tools to aid in setup/analysis of potential terms employing solution
scattering data.
 
this module provides functions to simplify the analysis of
solnScatPot.SolnScatPot potential terms.  

Classes
		Interp   class Interp       class for linear interpoation (/extrapolation)     Methods defined here: __call__(s, x)   return the result of interpolation (/extrapolation) to the point x. __init__(s, listOfTuples)   specify a list of (x,y) pairs sorted such that the x values are monotonically increasing.

Functions
		Pr(numBins, rMax, selection='known', weights=None)   return the unnormalized pairwise distance distribution function.   numBins specifies the granulaity of the distribution, and rMax specifies the upper distance cutoff.   The calculation is performed using all atoms in selection   [all atoms whose positions have been defined, by default].   The optional weights array specifies a weight for each atom. SolventAtomParams(volume=-1, radius=-1)   analyze(potList)   perform analysis of SolnScatPot terms and return nicely formatted summary. A Chi^2 value is calculated based on the assumption that the weights are 1/sigma_i^2, where sigma_i is the error in the observed value of I_i.   The deviation value should be nonzero only for EnsembleSimulation calculations with Ne>1. It is calculated as   Dev^2 = 1/Ne 1/Nk \sum_i \sum_j w_j * (I_ij-I_j)^2   where Nk is the number of datapoints and all values of I are normalized by calcdScale, and multiplied by globCorrect. analyze_chi2(term)   compute the Chi^2 value for the solnScatPot.SolnScatPot term argument. chi2(weights, I, expt, normalizeIndex=-3)   return chi^2 using the specified normalization method fitParams(scat, r0Start=None, r0End=None, r0Num=None, V0Start=None, V0End=None, V0Num=None, rhobStart=None, rhobEnd=None, rhobNum=None, writer=None, verbose=False)   given a SolnScatPot instance, optimize the boundary layer solvent density, the excluded volume effective radius, and excluded volume parameters. These parameters are the same as those optimized in the crysol program (J. Appl. Cryst. 28, 768-773 (1995)]   scat is a SolnScatPot instance      r0Start=0.9,  r0End=1.1,    r0Num=21,    V0Start=0.92, V0End=1.08,   V0Num=21,    rhobStart=0,  rhobEnd=0.02, rhobNum=20,   specify the ranges for the three fitting parameters r0, V0 and rhob. The r0 and V0 parameters specify a multiplicative factors relative to rm and Vm, respectively. Default values are specified above.   If writer is specified, it should be a function to take informational output. interpolateCurve(experiment, weights, numPoints)   given a curve with elements (q,I) and corresponding weights, return the corresponding linearly interpolated curves sampled uniformly over numPoints. normalize(weights, I, expt, normalizeIndex)        splineCurve(experiment, weights, numPoints)   given a curve with elements (q,I) and corresponding weights, return the corresponding splined curves sampled uniformly over numPoints. useGlobs(term, globTable=[], globRules=[], verbose=0, weightFunction=<function <lambda> at 0x1fef5f0>)   set up solnScatPot.SolnScatPot term to use the atom globbing approximation.   globTable contains a list of list of atoms with in user-defined globs. Atoms not specified in globTable are glob'ed by the pre-residue definitions in the globRules dictionary.   globRules is a dictionary whose keys are upper case residue names each entry containing a list of list of atom names to be globed.   weightFunction takes an atom as an argument and returns the relative weight to give it within the glob.   Atoms in term.selection() which are not specified by globTable or by globRules are placed into single-atom globs.

Data
		__package__ = None globRules = {'ADE': [('P', 'O1P', 'O2P'), ("O5'", "C5'"), ("O3'", "C3'"), ("O4'", "C4'"), ("C1'", "C2'"), ('N1', 'C2'), ('N3', 'C4'), ('C5', 'C6', 'N6'), ('N7', 'C8', 'N9')], 'ALA': [('C', 'O', 'N', 'HN'), ('CA', 'HA', 'CB', 'HB1', 'HB2', 'HB3')], 'ARG': [('C', 'O', 'N', 'HN'), ('CA', 'HA', 'CB', 'HB1', 'HB2', 'CG', 'HG1', 'HG2'), ('CD', 'HD1', 'HD2', 'NE', 'HE', 'CZ', 'NH1', 'NH2', 'HH11', 'HH12', 'HH21', 'HH22')], 'ASN': [('C', 'O', 'N', 'HN'), ('CA', 'HA', 'CB', 'HB1', 'HB2'), ('CG', 'OD1', 'ND2', 'HD21', 'HD22')], 'ASP': [('C', 'O', 'N', 'HN'), ('CA', 'HA', 'CB', 'HB1', 'HB2'), ('CG', 'OD1', 'OD2')], 'CYS': [('C', 'O', 'N', 'HN'), ('CA', 'HA', 'CB', 'HB1', 'HB2', 'SG', 'HG')], 'CYT': [('P', 'O1P', 'O2P'), ("O5'", "C5'"), ("O3'", "C3'"), ("O4'", "C4'"), ("C1'", "C2'"), ('N1', 'C2', 'O2'), ('N3', 'C4', 'N4'), ('C5', 'C6')], 'GLN': [('C', 'O', 'N', 'HN'), ('CA', 'HA', 'CB', 'HB1', 'HB2', 'CG', 'HG1', 'HG2'), ('CD', 'OE1', 'NE2', 'HE21', 'HE22')], 'GLU': [('C', 'O', 'N', 'HN'), ('CA', 'HA', 'CB', 'HB1', 'HB2', 'CG', 'HG1', 'HG2'), ('CD', 'OE1', 'OE2')], 'GLY': [('C', 'O', 'N', 'HN'), ('CA', 'HA1', 'HA2')], ...} params = {'Br': (26.52, 1.6824786822618245), 'C': (16.440000000000001, 1.4345829602682996), 'CH': (21.59, 1.5709991296307175), 'CH2': (26.739999999999998, 1.6871182809580803), 'CH3': (31.890000000000001, 1.7891355151247366), 'Ca': (31.890000000000001, 1.7891355151247366), 'Cl': (22.449999999999999, 1.5915874724077386), 'Cu(2)': (9.1999999999999993, 1.1821910653824932), 'Fe(2)': (8.3000000000000007, 1.1423111811746613), 'Fe(3)': (8.3000000000000007, 1.1423111811746613), ...} solventParamSets = {'svergun': {'C': (16.52189547022142, 1.5800000000000001), 'CH': (21.688370252755973, 1.73), 'CH2': (26.521848780380633, 1.8500000000000001), 'CH3': (32.024863534338337, 1.97), 'Ca': (32.024863534338337, 1.97), 'Cu': (8.7845297555481903, 1.28), 'Fe': (7.9864479354106468, 1.24), 'H': (5.131448118842135, 1.0700000000000001), 'MN': (9.2027720799157002, 1.3), 'Mg': (17.157284678805059, 1.6000000000000001), ...}, 'tiede': {'Br': (26.52, 1.6824786822618245), 'C': (9.0, 1.1735616258720787), 'CH': (20.0, 1.5314461446813734), 'CH2': (21.0, 1.5565562821123009), 'CH3': (33.0, 1.8096574578554767), 'Ca': (31.0, 1.7723342420376789), 'Cl': (22.449999999999999, 1.5915874724077386), 'Cu(2)': (9.1999999999999993, 1.1821910653824932), 'Fe(2)': (8.3000000000000007, 1.1423111811746613), 'Fe(3)': (8.3000000000000007, 1.1423111811746613), ...}, 'xiaobing': {'Br': (26.52, 1.6824786822618245), 'C': (16.440000000000001, 1.4345829602682996), 'CH': (21.59, 1.5709991296307175), 'CH2': (26.739999999999998, 1.6871182809580803), 'CH3': (31.890000000000001, 1.7891355151247366), 'Ca': (31.890000000000001, 1.7891355151247366), 'Cl': (22.449999999999999, 1.5915874724077386), 'Cu(2)': (9.1999999999999993, 1.1821910653824932), 'Fe(2)': (8.3000000000000007, 1.1423111811746613), 'Fe(3)': (8.3000000000000007, 1.1423111811746613), ...}} solventVolumeSets = {'svergun': {'C': (16.52189547022142, 1.5800000000000001), 'CH': (21.688370252755973, 1.73), 'CH2': (26.521848780380633, 1.8500000000000001), 'CH3': (32.024863534338337, 1.97), 'Ca': (32.024863534338337, 1.97), 'Cu': (8.7845297555481903, 1.28), 'Fe': (7.9864479354106468, 1.24), 'H': (5.131448118842135, 1.0700000000000001), 'MN': (9.2027720799157002, 1.3), 'Mg': (17.157284678805059, 1.6000000000000001), ...}, 'tiede': {'Br': (26.52, 1.6824786822618245), 'C': (9.0, 1.1735616258720787), 'CH': (20.0, 1.5314461446813734), 'CH2': (21.0, 1.5565562821123009), 'CH3': (33.0, 1.8096574578554767), 'Ca': (31.0, 1.7723342420376789), 'Cl': (22.449999999999999, 1.5915874724077386), 'Cu(2)': (9.1999999999999993, 1.1821910653824932), 'Fe(2)': (8.3000000000000007, 1.1423111811746613), 'Fe(3)': (8.3000000000000007, 1.1423111811746613), ...}, 'xiaobing': {'Br': (26.52, 1.6824786822618245), 'C': (16.440000000000001, 1.4345829602682996), 'CH': (21.59, 1.5709991296307175), 'CH2': (26.739999999999998, 1.6871182809580803), 'CH3': (31.890000000000001, 1.7891355151247366), 'Ca': (31.890000000000001, 1.7891355151247366), 'Cl': (22.449999999999999, 1.5915874724077386), 'Cu(2)': (9.1999999999999993, 1.1821910653824932), 'Fe(2)': (8.3000000000000007, 1.1423111811746613), 'Fe(3)': (8.3000000000000007, 1.1423111811746613), ...}}