solnScatPotTools
index
solnScatPotTools.py

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.  

 
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.
    
analyze(potList)
perform analysis of SolnScatPot terms and return nicely formatted summary
useGlobs(term, globTable=[], globRules=[], verbose=0, weightFunction=<function <lambda> at 0xe83488>)
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
        solventVolumeSets = {'svergun': {'C': 16.440000000000001, 'CH': 21.59, 'CH2': 26.739999999999998, 'CH3': 31.890000000000001, 'Ca': 31.890000000000001, 'Cu': 8.7799999999999994, 'Fe': 7.9900000000000002, 'H': 5.1500000000000004, 'MN': 9.1999999999999993, 'Mg': 17.16, ...}, 'tiede': {'Br': 26.52, 'C': 9.0, 'CH': 20.0, 'CH2': 21.0, 'CH3': 33.0, 'Ca': 31.0, 'Cl': 22.449999999999999, 'Cu(2)': 9.1999999999999993, 'Fe(2)': 8.3000000000000007, 'Fe(3)': 8.3000000000000007, ...}, 'xiaobing': {'Br': 26.52, 'C': 16.440000000000001, 'CH': 21.59, 'CH2': 26.739999999999998, 'CH3': 31.890000000000001, 'Ca': 31.890000000000001, 'Cl': 22.449999999999999, 'Cu(2)': 9.1999999999999993, 'Fe(2)': 8.3000000000000007, 'Fe(3)': 8.3000000000000007, ...}}
vol = {'Br': 26.52, 'C': 16.440000000000001, 'CH': 21.59, 'CH2': 26.739999999999998, 'CH3': 31.890000000000001, 'Ca': 31.890000000000001, 'Cl': 22.449999999999999, 'Cu(2)': 9.1999999999999993, 'Fe(2)': 8.3000000000000007, 'Fe(3)': 8.3000000000000007, ...}