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, weightByExpt=False, globProtons=0, radiusScale=1, 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.     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     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

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': 16.440000000000001, '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, ...}
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, ...}}

Data
		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': 16.440000000000001, '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, ...} 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, ...}}