Xplor-NIH: module sansPotTools

sansPotTools

Functions


absScattLength(atom)
return the abs values of the atom's scattering length

create_SANSPot(instanceName, aSelection='all', experiment=0, normalizeIndex=-2, preweighted=True, numPoints=None, weightByExpt=False, globProtons=0, radiusScale=1, volumeScale=None, fractionD2O=1, exchangeFraction=0.90000000000000002, simulation=0)
create a solnScatPot.SolnScatPot term appropriate for refining against solution neutron scattering data. For efficient refinement against scattering curves, the experimental SANS data should be extrapolated to q=0 and downsampled at constant spacing in q. aSelection specifies the atoms which the SANS experiment measures. normalizeIndex specifies which grid point to use to normalize data. A value of -2 denotes average normalization Other values mean no normalization. experiment is a string or filename which contains the lines of the form q I(q) w(q) the # symbol introduces a comment. If preweighted=False, the third entry is standard deviation instead of a weight, and the weight is computed as 1/sigma^2 if sigma!=0, else 0. If normalizeIndex>=0, sigma is also normalized. numPoints specifies the number of datapoints to sample. The experimental I(q) and errors/weights are fit to cubic splines and sampled uniformly over the entire range. No smoothing is performed. If the q values are evenly spaced or numPoints is specified, calcType is set to 'uniform'. If weightByExpt is true, weights are multiplied by (I(0)/I(q))^2, where I(q) is the scattering intensity at scattering amplitude q. globProtons specifies whether or not to glob protons on to their bonded heavy atoms radiusScale specifies a radius correction factor If specified, volumeScale is a separate scale factor for the effective volume. If it is not specified, this scale factor will be consistent with radiusScale fractionD2O specifies the fraction of D2O exchangeFraction specifies the percentage of exchangable protons which actually exchange.

exchangableName(atom)
return True if the atom is a proton exchangable with solvent

exp(...)
exp(x) Return e raised to the power of x.

groupProtons(sel='known')
return a list of heavy atom/proton groupings.

useGlobs(term, globTable=[], 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')], ...}, verbose=0)
set up solnScatPot.SolnScatPot term to use the atom globbing approximation for solution X-ray scattering. 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 atoms to be globed. Atoms in term.selection() which are not specified by globTable or by globRules are placed into single-atom globs.

Data

__package__ = None
exchangableProtons = {'ALA': ['HN'], 'ARG': ['HN', 'HE', 'HH21', 'HH22', 'HH11', 'HH12'], 'ASN': ['HN', 'HD21', 'HD22'], 'ASP': ['HN'], 'CYS': ['HN', 'HG'], 'GLN': ['HN', 'HE21', 'HE22'], 'GLU': ['HN'], 'GLY': ['HN'], 'HIS': ['HN', 'HD1'], 'ILE': ['HN'], ...}
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')], ...}
pi = 3.1415926535897931
scattLength = {'C': 0.66510000000000002, 'D': 0.66710000000000003, 'Fe': 0.95099999999999996, 'H': -0.37419999999999998, 'Mn': -0.35999999999999999, 'N': 0.93999999999999995, 'O': 0.58040000000000003, 'P': 0.51700000000000002, 'Pt': 0.94999999999999996, 'S': 0.28470000000000001}
solventVolume = {'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), ...}
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), ...}}

Data
		__package__ = None exchangableProtons = {'ALA': ['HN'], 'ARG': ['HN', 'HE', 'HH21', 'HH22', 'HH11', 'HH12'], 'ASN': ['HN', 'HD21', 'HD22'], 'ASP': ['HN'], 'CYS': ['HN', 'HG'], 'GLN': ['HN', 'HE21', 'HE22'], 'GLU': ['HN'], 'GLY': ['HN'], 'HIS': ['HN', 'HD1'], 'ILE': ['HN'], ...} 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')], ...} pi = 3.1415926535897931 scattLength = {'C': 0.66510000000000002, 'D': 0.66710000000000003, 'Fe': 0.95099999999999996, 'H': -0.37419999999999998, 'Mn': -0.35999999999999999, 'N': 0.93999999999999995, 'O': 0.58040000000000003, 'P': 0.51700000000000002, 'Pt': 0.94999999999999996, 'S': 0.28470000000000001} solventVolume = {'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), ...} 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), ...}}