Xplor-NIH: module residueAffPotTools

residueAffPotTools

The residue affinity potential encodes the arrangement of hydrophobic, polar and charged residues in a simple potential term. It can be used as a scoring function, or in refinement.

Functions


analyze(potList)
perform analysis of ResidueAffPot terms and return nicely formatted     summary

create_ResidueAffPot(name, sel='known', sequentialCutoff=3, interdomainContacts=False, potentialName='Thomas')
    The residue affinity potential encodes the arrangement of hydrophobic,     polar and charged residues in a simple potential term.     If an atom selection is given, only the specified residues will be     included in the term.     sequentialCutoff specifies the neighborhood in sequence about which     the potential term is not evaluated.     This potential term is implemented as a selNBPot.SelNBPot.     The flag interdomainContacts controls whether or not interactions between     domains are computed.     By default the 5-class contact potential parameters are used from     Thomas and Dill,     Proc. Natl. Acad. Sci. USA 93, 11628-11633 (1996).     Also available is the potential from     S. Miyazawa and R.L. Jernigan, PROTEINS 34, 49-68 (1999).     This can be used by specifying potentialName='Miyazawa'

transpose(...)

Data

potential = [[-0.65000000000000002], [0.040000000000000001, 0.050000000000000003], [-0.68000000000000005, -0.26000000000000001, -3.25], [0.32000000000000001, 0.12, 1.4199999999999999, 0.60999999999999999], [-0.17000000000000001, 0.17000000000000001, -0.089999999999999997, -0.42999999999999999, 1.9099999999999999]]
potential_Miyazawa = [[-1.1899999999999999, -0.54000000000000004, -0.029999999999999999, -0.02, -0.029999999999999999, 0.0, -0.029999999999999999, -0.059999999999999998, 0.16, 0.01, -0.029999999999999999, 0.12, 0.080000000000000002, 0.10000000000000001, 0.20999999999999999, 0.31, 0.26000000000000001, -0.01, 0.33000000000000002, 0.34999999999999998], [-0.60999999999999999, -0.69999999999999996, -0.19, -0.23999999999999999, -0.13, -0.12, -0.029999999999999999, -0.20999999999999999, -0.080000000000000002, 0.0, -0.10000000000000001, 0.089999999999999997, 0.19, 0.040000000000000001, 0.19, 0.16, 0.37, -0.02, 0.20999999999999999, 0.23999999999999999], [-0.67000000000000004, -0.82999999999999996, -0.88, -0.22, -0.11, -0.14000000000000001, -0.11, -0.080000000000000002, -0.02, -0.02, -0.16, 0.13, 0.10000000000000001, 0.070000000000000007, 0.22, 0.26000000000000001, 0.33000000000000002, 0.0, 0.20000000000000001, 0.22], [-0.64000000000000001, -0.66000000000000003, -0.72999999999999998, -0.73999999999999999, -0.17999999999999999, -0.20000000000000001, -0.16, -0.050000000000000003, 0.02, -0.070000000000000007, -0.17000000000000001, 0.080000000000000002, 0.20000000000000001, 0.12, 0.32000000000000001, 0.23999999999999999, 0.32000000000000001, 0.17999999999999999, 0.20999999999999999, 0.23000000000000001], [-0.65000000000000002, -0.69999999999999996, -0.80000000000000004, -0.81000000000000005, -0.83999999999999997, -0.19, -0.19, -0.029999999999999999, 0.0, -0.040000000000000001, -0.17999999999999999, 0.13, 0.20000000000000001, 0.14000000000000001, 0.26000000000000001, 0.28000000000000003, 0.40999999999999998, 0.17000000000000001, 0.20999999999999999, 0.23999999999999999], [-0.58999999999999997, -0.51000000000000001, -0.67000000000000004, -0.67000000000000004, -0.73999999999999999, -0.65000000000000002, -0.20000000000000001, -0.02, 0.080000000000000002, -0.070000000000000007, -0.089999999999999997, 0.10000000000000001, 0.16, 0.14999999999999999, 0.25, 0.27000000000000002, 0.40999999999999998, 0.19, 0.22, 0.22], [-0.66000000000000003, -0.72999999999999998, -0.68000000000000005, -0.59999999999999998, -0.62, -0.51000000000000001, -0.64000000000000001, -0.11, 0.01, 0.01, -0.029999999999999999, 0.19, 0.14999999999999999, 0.089999999999999997, 0.059999999999999998, 0.050000000000000003, 0.14999999999999999, -0.080000000000000002, -0.029999999999999999, 0.050000000000000003], [-0.39000000000000001, -0.56000000000000005, -0.57999999999999996, -0.48999999999999999, -0.55000000000000004, -0.38, -0.48999999999999999, -0.45000000000000001, 0.0, 0.050000000000000003, -0.029999999999999999, 0.080000000000000002, 0.040000000000000001, -0.059999999999999998, 0.02, -0.070000000000000007, -0.029999999999999999, -0.050000000000000003, -0.10000000000000001, -0.12], [-0.33000000000000002, -0.27000000000000002, -0.35999999999999999, -0.37, -0.38, -0.32000000000000001, -0.27000000000000002, -0.20000000000000001, -0.12, -0.089999999999999997, -0.050000000000000003, 0.0, 0.0, 0.080000000000000002, 0.070000000000000007, 0.17999999999999999, 0.10000000000000001, 0.10000000000000001, 0.17999999999999999, 0.13], [-0.31, -0.17000000000000001, -0.19, -0.13, -0.16, -0.14999999999999999, -0.25, -0.22, -0.080000000000000002, -0.28999999999999998, -0.26000000000000001, -0.080000000000000002, -0.10000000000000001, -0.01, -0.10000000000000001, 0.13, -0.059999999999999998, 0.040000000000000001, 0.02, 0.01], [-0.14999999999999999, -0.11, -0.14999999999999999, -0.14999999999999999, -0.14999999999999999, -0.070000000000000007, -0.02, -0.089999999999999997, 0.040000000000000001, -0.040000000000000001, -0.029999999999999999, -0.080000000000000002, -0.13, -0.089999999999999997, -0.12, -0.11, -0.13, -0.059999999999999998, -0.029999999999999999, -0.02], [-0.13, 0.050000000000000003, -0.12, 0.029999999999999999, -0.02, 0.040000000000000001, -0.01, -0.080000000000000002, 0.10000000000000001, -0.01, -0.040000000000000001, 0.050000000000000003, -0.17000000000000001, -0.040000000000000001, -0.12, -0.14000000000000001, -0.20000000000000001, -0.059999999999999998, -0.040000000000000001, -0.050000000000000003], [-0.070000000000000007, -0.059999999999999998, -0.11, -0.01, -0.040000000000000001, 0.080000000000000002, -0.02, -0.14000000000000001, 0.22, 0.13, -0.12, 0.22, 0.20000000000000001, -0.10000000000000001, -0.20000000000000001, -0.10000000000000001, -0.10000000000000001, 0.02, -0.14000000000000001, -0.17000000000000001], [-0.01, 0.040000000000000001, -0.01, 0.14000000000000001, 0.040000000000000001, 0.12, -0.10000000000000001, -0.11, 0.14999999999999999, -0.01, -0.040000000000000001, 0.089999999999999997, 0.059999999999999998, -0.059999999999999998, -0.27000000000000002, -0.19, -0.27000000000000002, -0.080000000000000002, -0.080000000000000002, -0.17999999999999999], [0.20000000000000001, 0.12, 0.14000000000000001, 0.17000000000000001, 0.17000000000000001, 0.26000000000000001, 0.0, -0.080000000000000002, 0.38, 0.32000000000000001, -0.16, 0.17999999999999999, 0.27000000000000002, 0.12, 0.46000000000000002, 0.029999999999999999, 0.040000000000000001, -0.19, -0.52000000000000002, -0.57999999999999996], [0.12, 0.29999999999999999, 0.17999999999999999, 0.22, 0.27000000000000002, 0.35999999999999999, 0.070000000000000007, -0.070000000000000007, 0.27000000000000002, 0.11, -0.11, 0.10000000000000001, 0.23999999999999999, 0.02, 0.44, 0.28999999999999998, -0.080000000000000002, -0.26000000000000001, -0.51000000000000001, -0.48999999999999999], [-0.35999999999999999, -0.28999999999999998, -0.34000000000000002, -0.13, -0.17999999999999999, -0.059999999999999998, -0.37, -0.29999999999999999, 0.070000000000000007, 0.0, -0.029999999999999999, 0.040000000000000001, 0.14999999999999999, 0.0, 0.0, -0.10000000000000001, -0.40000000000000002, -0.35999999999999999, -0.02, 0.10000000000000001], [0.080000000000000002, 0.029999999999999999, -0.050000000000000003, 0.0, -0.040000000000000001, 0.080000000000000002, -0.20999999999999999, -0.25, 0.23999999999999999, 0.089999999999999997, -0.11, 0.16, 0.089999999999999997, 0.10000000000000001, -0.22, -0.23999999999999999, 0.050000000000000003, 0.19, 0.029999999999999999, 0.28000000000000003], [0.33000000000000002, 0.28999999999999998, 0.19, 0.23999999999999999, 0.22, 0.28999999999999998, 0.089999999999999997, -0.050000000000000003, 0.40999999999999998, 0.28999999999999998, -0.33000000000000002, 0.35999999999999999, 0.28000000000000003, 0.22, -0.059999999999999998, -0.01, 0.38, 0.66000000000000003, 0.76000000000000001, 0.16], [-0.17999999999999999, -0.13, -0.19, -0.050000000000000003, -0.12, -0.050000000000000003, -0.37, -0.25, 0.14999999999999999, 0.02, -0.13, 0.20000000000000001, 0.17000000000000001, 0.17999999999999999, 0.37, 0.33000000000000002, 0.01, 0.17000000000000001, 0.46999999999999997, 0.11]]
potentials = {'Miyazawa': [[-1.1899999999999999, -0.54000000000000004, -0.029999999999999999, -0.02, -0.029999999999999999, 0.0, -0.029999999999999999, -0.059999999999999998, 0.16, 0.01, -0.029999999999999999, 0.12, 0.080000000000000002, 0.10000000000000001, 0.20999999999999999, 0.31, 0.26000000000000001, -0.01, 0.33000000000000002, 0.34999999999999998], [-0.60999999999999999, -0.69999999999999996, -0.19, -0.23999999999999999, -0.13, -0.12, -0.029999999999999999, -0.20999999999999999, -0.080000000000000002, 0.0, -0.10000000000000001, 0.089999999999999997, 0.19, 0.040000000000000001, 0.19, 0.16, 0.37, -0.02, 0.20999999999999999, 0.23999999999999999], [-0.67000000000000004, -0.82999999999999996, -0.88, -0.22, -0.11, -0.14000000000000001, -0.11, -0.080000000000000002, -0.02, -0.02, -0.16, 0.13, 0.10000000000000001, 0.070000000000000007, 0.22, 0.26000000000000001, 0.33000000000000002, 0.0, 0.20000000000000001, 0.22], [-0.64000000000000001, -0.66000000000000003, -0.72999999999999998, -0.73999999999999999, -0.17999999999999999, -0.20000000000000001, -0.16, -0.050000000000000003, 0.02, -0.070000000000000007, -0.17000000000000001, 0.080000000000000002, 0.20000000000000001, 0.12, 0.32000000000000001, 0.23999999999999999, 0.32000000000000001, 0.17999999999999999, 0.20999999999999999, 0.23000000000000001], [-0.65000000000000002, -0.69999999999999996, -0.80000000000000004, -0.81000000000000005, -0.83999999999999997, -0.19, -0.19, -0.029999999999999999, 0.0, -0.040000000000000001, -0.17999999999999999, 0.13, 0.20000000000000001, 0.14000000000000001, 0.26000000000000001, 0.28000000000000003, 0.40999999999999998, 0.17000000000000001, 0.20999999999999999, 0.23999999999999999], [-0.58999999999999997, -0.51000000000000001, -0.67000000000000004, -0.67000000000000004, -0.73999999999999999, -0.65000000000000002, -0.20000000000000001, -0.02, 0.080000000000000002, -0.070000000000000007, -0.089999999999999997, 0.10000000000000001, 0.16, 0.14999999999999999, 0.25, 0.27000000000000002, 0.40999999999999998, 0.19, 0.22, 0.22], [-0.66000000000000003, -0.72999999999999998, -0.68000000000000005, -0.59999999999999998, -0.62, -0.51000000000000001, -0.64000000000000001, -0.11, 0.01, 0.01, -0.029999999999999999, 0.19, 0.14999999999999999, 0.089999999999999997, 0.059999999999999998, 0.050000000000000003, 0.14999999999999999, -0.080000000000000002, -0.029999999999999999, 0.050000000000000003], [-0.39000000000000001, -0.56000000000000005, -0.57999999999999996, -0.48999999999999999, -0.55000000000000004, -0.38, -0.48999999999999999, -0.45000000000000001, 0.0, 0.050000000000000003, -0.029999999999999999, 0.080000000000000002, 0.040000000000000001, -0.059999999999999998, 0.02, -0.070000000000000007, -0.029999999999999999, -0.050000000000000003, -0.10000000000000001, -0.12], [-0.33000000000000002, -0.27000000000000002, -0.35999999999999999, -0.37, -0.38, -0.32000000000000001, -0.27000000000000002, -0.20000000000000001, -0.12, -0.089999999999999997, -0.050000000000000003, 0.0, 0.0, 0.080000000000000002, 0.070000000000000007, 0.17999999999999999, 0.10000000000000001, 0.10000000000000001, 0.17999999999999999, 0.13], [-0.31, -0.17000000000000001, -0.19, -0.13, -0.16, -0.14999999999999999, -0.25, -0.22, -0.080000000000000002, -0.28999999999999998, -0.26000000000000001, -0.080000000000000002, -0.10000000000000001, -0.01, -0.10000000000000001, 0.13, -0.059999999999999998, 0.040000000000000001, 0.02, 0.01], [-0.14999999999999999, -0.11, -0.14999999999999999, -0.14999999999999999, -0.14999999999999999, -0.070000000000000007, -0.02, -0.089999999999999997, 0.040000000000000001, -0.040000000000000001, -0.029999999999999999, -0.080000000000000002, -0.13, -0.089999999999999997, -0.12, -0.11, -0.13, -0.059999999999999998, -0.029999999999999999, -0.02], [-0.13, 0.050000000000000003, -0.12, 0.029999999999999999, -0.02, 0.040000000000000001, -0.01, -0.080000000000000002, 0.10000000000000001, -0.01, -0.040000000000000001, 0.050000000000000003, -0.17000000000000001, -0.040000000000000001, -0.12, -0.14000000000000001, -0.20000000000000001, -0.059999999999999998, -0.040000000000000001, -0.050000000000000003], [-0.070000000000000007, -0.059999999999999998, -0.11, -0.01, -0.040000000000000001, 0.080000000000000002, -0.02, -0.14000000000000001, 0.22, 0.13, -0.12, 0.22, 0.20000000000000001, -0.10000000000000001, -0.20000000000000001, -0.10000000000000001, -0.10000000000000001, 0.02, -0.14000000000000001, -0.17000000000000001], [-0.01, 0.040000000000000001, -0.01, 0.14000000000000001, 0.040000000000000001, 0.12, -0.10000000000000001, -0.11, 0.14999999999999999, -0.01, -0.040000000000000001, 0.089999999999999997, 0.059999999999999998, -0.059999999999999998, -0.27000000000000002, -0.19, -0.27000000000000002, -0.080000000000000002, -0.080000000000000002, -0.17999999999999999], [0.20000000000000001, 0.12, 0.14000000000000001, 0.17000000000000001, 0.17000000000000001, 0.26000000000000001, 0.0, -0.080000000000000002, 0.38, 0.32000000000000001, -0.16, 0.17999999999999999, 0.27000000000000002, 0.12, 0.46000000000000002, 0.029999999999999999, 0.040000000000000001, -0.19, -0.52000000000000002, -0.57999999999999996], [0.12, 0.29999999999999999, 0.17999999999999999, 0.22, 0.27000000000000002, 0.35999999999999999, 0.070000000000000007, -0.070000000000000007, 0.27000000000000002, 0.11, -0.11, 0.10000000000000001, 0.23999999999999999, 0.02, 0.44, 0.28999999999999998, -0.080000000000000002, -0.26000000000000001, -0.51000000000000001, -0.48999999999999999], [-0.35999999999999999, -0.28999999999999998, -0.34000000000000002, -0.13, -0.17999999999999999, -0.059999999999999998, -0.37, -0.29999999999999999, 0.070000000000000007, 0.0, -0.029999999999999999, 0.040000000000000001, 0.14999999999999999, 0.0, 0.0, -0.10000000000000001, -0.40000000000000002, -0.35999999999999999, -0.02, 0.10000000000000001], [0.080000000000000002, 0.029999999999999999, -0.050000000000000003, 0.0, -0.040000000000000001, 0.080000000000000002, -0.20999999999999999, -0.25, 0.23999999999999999, 0.089999999999999997, -0.11, 0.16, 0.089999999999999997, 0.10000000000000001, -0.22, -0.23999999999999999, 0.050000000000000003, 0.19, 0.029999999999999999, 0.28000000000000003], [0.33000000000000002, 0.28999999999999998, 0.19, 0.23999999999999999, 0.22, 0.28999999999999998, 0.089999999999999997, -0.050000000000000003, 0.40999999999999998, 0.28999999999999998, -0.33000000000000002, 0.35999999999999999, 0.28000000000000003, 0.22, -0.059999999999999998, -0.01, 0.38, 0.66000000000000003, 0.76000000000000001, 0.16], [-0.17999999999999999, -0.13, -0.19, -0.050000000000000003, -0.12, -0.050000000000000003, -0.37, -0.25, 0.14999999999999999, 0.02, -0.13, 0.20000000000000001, 0.17000000000000001, 0.17999999999999999, 0.37, 0.33000000000000002, 0.01, 0.17000000000000001, 0.46999999999999997, 0.11]], 'Thomas': [[-0.65000000000000002], [0.040000000000000001, 0.050000000000000003], [-0.68000000000000005, -0.26000000000000001, -3.25], [0.32000000000000001, 0.12, 1.4199999999999999, 0.60999999999999999], [-0.17000000000000001, 0.17000000000000001, -0.089999999999999997, -0.42999999999999999, 1.9099999999999999]]}
res = {'ALA': (('CB',), 8), 'ARG': (('NH*',), 17), 'ASN': (('OD1', 'ND2'), 13), 'ASP': (('OD*',), 15), 'CYS': (('SG',), 0), 'GLN': (('OE1', 'NE2'), 12), 'GLU': (('OE*',), 14), 'GLY': (('CA',), 9), 'HIS': (('ND1', 'CD2', 'CE1', 'NE2'), 16), 'ILE': (('CG2', 'CD1'), 3), ...}
residue = {'ALA': (('CB',), 0), 'ARG': (('NH*',), 4), 'ASN': (('OD1', 'ND2'), 1), 'ASP': (('OD*',), 3), 'CYS': (('SG',), 2), 'GLN': (('OE1', 'NE2'), 1), 'GLU': (('OE*',), 3), 'GLY': (('CA',), 1), 'HIS': (('ND1', 'CD2', 'CE1', 'NE2'), 1), 'ILE': (('CG2', 'CD1'), 0), ...}
residues = {'Miyazawa': {'ALA': (('CB',), 8), 'ARG': (('NH*',), 17), 'ASN': (('OD1', 'ND2'), 13), 'ASP': (('OD*',), 15), 'CYS': (('SG',), 0), 'GLN': (('OE1', 'NE2'), 12), 'GLU': (('OE*',), 14), 'GLY': (('CA',), 9), 'HIS': (('ND1', 'CD2', 'CE1', 'NE2'), 16), 'ILE': (('CG2', 'CD1'), 3), ...}, 'Thomas': {'ALA': (('CB',), 0), 'ARG': (('NH*',), 4), 'ASN': (('OD1', 'ND2'), 1), 'ASP': (('OD*',), 3), 'CYS': (('SG',), 2), 'GLN': (('OE1', 'NE2'), 1), 'GLU': (('OE*',), 3), 'GLY': (('CA',), 1), 'HIS': (('ND1', 'CD2', 'CE1', 'NE2'), 1), 'ILE': (('CG2', 'CD1'), 0), ...}}

Data
		potential = [[-0.65000000000000002], [0.040000000000000001, 0.050000000000000003], [-0.68000000000000005, -0.26000000000000001, -3.25], [0.32000000000000001, 0.12, 1.4199999999999999, 0.60999999999999999], [-0.17000000000000001, 0.17000000000000001, -0.089999999999999997, -0.42999999999999999, 1.9099999999999999]] potential_Miyazawa = [[-1.1899999999999999, -0.54000000000000004, -0.029999999999999999, -0.02, -0.029999999999999999, 0.0, -0.029999999999999999, -0.059999999999999998, 0.16, 0.01, -0.029999999999999999, 0.12, 0.080000000000000002, 0.10000000000000001, 0.20999999999999999, 0.31, 0.26000000000000001, -0.01, 0.33000000000000002, 0.34999999999999998], [-0.60999999999999999, -0.69999999999999996, -0.19, -0.23999999999999999, -0.13, -0.12, -0.029999999999999999, -0.20999999999999999, -0.080000000000000002, 0.0, -0.10000000000000001, 0.089999999999999997, 0.19, 0.040000000000000001, 0.19, 0.16, 0.37, -0.02, 0.20999999999999999, 0.23999999999999999], [-0.67000000000000004, -0.82999999999999996, -0.88, -0.22, -0.11, -0.14000000000000001, -0.11, -0.080000000000000002, -0.02, -0.02, -0.16, 0.13, 0.10000000000000001, 0.070000000000000007, 0.22, 0.26000000000000001, 0.33000000000000002, 0.0, 0.20000000000000001, 0.22], [-0.64000000000000001, -0.66000000000000003, -0.72999999999999998, -0.73999999999999999, -0.17999999999999999, -0.20000000000000001, -0.16, -0.050000000000000003, 0.02, -0.070000000000000007, -0.17000000000000001, 0.080000000000000002, 0.20000000000000001, 0.12, 0.32000000000000001, 0.23999999999999999, 0.32000000000000001, 0.17999999999999999, 0.20999999999999999, 0.23000000000000001], [-0.65000000000000002, -0.69999999999999996, -0.80000000000000004, -0.81000000000000005, -0.83999999999999997, -0.19, -0.19, -0.029999999999999999, 0.0, -0.040000000000000001, -0.17999999999999999, 0.13, 0.20000000000000001, 0.14000000000000001, 0.26000000000000001, 0.28000000000000003, 0.40999999999999998, 0.17000000000000001, 0.20999999999999999, 0.23999999999999999], [-0.58999999999999997, -0.51000000000000001, -0.67000000000000004, -0.67000000000000004, -0.73999999999999999, -0.65000000000000002, -0.20000000000000001, -0.02, 0.080000000000000002, -0.070000000000000007, -0.089999999999999997, 0.10000000000000001, 0.16, 0.14999999999999999, 0.25, 0.27000000000000002, 0.40999999999999998, 0.19, 0.22, 0.22], [-0.66000000000000003, -0.72999999999999998, -0.68000000000000005, -0.59999999999999998, -0.62, -0.51000000000000001, -0.64000000000000001, -0.11, 0.01, 0.01, -0.029999999999999999, 0.19, 0.14999999999999999, 0.089999999999999997, 0.059999999999999998, 0.050000000000000003, 0.14999999999999999, -0.080000000000000002, -0.029999999999999999, 0.050000000000000003], [-0.39000000000000001, -0.56000000000000005, -0.57999999999999996, -0.48999999999999999, -0.55000000000000004, -0.38, -0.48999999999999999, -0.45000000000000001, 0.0, 0.050000000000000003, -0.029999999999999999, 0.080000000000000002, 0.040000000000000001, -0.059999999999999998, 0.02, -0.070000000000000007, -0.029999999999999999, -0.050000000000000003, -0.10000000000000001, -0.12], [-0.33000000000000002, -0.27000000000000002, -0.35999999999999999, -0.37, -0.38, -0.32000000000000001, -0.27000000000000002, -0.20000000000000001, -0.12, -0.089999999999999997, -0.050000000000000003, 0.0, 0.0, 0.080000000000000002, 0.070000000000000007, 0.17999999999999999, 0.10000000000000001, 0.10000000000000001, 0.17999999999999999, 0.13], [-0.31, -0.17000000000000001, -0.19, -0.13, -0.16, -0.14999999999999999, -0.25, -0.22, -0.080000000000000002, -0.28999999999999998, -0.26000000000000001, -0.080000000000000002, -0.10000000000000001, -0.01, -0.10000000000000001, 0.13, -0.059999999999999998, 0.040000000000000001, 0.02, 0.01], [-0.14999999999999999, -0.11, -0.14999999999999999, -0.14999999999999999, -0.14999999999999999, -0.070000000000000007, -0.02, -0.089999999999999997, 0.040000000000000001, -0.040000000000000001, -0.029999999999999999, 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0.070000000000000007, 0.0, -0.029999999999999999, 0.040000000000000001, 0.14999999999999999, 0.0, 0.0, -0.10000000000000001, -0.40000000000000002, -0.35999999999999999, -0.02, 0.10000000000000001], [0.080000000000000002, 0.029999999999999999, -0.050000000000000003, 0.0, -0.040000000000000001, 0.080000000000000002, -0.20999999999999999, -0.25, 0.23999999999999999, 0.089999999999999997, -0.11, 0.16, 0.089999999999999997, 0.10000000000000001, -0.22, -0.23999999999999999, 0.050000000000000003, 0.19, 0.029999999999999999, 0.28000000000000003], [0.33000000000000002, 0.28999999999999998, 0.19, 0.23999999999999999, 0.22, 0.28999999999999998, 0.089999999999999997, -0.050000000000000003, 0.40999999999999998, 0.28999999999999998, -0.33000000000000002, 0.35999999999999999, 0.28000000000000003, 0.22, -0.059999999999999998, -0.01, 0.38, 0.66000000000000003, 0.76000000000000001, 0.16], [-0.17999999999999999, -0.13, -0.19, -0.050000000000000003, -0.12, -0.050000000000000003, -0.37, -0.25, 0.14999999999999999, 0.02, -0.13, 0.20000000000000001, 0.17000000000000001, 0.17999999999999999, 0.37, 0.33000000000000002, 0.01, 0.17000000000000001, 0.46999999999999997, 0.11]] potentials = {'Miyazawa': [[-1.1899999999999999, -0.54000000000000004, -0.029999999999999999, -0.02, -0.029999999999999999, 0.0, -0.029999999999999999, -0.059999999999999998, 0.16, 0.01, -0.029999999999999999, 0.12, 0.080000000000000002, 0.10000000000000001, 0.20999999999999999, 0.31, 0.26000000000000001, -0.01, 0.33000000000000002, 0.34999999999999998], [-0.60999999999999999, -0.69999999999999996, -0.19, -0.23999999999999999, -0.13, -0.12, -0.029999999999999999, -0.20999999999999999, -0.080000000000000002, 0.0, -0.10000000000000001, 0.089999999999999997, 0.19, 0.040000000000000001, 0.19, 0.16, 0.37, -0.02, 0.20999999999999999, 0.23999999999999999], [-0.67000000000000004, -0.82999999999999996, -0.88, -0.22, -0.11, -0.14000000000000001, -0.11, -0.080000000000000002, -0.02, -0.02, -0.16, 0.13, 0.10000000000000001, 0.070000000000000007, 0.22, 0.26000000000000001, 0.33000000000000002, 0.0, 0.20000000000000001, 0.22], [-0.64000000000000001, -0.66000000000000003, -0.72999999999999998, -0.73999999999999999, -0.17999999999999999, -0.20000000000000001, -0.16, -0.050000000000000003, 0.02, -0.070000000000000007, -0.17000000000000001, 0.080000000000000002, 0.20000000000000001, 0.12, 0.32000000000000001, 0.23999999999999999, 0.32000000000000001, 0.17999999999999999, 0.20999999999999999, 0.23000000000000001], [-0.65000000000000002, -0.69999999999999996, -0.80000000000000004, -0.81000000000000005, -0.83999999999999997, -0.19, -0.19, -0.029999999999999999, 0.0, -0.040000000000000001, -0.17999999999999999, 0.13, 0.20000000000000001, 0.14000000000000001, 0.26000000000000001, 0.28000000000000003, 0.40999999999999998, 0.17000000000000001, 0.20999999999999999, 0.23999999999999999], [-0.58999999999999997, -0.51000000000000001, -0.67000000000000004, -0.67000000000000004, -0.73999999999999999, -0.65000000000000002, -0.20000000000000001, -0.02, 0.080000000000000002, -0.070000000000000007, -0.089999999999999997, 0.10000000000000001, 0.16, 0.14999999999999999, 0.25, 0.27000000000000002, 0.40999999999999998, 0.19, 0.22, 0.22], [-0.66000000000000003, -0.72999999999999998, -0.68000000000000005, -0.59999999999999998, -0.62, -0.51000000000000001, -0.64000000000000001, -0.11, 0.01, 0.01, -0.029999999999999999, 0.19, 0.14999999999999999, 0.089999999999999997, 0.059999999999999998, 0.050000000000000003, 0.14999999999999999, -0.080000000000000002, -0.029999999999999999, 0.050000000000000003], [-0.39000000000000001, -0.56000000000000005, -0.57999999999999996, -0.48999999999999999, -0.55000000000000004, -0.38, -0.48999999999999999, -0.45000000000000001, 0.0, 0.050000000000000003, -0.029999999999999999, 0.080000000000000002, 0.040000000000000001, -0.059999999999999998, 0.02, -0.070000000000000007, -0.029999999999999999, -0.050000000000000003, -0.10000000000000001, -0.12], [-0.33000000000000002, -0.27000000000000002, -0.35999999999999999, -0.37, -0.38, -0.32000000000000001, -0.27000000000000002, -0.20000000000000001, -0.12, -0.089999999999999997, -0.050000000000000003, 0.0, 0.0, 0.080000000000000002, 0.070000000000000007, 0.17999999999999999, 0.10000000000000001, 0.10000000000000001, 0.17999999999999999, 0.13], [-0.31, -0.17000000000000001, -0.19, -0.13, -0.16, -0.14999999999999999, -0.25, -0.22, -0.080000000000000002, -0.28999999999999998, -0.26000000000000001, -0.080000000000000002, -0.10000000000000001, -0.01, -0.10000000000000001, 0.13, -0.059999999999999998, 0.040000000000000001, 0.02, 0.01], [-0.14999999999999999, -0.11, -0.14999999999999999, -0.14999999999999999, -0.14999999999999999, -0.070000000000000007, -0.02, -0.089999999999999997, 0.040000000000000001, -0.040000000000000001, -0.029999999999999999, -0.080000000000000002, -0.13, -0.089999999999999997, -0.12, -0.11, -0.13, -0.059999999999999998, -0.029999999999999999, -0.02], [-0.13, 0.050000000000000003, -0.12, 0.029999999999999999, -0.02, 0.040000000000000001, -0.01, -0.080000000000000002, 0.10000000000000001, -0.01, -0.040000000000000001, 0.050000000000000003, -0.17000000000000001, -0.040000000000000001, -0.12, -0.14000000000000001, -0.20000000000000001, -0.059999999999999998, -0.040000000000000001, -0.050000000000000003], [-0.070000000000000007, -0.059999999999999998, -0.11, -0.01, -0.040000000000000001, 0.080000000000000002, -0.02, -0.14000000000000001, 0.22, 0.13, -0.12, 0.22, 0.20000000000000001, -0.10000000000000001, -0.20000000000000001, -0.10000000000000001, -0.10000000000000001, 0.02, -0.14000000000000001, -0.17000000000000001], [-0.01, 0.040000000000000001, -0.01, 0.14000000000000001, 0.040000000000000001, 0.12, -0.10000000000000001, -0.11, 0.14999999999999999, -0.01, -0.040000000000000001, 0.089999999999999997, 0.059999999999999998, -0.059999999999999998, -0.27000000000000002, -0.19, -0.27000000000000002, -0.080000000000000002, -0.080000000000000002, -0.17999999999999999], [0.20000000000000001, 0.12, 0.14000000000000001, 0.17000000000000001, 0.17000000000000001, 0.26000000000000001, 0.0, -0.080000000000000002, 0.38, 0.32000000000000001, -0.16, 0.17999999999999999, 0.27000000000000002, 0.12, 0.46000000000000002, 0.029999999999999999, 0.040000000000000001, -0.19, -0.52000000000000002, -0.57999999999999996], [0.12, 0.29999999999999999, 0.17999999999999999, 0.22, 0.27000000000000002, 0.35999999999999999, 0.070000000000000007, -0.070000000000000007, 0.27000000000000002, 0.11, -0.11, 0.10000000000000001, 0.23999999999999999, 0.02, 0.44, 0.28999999999999998, -0.080000000000000002, -0.26000000000000001, -0.51000000000000001, -0.48999999999999999], [-0.35999999999999999, -0.28999999999999998, -0.34000000000000002, -0.13, -0.17999999999999999, -0.059999999999999998, -0.37, -0.29999999999999999, 0.070000000000000007, 0.0, -0.029999999999999999, 0.040000000000000001, 0.14999999999999999, 0.0, 0.0, -0.10000000000000001, -0.40000000000000002, -0.35999999999999999, -0.02, 0.10000000000000001], [0.080000000000000002, 0.029999999999999999, -0.050000000000000003, 0.0, -0.040000000000000001, 0.080000000000000002, -0.20999999999999999, -0.25, 0.23999999999999999, 0.089999999999999997, -0.11, 0.16, 0.089999999999999997, 0.10000000000000001, -0.22, -0.23999999999999999, 0.050000000000000003, 0.19, 0.029999999999999999, 0.28000000000000003], [0.33000000000000002, 0.28999999999999998, 0.19, 0.23999999999999999, 0.22, 0.28999999999999998, 0.089999999999999997, -0.050000000000000003, 0.40999999999999998, 0.28999999999999998, -0.33000000000000002, 0.35999999999999999, 0.28000000000000003, 0.22, -0.059999999999999998, -0.01, 0.38, 0.66000000000000003, 0.76000000000000001, 0.16], [-0.17999999999999999, -0.13, -0.19, -0.050000000000000003, -0.12, -0.050000000000000003, -0.37, -0.25, 0.14999999999999999, 0.02, -0.13, 0.20000000000000001, 0.17000000000000001, 0.17999999999999999, 0.37, 0.33000000000000002, 0.01, 0.17000000000000001, 0.46999999999999997, 0.11]], 'Thomas': [[-0.65000000000000002], [0.040000000000000001, 0.050000000000000003], [-0.68000000000000005, -0.26000000000000001, -3.25], [0.32000000000000001, 0.12, 1.4199999999999999, 0.60999999999999999], [-0.17000000000000001, 0.17000000000000001, -0.089999999999999997, -0.42999999999999999, 1.9099999999999999]]} res = {'ALA': (('CB',), 8), 'ARG': (('NH',), 17), 'ASN': (('OD1', 'ND2'), 13), 'ASP': (('OD',), 15), 'CYS': (('SG',), 0), 'GLN': (('OE1', 'NE2'), 12), 'GLU': (('OE',), 14), 'GLY': (('CA',), 9), 'HIS': (('ND1', 'CD2', 'CE1', 'NE2'), 16), 'ILE': (('CG2', 'CD1'), 3), ...} residue* = {'ALA': (('CB',), 0), 'ARG': (('NH',), 4), 'ASN': (('OD1', 'ND2'), 1), 'ASP': (('OD',), 3), 'CYS': (('SG',), 2), 'GLN': (('OE1', 'NE2'), 1), 'GLU': (('OE',), 3), 'GLY': (('CA',), 1), 'HIS': (('ND1', 'CD2', 'CE1', 'NE2'), 1), 'ILE': (('CG2', 'CD1'), 0), ...} residues* = {'Miyazawa': {'ALA': (('CB',), 8), 'ARG': (('NH',), 17), 'ASN': (('OD1', 'ND2'), 13), 'ASP': (('OD',), 15), 'CYS': (('SG',), 0), 'GLN': (('OE1', 'NE2'), 12), 'GLU': (('OE',), 14), 'GLY': (('CA',), 9), 'HIS': (('ND1', 'CD2', 'CE1', 'NE2'), 16), 'ILE': (('CG2', 'CD1'), 3), ...}, 'Thomas': {'ALA': (('CB',), 0), 'ARG': (('NH',), 4), 'ASN': (('OD1', 'ND2'), 1), 'ASP': (('OD',), 3), 'CYS': (('SG',), 2), 'GLN': (('OE1', 'NE2'), 1), 'GLU': (('OE',), 3), 'GLY': (('CA',), 1), 'HIS': (('ND1', 'CD2', 'CE1', 'NE2'), 1), 'ILE': (('CG2', 'CD1'), 0), ...}}