_proc=False)#: Average pairs of electron density maps, second half to first half.

average_two(rho1, rho2, abort_event=None)#: Align two electron density maps and return the average.

binary_average(rhos, cores=1, abort_event=None, single_proc=False)#: Generate a reference electron density map using binary averaging.

calc_chi2(Iq_exp, Iq_calc, scale=True, offset=False, interpolation=True, return_sf=False, return_fit=False, use_sasrec=True, D=None)#

Calculates a chi2 comparing experimental vs calculated intensity profiles using interpolation.

Iq_exp (ndarray) - Experimental data, q, I, sigq (required) Iq_calc (ndarray) - calculated scattering profile’s q, I, and sigq (required) scale (bool) - whether to allow scaling of Iq_exp to Iq_calc offset (bool) - whether to allow offset of Iq_exp to Iq_calc interpolation (bool) - whether to allow fine interpolation of Icalc to qexp using cubic spline return_sf (bool) - return scale factor of Iq_exp return_fit (bool) - return fit formatted as Nx4 array of [qexp, c*Iexp+b, c*err, Icalc], where c,b are scale and offset

calc_fsc(rho1, rho2, side)#: Calculate the Fourier Shell Correlation between two electron density maps.

calc_rg_I0_by_guinier(Iq, nb=None, ne=None)#: calculate Rg, I(0) by fitting Guinier equation to data. Use only desired q range in input arrays.

calc_rg_by_guinier_first_2_points(q, I, DENSS_GPU=False)#: calculate Rg using Guinier law, but only use the first two data points. This is meant to be used with a calculated scattering profile, such as Imean from denss().

calc_rg_by_guinier_peak(Iq, exp=1, nb=0, ne=None)#: roughly estimate Rg using the Guinier peak method. Use only desired q range in input arrays. exp - the exponent in q^exp * I(q)

calc_rho0(mw, conc)#: Estimate bulk solvent density, rho0, from list of molecular weights and molar concentrations of components. mw and conc can be lists (nth element of mw corresponds to nth element of concentration) mw in g/mol concentration in mol/L.

calc_uniform_shell(pdb, x, y, z, thickness=2.8, distance=1.4)#

Create a uniform density hydration shell around the particle.

pdb - instance of PDB class (required) x,y,z - meshgrids for x, y, and z (required) thickness - thickness of the shell (e.g. water diameter) distance - distance from the protein surface defining the center of the shell (e.g., water radius)

cap_heights(r1, r2, d)#: Calculate the heights h1, h2 of spherical caps from overlapping spheres of radii r1, r2 a distance d apart

center_of_circle_from_sphere_intersection(x1, y1, z1, r1, x2, y2, z2, r2, a, b, c, d)#: Calculate the center of the circle formed by the intersection of two spheres

center_rho(rho, centering='com', return_shift=False, maxfirst=True, iterations=1)#

Move electron density map so its center of mass aligns with the center of the grid

centering - which part of the density to center on. By default, center on the: center of mass (“com”). Can also center on maximum density value (“max”).

center_rho_roll(rho, recenter_mode='com', maxfirst=True, return_shift=False)#

Move electron density map so its center of mass aligns with the center of the grid

rho - electron density array recenter_mode - a string either com (center of mass) or max (maximum density)

check_if_raw_data(Iq)#

Check if an I(q) profile is a smooth fitted profile, or raw data.

Iq - N x 3 numpy array, where N is the number of data points, and the: three columns are q, I, error.

This performs a very simple check. It simply checks if there exists a q = 0 term. The Iq profile given should be first cleaned up by clean_up_data() function, which will remove I=0 and sig=0 data points.

chi2(exp, calc, sig)#: Return the chi2 discrepancy between experimental and calculated data

clean_up_data(Iq)#

Do a quick cleanup by removing zero intensities and zero errors.

Iq - N x 3 numpy array, where N is the number of data points, and the three columns are q, I, error.

coarse_then_fine_alignment(refrho, movrho, coarse=True, topn=1, abort_event=None)#: Course alignment followed by fine alignment. Select the topn candidates from the grid search and minimize each, selecting the best fine alignment.

create_lowq(q)#: Create a calculated q range for Sasrec for low q out to q=0. Just the q values, not any extrapolation of intensities.

denss_3DFs(rho_start, dmax, ne=None, voxel=5.0, oversampling=3.0, positivity=True, output='map', steps=2001, seed=None, shrinkwrap=True, shrinkwrap_sigma_start=3, shrinkwrap_sigma_end=1.5, shrinkwrap_sigma_decay=0.99, shrinkwrap_threshold_fraction=0.2, shrinkwrap_iter=20, shrinkwrap_minstep=50, write_freq=100, support=None, enforce_connectivity=True, enforce_connectivity_steps=[6000], quiet=False)#: Calculate electron density from starting map by refining phases only.

direct_I2P(q, I, D=None)#

ecdf(x)#: convenience function for computing the empirical CDF

equation_of_plane_from_sphere_intersection(x1, y1, z1, r1, x2, y2, z2, r2)#: Calculate coefficients a,b,c,d of equation of a plane (ax+by+cz+d=0) formed by the intersection of two spheres with centers (x1,y1,z1), (x2,y2,z2) and radii r1,r2. from: http://ambrnet.com/TrigoCalc/Sphere/TwoSpheres/Intersection.htm

estimate_dmax(Iq, dmax=None, clean_up=True)#: Attempt to roughly estimate Dmax directly from data.

estimate_side_from_pdb(pdb, use_convex_hull=False)#

euler2matrix(alpha=0.0, beta=0.0, gamma=0.0)#

Convert Euler angles alpha, beta, gamma to a standard rotation matrix.

alpha - yaw, counterclockwise rotation about z-axis, upper-left quadrant beta - pitch, counterclockwise rotation about y-axis, four-corners gamma - roll, counterclockwise rotation about x-axis, lower-right quadrant all angles given in radians

euler_grid_search(refrho, movrho, topn=1, abort_event=None)#: Simple grid search on uniformly sampled sphere to optimize alignment. Return the topn candidate maps (default=1, i.e. the best candidate).

filter_P(r, P, sigr=None, qmax=0.5, cutoff=0.75, qmin=0.0, cutoffmin=1.25)#: Filter P(r) and sigr of oscillations.

find_nearest_i(array, value)#: Return the index of the array item nearest to specified value

formfactor(element, q=array([0.001, 0.002, 0.003, 0.004, 0.005, 0.006, 0.007, 0.008, 0.009, 0.01, 0.011, 0.012, 0.013, 0.014, 0.015, 0.016, 0.017, 0.018, 0.019, 0.02, 0.021, 0.022, 0.023, 0.024, 0.025, 0.026, 0.027, 0.028, 0.029, 0.03, 0.031, 0.032, 0.033, 0.034, 0.035, 0.036, 0.037, 0.038, 0.039, 0.04, 0.041, 0.042, 0.043, 0.044, 0.045, 0.046, 0.047, 0.048, 0.049, 0.05, 0.051, 0.052, 0.053, 0.054, 0.055, 0.056, 0.057, 0.058, 0.059, 0.06, 0.061, 0.062, 0.063, 0.064, 0.065, 0.066, 0.067, 0.068, 0.069, 0.07, 0.071, 0.072, 0.073, 0.074, 0.075, 0.076, 0.077, 0.078, 0.079, 0.08, 0.081, 0.082, 0.083, 0.084, 0.085, 0.086, 0.087, 0.088, 0.089, 0.09, 0.091, 0.092, 0.093, 0.094, 0.095, 0.096, 0.097, 0.098, 0.099, 0.1, 0.101, 0.102, 0.103, 0.104, 0.105, 0.106, 0.107, 0.108, 0.109, 0.11, 0.111, 0.112, 0.113, 0.114, 0.115, 0.116, 0.117, 0.118, 0.119, 0.12, 0.121, 0.122, 0.123, 0.124, 0.125, 0.126, 0.127, 0.128, 0.129, 0.13, 0.131, 0.132, 0.133, 0.134, 0.135, 0.136, 0.137, 0.138, 0.139, 0.14, 0.141, 0.142, 0.143, 0.144, 0.145, 0.146, 0.147, 0.148, 0.149, 0.15, 0.151, 0.152, 0.153, 0.154, 0.155, 0.156, 0.157, 0.158, 0.159, 0.16, 0.161, 0.162, 0.163, 0.164, 0.165, 0.166, 0.167, 0.168, 0.169, 0.17, 0.171, 0.172, 0.173, 0.174, 0.175, 0.176, 0.177, 0.178, 0.179, 0.18, 0.181, 0.182, 0.183, 0.184, 0.185, 0.186, 0.187, 0.188, 0.189, 0.19, 0.191, 0.192, 0.193, 0.194, 0.195, 0.196, 0.197, 0.198, 0.199, 0.2, 0.201, 0.202, 0.203, 0.204, 0.205, 0.206, 0.207, 0.208, 0.209, 0.21, 0.211, 0.212, 0.213, 0.214, 0.215, 0.216, 0.217, 0.218, 0.219, 0.22, 0.221, 0.222, 0.223, 0.224, 0.225, 0.226, 0.227, 0.228, 0.229, 0.23, 0.231, 0.232, 0.233, 0.234, 0.235, 0.236, 0.237, 0.238, 0.239, 0.24, 0.241, 0.242, 0.243, 0.244, 0.245, 0.246, 0.247, 0.248, 0.249, 0.25, 0.251, 0.252, 0.253, 0.254, 0.255, 0.256, 0.257, 0.258, 0.259, 0.26, 0.261, 0.262, 0.263, 0.264, 0.265, 0.266, 0.267, 0.268, 0.269, 0.27, 0.271, 0.272, 0.273, 0.274, 0.275, 0.276, 0.277, 0.278, 0.279, 0.28, 0.281, 0.282, 0.283, 0.284, 0.285, 0.286, 0.287, 0.288, 0.289, 0.29, 0.291, 0.292, 0.293, 0.294, 0.295, 0.296, 0.297, 0.298, 0.299, 0.3, 0.301, 0.302, 0.303, 0.304, 0.305, 0.306, 0.307, 0.308, 0.309, 0.31, 0.311, 0.312, 0.313, 0.314, 0.315, 0.316, 0.317, 0.318, 0.319, 0.32, 0.321, 0.322, 0.323, 0.324, 0.325, 0.326, 0.327, 0.328, 0.329, 0.33, 0.331, 0.332, 0.333, 0.334, 0.335, 0.336, 0.337, 0.338, 0.339, 0.34, 0.341, 0.342, 0.343, 0.344, 0.345, 0.346, 0.347, 0.348, 0.349, 0.35, 0.351, 0.352, 0.353, 0.354, 0.355, 0.356, 0.357, 0.358, 0.359, 0.36, 0.361, 0.362, 0.363, 0.364, 0.365, 0.366, 0.367, 0.368, 0.369, 0.37, 0.371, 0.372, 0.373, 0.374, 0.375, 0.376, 0.377, 0.378, 0.379, 0.38, 0.381, 0.382, 0.383, 0.384, 0.385, 0.386, 0.387, 0.388, 0.389, 0.39, 0.391, 0.392, 0.393, 0.394, 0.395, 0.396, 0.397, 0.398, 0.399, 0.4, 0.401, 0.402, 0.403, 0.404, 0.405, 0.406, 0.407, 0.408, 0.409, 0.41, 0.411, 0.412, 0.413, 0.414, 0.415, 0.416, 0.417, 0.418, 0.419, 0.42, 0.421, 0.422, 0.423, 0.424, 0.425, 0.426, 0.427, 0.428, 0.429, 0.43, 0.431, 0.432, 0.433, 0.434, 0.435, 0.436, 0.437, 0.438, 0.439, 0.44, 0.441, 0.442, 0.443, 0.444, 0.445, 0.446, 0.447, 0.448, 0.449, 0.45, 0.451, 0.452, 0.453, 0.454, 0.455, 0.456, 0.457, 0.458, 0.459, 0.46, 0.461, 0.462, 0.463, 0.464, 0.465, 0.466, 0.467, 0.468, 0.469, 0.47, 0.471, 0.472, 0.473, 0.474, 0.475, 0.476, 0.477, 0.478, 0.479, 0.48, 0.481, 0.482, 0.483, 0.484, 0.485, 0.486, 0.487, 0.488, 0.489, 0.49, 0.491, 0.492, 0.493, 0.494, 0.495, 0.496, 0.497, 0.498, 0.499, 0.5]), B=None)#: Calculate atomic form factors

fsc2res(fsc, cutoff=0.5, return_plot=False)#

Calculate resolution from the FSC curve using the cutoff given.

fsc - an Nx2 array, where the first column is the x axis given as: as 1/resolution (angstrom).

cutoff - the fsc value at which to estimate resolution, default=0.5. return_plot - return additional arrays for plotting (x, y, resx)

generate_enantiomers(rho)#: Generate all enantiomers of given density map. Output maps are original, and flipped over z.

grid_center(rho)#

inertia_tensor(rho, side)#: Calculate the moment of inertia tensor for the given electron density map.

largest_indices(a, n)#: Returns the n largest indices from a numpy array.

loadDatFile(filename)#: Loads a Primus .dat format file. Taken from the BioXTAS RAW software package, used with permission under the GPL license.

loadFitFile(filename)#: Loads a four column .fit format file (q, I, err, fit). Taken from the BioXTAS RAW software package, used with permission under the GPL license.

loadOldFitFile(filename)#: Loads a old denss _fit.dat format file. Taken from the BioXTAS RAW software package, used with permission under the GPL license.

loadOutFile(filename)#: Loads a GNOM .out file and returns q, Ireg, sqrt(Ireg), and a dictionary of miscellaneous results from GNOM. Taken from the BioXTAS RAW software package, used with permission under the GPL license.

loadProfile(fname, units='a')#: Determines which loading function to run, and then runs it.

class map#

Bases: object

map(func, *iterables) –> map object

Make an iterator that computes the function using arguments from each of the iterables. Stops when the shortest iterable is exhausted.

minimize_rho(refrho, movrho, T=array([0., 0., 0., 0., 0., 0.]))#: Optimize superposition of electron density maps. Move movrho to refrho.

minimize_rho_score(T, refrho, movrho)#

Scoring function for superposition of electron density maps.

refrho - fixed, reference rho movrho - moving rho T - 6-element list containing alpha, beta, gamma, Tx, Ty, Tz in that order to move movrho by.

multi_average_two(niter, **kwargs)#: Wrapper script for averaging two maps for multiprocessing.

myabs(x, out=None, DENSS_GPU=False)#

mybinmean(xravel, binsravel, xcount=None, DENSS_GPU=False)#

mybinmean_optimized(xravel, binsravel, xcount=None, out=None)#

myfftn(x, DENSS_GPU=False)#

myifftn(x, DENSS_GPU=False)#

myirfftn(x, DENSS_GPU=False)#

mylog(x, DENSS_GPU=False)#

mymean(x, DENSS_GPU=False)#

myones(x, DENSS_GPU=False)#

myrfftn(x, DENSS_GPU=False)#

mysqrt(x, DENSS_GPU=False)#

mystd(x, DENSS_GPU=False)#

mysum(x, out=None, DENSS_GPU=False)#

myzeros(x, DENSS_GPU=False)#

myzeros_like(x, DENSS_GPU=False)#

class object#

Bases:

The base class of the class hierarchy.

When called, it accepts no arguments and returns a new featureless instance that has no instance attributes and cannot be given any.

pad_rho(rho, newshape)#: Pad rho with zeros to achieve new shape

parse_arguments(parser, data_proxy=None, return_args=False)#

class partial#

Bases: object

partial(func, *args, **keywords) - new function with partial application of the given arguments and keywords.

args#: tuple of arguments to future partial calls

func#: function object to use in future partial calls

keywords#: dictionary of keyword arguments to future partial calls

pdb2F_multigauss(pdb, qx, qy, qz, qr=None, radii=None, B=None)#

Calculate structure factors F from pdb coordinates.

pdb - instance of PDB class (required) x,y,z - meshgrids for x, y, and z (required) radii - float or list of radii of atoms in pdb (optional, uses spherical form factor rather than Kromer-Mann)

pdb2F_simple_gauss_by_radius(pdb, qx, qy, qz, qr=None, rho0=0.334, radii=None, B=None)#

Calculate structure factors F from pdb coordinates.

pdb - instance of PDB class (required) x,y,z - meshgrids for x, y, and z (required) radii - float or list of radii of atoms in pdb (optional, uses spherical form factor rather than Kromer-Mann)

pdb2map_FFT(pdb, x, y, z, radii=None, restrict=True)#

Calculate electron density from pdb coordinates by FFT of Fs.

pdb - instance of PDB class (required) x,y,z - meshgrids for x, y, and z (required) radii - float or list of radii of atoms in pdb (optional, uses spherical form factor rather than Kromer-Mann)

pdb2map_multigauss(pdb, x, y, z, cutoff=3.0, global_B=None, use_b=False, ignore_waters=True)#

5-term gaussian sum at coordinate locations using Cromer-Mann coefficients.

This function only calculates the values at grid points near the atom for speed.

pdb - instance of PDB class (required) x,y,z - meshgrids for x, y, and z (required) cutoff - maximum distance from atom to calculate density global_B - desired resolution of density map, calculated as a B-factor corresonding to atomic displacement equal to resolution.

pdb2map_simple_gauss_by_radius(pdb, x, y, z, cutoff=3.0, global_B=None, rho0=0.334, ignore_waters=True)#

Simple isotropic single gaussian sum at coordinate locations.

This function only calculates the values at grid points near the atom for speed.

pdb - instance of PDB class (required, must have pdb.radius attribute) x,y,z - meshgrids for x, y, and z (required) cutoff - maximum distance from atom to calculate density rho0 - average bulk solvent density used for excluded volume estimation (0.334 for water)

pdb2support_SES(pdb, x, y, z, radius=None, probe=1.4)#

Return a 3D Boolean array of the Solvent Excluded Surface from a set of coordinates.

pdb - instance of PDB() class x,y,z - meshgrid arrays containing x, y, and z coordinates for all voxels of 3D support space probe - probe radius for ses determination (defaults to 1.4 for water)

pdb2support_fast(pdb, x, y, z, radius=None, probe=0.0)#: Return a boolean 3D density map with support from PDB coordinates

pdb2support_vdW(pdb, x, y, z, radius=None, probe=0.0)#: Return a boolean 3D density map with support from PDB coordinates

principal_axes(I)#: Calculate the principal inertia axes and order them Ia < Ib < Ic.

principal_axis_alignment(refrho, movrho)#: Align movrho principal axes to refrho.

class range(stop)#

class range(start, stop[, step]) → range object

Bases: object

Return an object that produces a sequence of integers from start (inclusive) to stop (exclusive) by step. range(i, j) produces i, i+1, i+2, …, j-1. start defaults to 0, and stop is omitted! range(4) produces 0, 1, 2, 3. These are exactly the valid indices for a list of 4 elements. When step is given, it specifies the increment (or decrement).

count(value) → integer -- return number of occurrences of value#

index(value) → integer -- return index of value.#: Raise ValueError if the value is not present.

start#

step#

stop#

read_mrc(filename='map.mrc', returnABC=False, float64=True)#: See MRC format at http://bio3d.colorado.edu/imod/doc/mrc_format.txt for offsets

real_space_correlation_coefficient(rho1, rho2, threshold=None)#

Real space correlation coefficient between two density maps.

threshold - fraction of max(rho1)

realspace_formfactor(element, r=array([0., 0.001, 0.002, 0.003, 0.004, 0.005, 0.006, 0.007, 0.008, 0.009, 0.01, 0.011, 0.012, 0.013, 0.014, 0.015, 0.016, 0.017, 0.018, 0.019, 0.02, 0.021, 0.022, 0.023, 0.024, 0.025, 0.026, 0.027, 0.028, 0.029, 0.03, 0.031, 0.032, 0.033, 0.034, 0.035, 0.036, 0.037, 0.038, 0.039, 0.04, 0.041, 0.042, 0.043, 0.044, 0.045, 0.046, 0.047, 0.048, 0.049, 0.05, 0.051, 0.052, 0.053, 0.054, 0.055, 0.056, 0.057, 0.058, 0.059, 0.06, 0.061, 0.062, 0.063, 0.064, 0.065, 0.066, 0.067, 0.068, 0.069, 0.07, 0.071, 0.072, 0.073, 0.074, 0.075, 0.076, 0.077, 0.078, 0.079, 0.08, 0.081, 0.082, 0.083, 0.084, 0.085, 0.086, 0.087, 0.088, 0.089, 0.09, 0.091, 0.092, 0.093, 0.094, 0.095, 0.096, 0.097, 0.098, 0.099, 0.1, 0.101, 0.102, 0.103, 0.104, 0.105, 0.106, 0.107, 0.108, 0.109, 0.11, 0.111, 0.112, 0.113, 0.114, 0.115, 0.116, 0.117, 0.118, 0.119, 0.12, 0.121, 0.122, 0.123, 0.124, 0.125, 0.126, 0.127, 0.128, 0.129, 0.13, 0.131, 0.132, 0.133, 0.134, 0.135, 0.136, 0.137, 0.138, 0.139, 0.14, 0.141, 0.142, 0.143, 0.144, 0.145, 0.146, 0.147, 0.148, 0.149, 0.15, 0.151, 0.152, 0.153, 0.154, 0.155, 0.156, 0.157, 0.158, 0.159, 0.16, 0.161, 0.162, 0.163, 0.164, 0.165, 0.166, 0.167, 0.168, 0.169, 0.17, 0.171, 0.172, 0.173, 0.174, 0.175, 0.176, 0.177, 0.178, 0.179, 0.18, 0.181, 0.182, 0.183, 0.184, 0.185, 0.186, 0.187, 0.188, 0.189, 0.19, 0.191, 0.192, 0.193, 0.194, 0.195, 0.196, 0.197, 0.198, 0.199, 0.2, 0.201, 0.202, 0.203, 0.204, 0.205, 0.206, 0.207, 0.208, 0.209, 0.21, 0.211, 0.212, 0.213, 0.214, 0.215, 0.216, 0.217, 0.218, 0.219, 0.22, 0.221, 0.222, 0.223, 0.224, 0.225, 0.226, 0.227, 0.228, 0.229, 0.23, 0.231, 0.232, 0.233, 0.234, 0.235, 0.236, 0.237, 0.238, 0.239, 0.24, 0.241, 0.242, 0.243, 0.244, 0.245, 0.246, 0.247, 0.248, 0.249, 0.25, 0.251, 0.252, 0.253, 0.254, 0.255, 0.256, 0.257, 0.258, 0.259, 0.26, 0.261, 0.262, 0.263, 0.264, 0.265, 0.266, 0.267, 0.268, 0.269, 0.27, 0.271, 0.272, 0.273, 0.274, 0.275, 0.276, 0.277, 0.278, 0.279, 0.28, 0.281, 0.282, 0.283, 0.284, 0.285, 0.286, 0.287, 0.288, 0.289, 0.29, 0.291, 0.292, 0.293, 0.294, 0.295, 0.296, 0.297, 0.298, 0.299, 0.3, 0.301, 0.302, 0.303, 0.304, 0.305, 0.306, 0.307, 0.308, 0.309, 0.31, 0.311, 0.312, 0.313, 0.314, 0.315, 0.316, 0.317, 0.318, 0.319, 0.32, 0.321, 0.322, 0.323, 0.324, 0.325, 0.326, 0.327, 0.328, 0.329, 0.33, 0.331, 0.332, 0.333, 0.334, 0.335, 0.336, 0.337, 0.338, 0.339, 0.34, 0.341, 0.342, 0.343, 0.344, 0.345, 0.346, 0.347, 0.348, 0.349, 0.35, 0.351, 0.352, 0.353, 0.354, 0.355, 0.356, 0.357, 0.358, 0.359, 0.36, 0.361, 0.362, 0.363, 0.364, 0.365, 0.366, 0.367, 0.368, 0.369, 0.37, 0.371, 0.372, 0.373, 0.374, 0.375, 0.376, 0.377, 0.378, 0.379, 0.38, 0.381, 0.382, 0.383, 0.384, 0.385, 0.386, 0.387, 0.388, 0.389, 0.39, 0.391, 0.392, 0.393, 0.394, 0.395, 0.396, 0.397, 0.398, 0.399, 0.4, 0.401, 0.402, 0.403, 0.404, 0.405, 0.406, 0.407, 0.408, 0.409, 0.41, 0.411, 0.412, 0.413, 0.414, 0.415, 0.416, 0.417, 0.418, 0.419, 0.42, 0.421, 0.422, 0.423, 0.424, 0.425, 0.426, 0.427, 0.428, 0.429, 0.43, 0.431, 0.432, 0.433, 0.434, 0.435, 0.436, 0.437, 0.438, 0.439, 0.44, 0.441, 0.442, 0.443, 0.444, 0.445, 0.446, 0.447, 0.448, 0.449, 0.45, 0.451, 0.452, 0.453, 0.454, 0.455, 0.456, 0.457, 0.458, 0.459, 0.46, 0.461, 0.462, 0.463, 0.464, 0.465, 0.466, 0.467, 0.468, 0.469, 0.47, 0.471, 0.472, 0.473, 0.474, 0.475, 0.476, 0.477, 0.478, 0.479, 0.48, 0.481, 0.482, 0.483, 0.484, 0.485, 0.486, 0.487, 0.488, 0.489, 0.49, 0.491, 0.492, 0.493, 0.494, 0.495, 0.496, 0.497, 0.498, 0.499, 0.5]), B=None)#: Calculate real space atomic form factors

realspace_gaussian_formfactor(r=array([-3., -2.94, -2.88, -2.82, -2.76, -2.7, -2.64, -2.58, -2.52, -2.46, -2.4, -2.34, -2.28, -2.22, -2.16, -2.1, -2.04, -1.98, -1.92, -1.86, -1.8, -1.74, -1.68, -1.62, -1.56, -1.5, -1.44, -1.38, -1.32, -1.26, -1.2, -1.14, -1.08, -1.02, -0.96, -0.9, -0.84, -0.78, -0.72, -0.66, -0.6, -0.54, -0.48, -0.42, -0.36, -0.3, -0.24, -0.18, -0.12, -0.06, 0., 0.06, 0.12, 0.18, 0.24, 0.3, 0.36, 0.42, 0.48, 0.54, 0.6, 0.66, 0.72, 0.78, 0.84, 0.9, 0.96, 1.02, 1.08, 1.14, 1.2, 1.26, 1.32, 1.38, 1.44, 1.5, 1.56, 1.62, 1.68, 1.74, 1.8, 1.86, 1.92, 1.98, 2.04, 2.1, 2.16, 2.22, 2.28, 2.34, 2.4, 2.46, 2.52, 2.58, 2.64, 2.7, 2.76, 2.82, 2.88, 2.94, 3.]), rho0=0.334, V=None, radius=None, B=None)#: Calculate real space atomic form factors assuming an isotropic gaussian sphere (for excluded volume).

reciprocalspace_gaussian_formfactor(q=array([0., 0.001, 0.002, 0.003, 0.004, 0.005, 0.006, 0.007, 0.008, 0.009, 0.01, 0.011, 0.012, 0.013, 0.014, 0.015, 0.016, 0.017, 0.018, 0.019, 0.02, 0.021, 0.022, 0.023, 0.024, 0.025, 0.026, 0.027, 0.028, 0.029, 0.03, 0.031, 0.032, 0.033, 0.034, 0.035, 0.036, 0.037, 0.038, 0.039, 0.04, 0.041, 0.042, 0.043, 0.044, 0.045, 0.046, 0.047, 0.048, 0.049, 0.05, 0.051, 0.052, 0.053, 0.054, 0.055, 0.056, 0.057, 0.058, 0.059, 0.06, 0.061, 0.062, 0.063, 0.064, 0.065, 0.066, 0.067, 0.068, 0.069, 0.07, 0.071, 0.072, 0.073, 0.074, 0.075, 0.076, 0.077, 0.078, 0.079, 0.08, 0.081, 0.082, 0.083, 0.084, 0.085, 0.086, 0.087, 0.088, 0.089, 0.09, 0.091, 0.092, 0.093, 0.094, 0.095, 0.096, 0.097, 0.098, 0.099, 0.1, 0.101, 0.102, 0.103, 0.104, 0.105, 0.106, 0.107, 0.108, 0.109, 0.11, 0.111, 0.112, 0.113, 0.114, 0.115, 0.116, 0.117, 0.118, 0.119, 0.12, 0.121, 0.122, 0.123, 0.124, 0.125, 0.126, 0.127, 0.128, 0.129, 0.13, 0.131, 0.132, 0.133, 0.134, 0.135, 0.136, 0.137, 0.138, 0.139, 0.14, 0.141, 0.142, 0.143, 0.144, 0.145, 0.146, 0.147, 0.148, 0.149, 0.15, 0.151, 0.152, 0.153, 0.154, 0.155, 0.156, 0.157, 0.158, 0.159, 0.16, 0.161, 0.162, 0.163, 0.164, 0.165, 0.166, 0.167, 0.168, 0.169, 0.17, 0.171, 0.172, 0.173, 0.174, 0.175, 0.176, 0.177, 0.178, 0.179, 0.18, 0.181, 0.182, 0.183, 0.184, 0.185, 0.186, 0.187, 0.188, 0.189, 0.19, 0.191, 0.192, 0.193, 0.194, 0.195, 0.196, 0.197, 0.198, 0.199, 0.2, 0.201, 0.202, 0.203, 0.204, 0.205, 0.206, 0.207, 0.208, 0.209, 0.21, 0.211, 0.212, 0.213, 0.214, 0.215, 0.216, 0.217, 0.218, 0.219, 0.22, 0.221, 0.222, 0.223, 0.224, 0.225, 0.226, 0.227, 0.228, 0.229, 0.23, 0.231, 0.232, 0.233, 0.234, 0.235, 0.236, 0.237, 0.238, 0.239, 0.24, 0.241, 0.242, 0.243, 0.244, 0.245, 0.246, 0.247, 0.248, 0.249, 0.25, 0.251, 0.252, 0.253, 0.254, 0.255, 0.256, 0.257, 0.258, 0.259, 0.26, 0.261, 0.262, 0.263, 0.264, 0.265, 0.266, 0.267, 0.268, 0.269, 0.27, 0.271, 0.272, 0.273, 0.274, 0.275, 0.276, 0.277, 0.278, 0.279, 0.28, 0.281, 0.282, 0.283, 0.284, 0.285, 0.286, 0.287, 0.288, 0.289, 0.29, 0.291, 0.292, 0.293, 0.294, 0.295, 0.296, 0.297, 0.298, 0.299, 0.3, 0.301, 0.302, 0.303, 0.304, 0.305, 0.306, 0.307, 0.308, 0.309, 0.31, 0.311, 0.312, 0.313, 0.314, 0.315, 0.316, 0.317, 0.318, 0.319, 0.32, 0.321, 0.322, 0.323, 0.324, 0.325, 0.326, 0.327, 0.328, 0.329, 0.33, 0.331, 0.332, 0.333, 0.334, 0.335, 0.336, 0.337, 0.338, 0.339, 0.34, 0.341, 0.342, 0.343, 0.344, 0.345, 0.346, 0.347, 0.348, 0.349, 0.35, 0.351, 0.352, 0.353, 0.354, 0.355, 0.356, 0.357, 0.358, 0.359, 0.36, 0.361, 0.362, 0.363, 0.364, 0.365, 0.366, 0.367, 0.368, 0.369, 0.37, 0.371, 0.372, 0.373, 0.374, 0.375, 0.376, 0.377, 0.378, 0.379, 0.38, 0.381, 0.382, 0.383, 0.384, 0.385, 0.386, 0.387, 0.388, 0.389, 0.39, 0.391, 0.392, 0.393, 0.394, 0.395, 0.396, 0.397, 0.398, 0.399, 0.4, 0.401, 0.402, 0.403, 0.404, 0.405, 0.406, 0.407, 0.408, 0.409, 0.41, 0.411, 0.412, 0.413, 0.414, 0.415, 0.416, 0.417, 0.418, 0.419, 0.42, 0.421, 0.422, 0.423, 0.424, 0.425, 0.426, 0.427, 0.428, 0.429, 0.43, 0.431, 0.432, 0.433, 0.434, 0.435, 0.436, 0.437, 0.438, 0.439, 0.44, 0.441, 0.442, 0.443, 0.444, 0.445, 0.446, 0.447, 0.448, 0.449, 0.45, 0.451, 0.452, 0.453, 0.454, 0.455, 0.456, 0.457, 0.458, 0.459, 0.46, 0.461, 0.462, 0.463, 0.464, 0.465, 0.466, 0.467, 0.468, 0.469, 0.47, 0.471, 0.472, 0.473, 0.474, 0.475, 0.476, 0.477, 0.478, 0.479, 0.48, 0.481, 0.482, 0.483, 0.484, 0.485, 0.486, 0.487, 0.488, 0.489, 0.49, 0.491, 0.492, 0.493, 0.494, 0.495, 0.496, 0.497, 0.498, 0.499, 0.5]), rho0=0.334, V=None, radius=None, B=None)#: Calculate reciprocal space atomic form factors assuming an isotropic gaussian sphere (for excluded volume).

reconstruct_abinitio_from_scattering_profile(q, I, sigq, dmax, qraw=None, Iraw=None, sigqraw=None, ne=None, voxel=5.0, oversampling=3.0, recenter=True, recenter_steps=None, recenter_mode='com', positivity=True, positivity_steps=None, extrapolate=True, output='map', steps=None, seed=None, rho_start=None, support_start=None, add_noise=None, shrinkwrap=True, shrinkwrap_old_method=False, shrinkwrap_sigma_start=3, shrinkwrap_sigma_end=1.5, shrinkwrap_sigma_decay=0.99, shrinkwrap_threshold_fraction=0.2, shrinkwrap_iter=20, shrinkwrap_minstep=100, chi_end_fraction=0.01, write_xplor_format=False, write_freq=100, enforce_connectivity=True, enforce_connectivity_steps=[500], enforce_connectivity_max_features=1, cutout=True, quiet=False, ncs=0, ncs_steps=[500], ncs_axis=1, ncs_type='cyclical', abort_event=None, my_logger=<RootLogger root (WARNING)>, path='.', gui=False, DENSS_GPU=False, progress_cb=None)#: Calculate electron density from scattering data.

regrid_Iq(Iq, qmin=None, qmax=None, nq=None, qc=None, use_sasrec=False, D=None)#: Interpolate Iq_calc to desired qgrid. qmax - maximum desired q value (e.g. 0.5, optional) nq - number of q points desired (equispaced from qmin to qmax, e.g., 501, optional) qc - desired q grid (takes precedence over qmax/nq) use_sasrec - rather than using simple scipy interpolation, use the more accurate (but slower) sasrec for interpolation D - maximum dimension of particle (useful for sasrec, if not given, estimated automatically from the data)

rho2rg(rho, side=None, r=None, support=None, dx=None)#: Calculate radius of gyration from an electron density map.

rho_overlap_score(rho1, rho2, threshold=None)#: Scoring function for superposition of electron density maps.

rotate_coordinates(coordinates, degrees_x=0, degrees_y=0, degrees_z=0)#

running_mean(x, N)#

select_best_enantiomer(refrho, rho, abort_event=None)#: Generate, align and select the enantiomer that best fits the reference map.

select_best_enantiomers(rhos, refrho=None, cores=1, avg_queue=None, abort_event=None, single_proc=False)#: Select the best enantiomer from each map in the set (or a single map). refrho should not be binary averaged from the original denss maps, since that would likely lose handedness. By default, refrho will be set to the first map.

shrinkwrap_by_density_value(rho, absv=True, sigma=3.0, threshold=0.2, recenter=True, recenter_mode='com')#

Create support using shrinkwrap method based on threshold as fraction of maximum density

rho - electron density; numpy array absv - boolean, whether or not to take the absolute value of the density sigma - sigma, in pixels, for gaussian filter threshold - fraction of maximum gaussian filtered density (0 to 1) recenter - boolean, whether or not to recenter the density prior to calculating support recenter_mode - either com (center of mass) or max (maximum density value)

shrinkwrap_by_volume(rho, N, absv=True, sigma=3.0, recenter=True, recenter_mode='com')#

Create support using shrinkwrap method based on threshold as fraction of maximum density

rho - electron density; numpy array absv - boolean, whether or not to take the absolute value of the density sigma - sigma, in pixels, for gaussian filter N - set the threshold such that N voxels are in the support (must precalculate this based on volume) recenter - boolean, whether or not to recenter the density prior to calculating support recenter_mode - either com (center of mass) or max (maximum density value)

sigmoid(x, x0, k, b, L)#

sigmoid_find_x_value_given_y(y, x0, k, b, L)#: find the corresponding x value given a desired y value on a sigmoid curve

sphere(R, q=array([0., 0.001, 0.002, 0.003, 0.004, 0.005, 0.006, 0.007, 0.008, 0.009, 0.01, 0.011, 0.012, 0.013, 0.014, 0.015, 0.016, 0.017, 0.018, 0.019, 0.02, 0.021, 0.022, 0.023, 0.024, 0.025, 0.026, 0.027, 0.028, 0.029, 0.03, 0.031, 0.032, 0.033, 0.034, 0.035, 0.036, 0.037, 0.038, 0.039, 0.04, 0.041, 0.042, 0.043, 0.044, 0.045, 0.046, 0.047, 0.048, 0.049, 0.05, 0.051, 0.052, 0.053, 0.054, 0.055, 0.056, 0.057, 0.058, 0.059, 0.06, 0.061, 0.062, 0.063, 0.064, 0.065, 0.066, 0.067, 0.068, 0.069, 0.07, 0.071, 0.072, 0.073, 0.074, 0.075, 0.076, 0.077, 0.078, 0.079, 0.08, 0.081, 0.082, 0.083, 0.084, 0.085, 0.086, 0.087, 0.088, 0.089, 0.09, 0.091, 0.092, 0.093, 0.094, 0.095, 0.096, 0.097, 0.098, 0.099, 0.1, 0.101, 0.102, 0.103, 0.104, 0.105, 0.106, 0.107, 0.108, 0.109, 0.11, 0.111, 0.112, 0.113, 0.114, 0.115, 0.116, 0.117, 0.118, 0.119, 0.12, 0.121, 0.122, 0.123, 0.124, 0.125, 0.126, 0.127, 0.128, 0.129, 0.13, 0.131, 0.132, 0.133, 0.134, 0.135, 0.136, 0.137, 0.138, 0.139, 0.14, 0.141, 0.142, 0.143, 0.144, 0.145, 0.146, 0.147, 0.148, 0.149, 0.15, 0.151, 0.152, 0.153, 0.154, 0.155, 0.156, 0.157, 0.158, 0.159, 0.16, 0.161, 0.162, 0.163, 0.164, 0.165, 0.166, 0.167, 0.168, 0.169, 0.17, 0.171, 0.172, 0.173, 0.174, 0.175, 0.176, 0.177, 0.178, 0.179, 0.18, 0.181, 0.182, 0.183, 0.184, 0.185, 0.186, 0.187, 0.188, 0.189, 0.19, 0.191, 0.192, 0.193, 0.194, 0.195, 0.196, 0.197, 0.198, 0.199, 0.2, 0.201, 0.202, 0.203, 0.204, 0.205, 0.206, 0.207, 0.208, 0.209, 0.21, 0.211, 0.212, 0.213, 0.214, 0.215, 0.216, 0.217, 0.218, 0.219, 0.22, 0.221, 0.222, 0.223, 0.224, 0.225, 0.226, 0.227, 0.228, 0.229, 0.23, 0.231, 0.232, 0.233, 0.234, 0.235, 0.236, 0.237, 0.238, 0.239, 0.24, 0.241, 0.242, 0.243, 0.244, 0.245, 0.246, 0.247, 0.248, 0.249, 0.25, 0.251, 0.252, 0.253, 0.254, 0.255, 0.256, 0.257, 0.258, 0.259, 0.26, 0.261, 0.262, 0.263, 0.264, 0.265, 0.266, 0.267, 0.268, 0.269, 0.27, 0.271, 0.272, 0.273, 0.274, 0.275, 0.276, 0.277, 0.278, 0.279, 0.28, 0.281, 0.282, 0.283, 0.284, 0.285, 0.286, 0.287, 0.288, 0.289, 0.29, 0.291, 0.292, 0.293, 0.294, 0.295, 0.296, 0.297, 0.298, 0.299, 0.3, 0.301, 0.302, 0.303, 0.304, 0.305, 0.306, 0.307, 0.308, 0.309, 0.31, 0.311, 0.312, 0.313, 0.314, 0.315, 0.316, 0.317, 0.318, 0.319, 0.32, 0.321, 0.322, 0.323, 0.324, 0.325, 0.326, 0.327, 0.328, 0.329, 0.33, 0.331, 0.332, 0.333, 0.334, 0.335, 0.336, 0.337, 0.338, 0.339, 0.34, 0.341, 0.342, 0.343, 0.344, 0.345, 0.346, 0.347, 0.348, 0.349, 0.35, 0.351, 0.352, 0.353, 0.354, 0.355, 0.356, 0.357, 0.358, 0.359, 0.36, 0.361, 0.362, 0.363, 0.364, 0.365, 0.366, 0.367, 0.368, 0.369, 0.37, 0.371, 0.372, 0.373, 0.374, 0.375, 0.376, 0.377, 0.378, 0.379, 0.38, 0.381, 0.382, 0.383, 0.384, 0.385, 0.386, 0.387, 0.388, 0.389, 0.39, 0.391, 0.392, 0.393, 0.394, 0.395, 0.396, 0.397, 0.398, 0.399, 0.4, 0.401, 0.402, 0.403, 0.404, 0.405, 0.406, 0.407, 0.408, 0.409, 0.41, 0.411, 0.412, 0.413, 0.414, 0.415, 0.416, 0.417, 0.418, 0.419, 0.42, 0.421, 0.422, 0.423, 0.424, 0.425, 0.426, 0.427, 0.428, 0.429, 0.43, 0.431, 0.432, 0.433, 0.434, 0.435, 0.436, 0.437, 0.438, 0.439, 0.44, 0.441, 0.442, 0.443, 0.444, 0.445, 0.446, 0.447, 0.448, 0.449, 0.45, 0.451, 0.452, 0.453, 0.454, 0.455, 0.456, 0.457, 0.458, 0.459, 0.46, 0.461, 0.462, 0.463, 0.464, 0.465, 0.466, 0.467, 0.468, 0.469, 0.47, 0.471, 0.472, 0.473, 0.474, 0.475, 0.476, 0.477, 0.478, 0.479, 0.48, 0.481, 0.482, 0.483, 0.484, 0.485, 0.486, 0.487, 0.488, 0.489, 0.49, 0.491, 0.492, 0.493, 0.494, 0.495, 0.496, 0.497, 0.498, 0.499, 0.5]), I0=1.0, amp=False)#: Calculate the scattering of a uniform sphere.

sphere_radius_from_volume(V)#

sphere_volume_from_radius(R)#

spherical_cap_volume(R, h)#

spherical_to_euler(phi, theta)#: Convert spherical coordinates (phi, theta) to Euler angles (alpha, beta, gamma).

store_parameters_as_string(sasrec)#

class str(object='')#

class str(bytes_or_buffer[, encoding[, errors]]) → str

Bases: object

Create a new string object from the given object. If encoding or errors is specified, then the object must expose a data buffer that will be decoded using the given encoding and error handler. Otherwise, returns the result of object.__str__() (if defined) or repr(object). encoding defaults to sys.getdefaultencoding(). errors defaults to ‘strict’.

capitalize()#

Return a capitalized version of the string.

More specifically, make the first character have upper case and the rest lower case.

casefold()#: Return a version of the string suitable for caseless comparisons.

center(width, fillchar=' ', /)#

Return a centered string of length width.

Padding is done using the specified fill character (default is a space).

count(sub[, start[, end]]) → int#: Return the number of non-overlapping occurrences of substring sub in string S[start:end]. Optional arguments start and end are interpreted as in slice notation.

encode(encoding='utf-8', errors='strict')#

Encode the string using the codec registered for encoding.

encoding: The encoding in which to encode the string.
errors: The error handling scheme to use for encoding errors. The default is ‘strict’ meaning that encoding errors raise a UnicodeEncodeError. Other possible values are ‘ignore’, ‘replace’ and ‘xmlcharrefreplace’ as well as any other name registered with codecs.register_error that can handle UnicodeEncodeErrors.

endswith(suffix[, start[, end]]) → bool#: Return True if S ends with the specified suffix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. suffix can also be a tuple of strings to try.

expandtabs(tabsize=8)#

Return a copy where all tab characters are expanded using spaces.

If tabsize is not given, a tab size of 8 characters is assumed.

find(sub[, start[, end]]) → int#

Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Return -1 on failure.

format(*args, **kwargs) → str#: Return a formatted version of S, using substitutions from args and kwargs. The substitutions are identified by braces (‘{’ and ‘}’).

format_map(mapping) → str#: Return a formatted version of S, using substitutions from mapping. The substitutions are identified by braces (‘{’ and ‘}’).

index(sub[, start[, end]]) → int#

Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Raises ValueError when the substring is not found.

isalnum()#

Return True if the string is an alpha-numeric string, False otherwise.

A string is alpha-numeric if all characters in the string are alpha-numeric and there is at least one character in the string.

isalpha()#

Return True if the string is an alphabetic string, False otherwise.

A string is alphabetic if all characters in the string are alphabetic and there is at least one character in the string.

isascii()#

Return True if all characters in the string are ASCII, False otherwise.

ASCII characters have code points in the range U+0000-U+007F. Empty string is ASCII too.

isdecimal()#

Return True if the string is a decimal string, False otherwise.

A string is a decimal string if all characters in the string are decimal and there is at least one character in the string.

isdigit()#

Return True if the string is a digit string, False otherwise.

A string is a digit string if all characters in the string are digits and there is at least one character in the string.

isidentifier()#

Return True if the string is a valid Python identifier, False otherwise.

Call keyword.iskeyword(s) to test whether string s is a reserved identifier, such as “def” or “class”.

islower()#

Return True if the string is a lowercase string, False otherwise.

A string is lowercase if all cased characters in the string are lowercase and there is at least one cased character in the string.

isnumeric()#

Return True if the string is a numeric string, False otherwise.

A string is numeric if all characters in the string are numeric and there is at least one character in the string.

isprintable()#

Return True if the string is printable, False otherwise.

A string is printable if all of its characters are considered printable in repr() or if it is empty.

isspace()#

Return True if the string is a whitespace string, False otherwise.

A string is whitespace if all characters in the string are whitespace and there is at least one character in the string.

istitle()#

Return True if the string is a title-cased string, False otherwise.

In a title-cased string, upper- and title-case characters may only follow uncased characters and lowercase characters only cased ones.

isupper()#

Return True if the string is an uppercase string, False otherwise.

A string is uppercase if all cased characters in the string are uppercase and there is at least one cased character in the string.

join(iterable, /)#

Concatenate any number of strings.

The string whose method is called is inserted in between each given string. The result is returned as a new string.

Example: ‘.’.join([‘ab’, ‘pq’, ‘rs’]) -> ‘ab.pq.rs’

ljust(width, fillchar=' ', /)#

Return a left-justified string of length width.

Padding is done using the specified fill character (default is a space).

lower()#: Return a copy of the string converted to lowercase.

lstrip(chars=None, /)#

Return a copy of the string with leading whitespace removed.

If chars is given and not None, remove characters in chars instead.

static maketrans()#

Return a translation table usable for str.translate().

If there is only one argument, it must be a dictionary mapping Unicode ordinals (integers) or characters to Unicode ordinals, strings or None. Character keys will be then converted to ordinals. If there are two arguments, they must be strings of equal length, and in the resulting dictionary, each character in x will be mapped to the character at the same position in y. If there is a third argument, it must be a string, whose characters will be mapped to None in the result.

partition(sep, /)#

Partition the string into three parts using the given separator.

This will search for the separator in the string. If the separator is found, returns a 3-tuple containing the part before the separator, the separator itself, and the part after it.

If the separator is not found, returns a 3-tuple containing the original string and two empty strings.

removeprefix(prefix, /)#

Return a str with the given prefix string removed if present.

If the string starts with the prefix string, return string[len(prefix):]. Otherwise, return a copy of the original string.

removesuffix(suffix, /)#

Return a str with the given suffix string removed if present.

If the string ends with the suffix string and that suffix is not empty, return string[:-len(suffix)]. Otherwise, return a copy of the original string.

replace(old, new, count=-1, /)#

Return a copy with all occurrences of substring old replaced by new.

count
Maximum number of occurrences to replace. -1 (the default value) means replace all occurrences.

If the optional argument count is given, only the first count occurrences are replaced.

rfind(sub[, start[, end]]) → int#

Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Return -1 on failure.

rindex(sub[, start[, end]]) → int#

Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Raises ValueError when the substring is not found.

rjust(width, fillchar=' ', /)#

Return a right-justified string of length width.

Padding is done using the specified fill character (default is a space).

rpartition(sep, /)#

Partition the string into three parts using the given separator.

This will search for the separator in the string, starting at the end. If the separator is found, returns a 3-tuple containing the part before the separator, the separator itself, and the part after it.

If the separator is not found, returns a 3-tuple containing two empty strings and the original string.

rsplit(sep=None, maxsplit=-1)#

Return a list of the substrings in the string, using sep as the separator string.

sep
The separator used to split the string.

When set to None (the default value), will split on any whitespace character (including n r t f and spaces) and will discard empty strings from the result.

maxsplit
Maximum number of splits. -1 (the default value) means no limit.

Splitting starts at the end of the string and works to the front.

rstrip(chars=None, /)#

Return a copy of the string with trailing whitespace removed.

If chars is given and not None, remove characters in chars instead.

split(sep=None, maxsplit=-1)#

Return a list of the substrings in the string, using sep as the separator string.

sep
The separator used to split the string.

When set to None (the default value), will split on any whitespace character (including n r t f and spaces) and will discard empty strings from the result.

maxsplit
Maximum number of splits. -1 (the default value) means no limit.

Splitting starts at the front of the string and works to the end.

Note, str.split() is mainly useful for data that has been intentionally delimited. With natural text that includes punctuation, consider using the regular expression module.

splitlines(keepends=False)#

Return a list of the lines in the string, breaking at line boundaries.

Line breaks are not included in the resulting list unless keepends is given and true.

startswith(prefix[, start[, end]]) → bool#: Return True if S starts with the specified prefix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. prefix can also be a tuple of strings to try.

strip(chars=None, /)#

Return a copy of the string with leading and trailing whitespace removed.

If chars is given and not None, remove characters in chars instead.

swapcase()#: Convert uppercase characters to lowercase and lowercase characters to uppercase.

title()#

Return a version of the string where each word is titlecased.

More specifically, words start with uppercased characters and all remaining cased characters have lower case.

translate(table, /)#

Replace each character in the string using the given translation table.

table
Translation table, which must be a mapping of Unicode ordinals to Unicode ordinals, strings, or None.

The table must implement lookup/indexing via __getitem__, for instance a dictionary or list. If this operation raises LookupError, the character is left untouched. Characters mapped to None are deleted.

upper()#: Return a copy of the string converted to uppercase.

zfill(width, /)#

Pad a numeric string with zeros on the left, to fill a field of the given width.

The string is never truncated.

transform_rho(rho, T, order=1)#: Rotate and translate electron density map by T vector. T = [alpha, beta, gamma, x, y, z], angles in radians order = interpolation order (0-5)

u2B(u)#: Calculate B-factor from atomic displacement, u

v2B(v)#: Calculate B-factor from atomic volume displacement, v

write_mrc(rho, side, filename='map.mrc')#: Write an MRC formatted electron density map. See here: http://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/image-processing-software/#image

write_xplor(rho, side, filename='map.xplor')#: Write an XPLOR formatted electron density map.

class zip#

Bases: object

zip(*iterables, strict=False) –> Yield tuples until an input is exhausted.

>>> list(zip('abcdefg', range(3), range(4)))
[('a', 0, 0), ('b', 1, 1), ('c', 2, 2)]

The zip object yields n-length tuples, where n is the number of iterables passed as positional arguments to zip(). The i-th element in every tuple comes from the i-th iterable argument to zip(). This continues until the shortest argument is exhausted.

If strict is true and one of the arguments is exhausted before the others, raise a ValueError.

zoom_rho(rho, vx, dx)#

Resample rho to have new voxel size.

rho - map to resample (3D array) vx - length of voxel of rho, float or tuple of three sides (a,b,c) dx - desired voxel size (only float allowed, assumes cubic grid desired)

DENSS.denss

Contents

DENSS.denss#

Submodules#

Submodules#