residueAffPotTools		 index


 
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.
 
This term is described in
  Y. Ryabov, J.-Y.  Suh, A. Grishaev,  G.M. Clore and C.D.
  Schwieters, ``Using the experimentally determined
  components of the overall rotational diffusion tensor to restrain
  molecular shape and size in NMR structure determination of globular
  proteins and protein-protein complexes}{J. Am. Chem. Soc. 131, 9522-9531
  (2009)

 
Functions
       
analyze(potList)
perform analysis of ResidueAffPot terms and return nicely formatted
summary
create_ResidueAffPot(name, sel='known and not PSEUDO', sequentialCutoff=3, intradomainContacts=True, interdomainContacts=False, selectionPairs=[], 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 flags interdomainContacts and intradomainContacts control whether or
not interactions between domains are computed. Domain identity is
determined by segid.
 
Alternatively, active interactions can be specified using the selectionPairs
argument, a list of pairs of atom selections, the interactions
between which are not nonzero. If selectionPairs is specified,
intradomainContacts and interdomainContacts arguments are ignored.
 
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'

 
Data
        potential = [[-0.65], [0.04, 0.05], [-0.68, -0.26, -3.25], [0.32, 0.12, 1.42, 0.61], [-0.17, 0.17, -0.09, -0.43, 1.91]]
potential_Miyazawa = [[-1.19, -0.54, -0.03, -0.02, -0.03, 0.0, -0.03, -0.06, 0.16, 0.01, -0.03, 0.12, 0.08, 0.1, 0.21, 0.31, 0.26, -0.01, 0.33, 0.35], [-0.61, -0.7, -0.19, -0.24, -0.13, -0.12, -0.03, -0.21, -0.08, 0.0, -0.1, 0.09, 0.19, 0.04, 0.19, 0.16, 0.37, -0.02, 0.21, 0.24], [-0.67, -0.83, -0.88, -0.22, -0.11, -0.14, -0.11, -0.08, -0.02, -0.02, -0.16, 0.13, 0.1, 0.07, 0.22, 0.26, 0.33, 0.0, 0.2, 0.22], [-0.64, -0.66, -0.73, -0.74, -0.18, -0.2, -0.16, -0.05, 0.02, -0.07, -0.17, 0.08, 0.2, 0.12, 0.32, 0.24, 0.32, 0.18, 0.21, 0.23], [-0.65, -0.7, -0.8, -0.81, -0.84, -0.19, -0.19, -0.03, 0.0, -0.04, -0.18, 0.13, 0.2, 0.14, 0.26, 0.28, 0.41, 0.17, 0.21, 0.24], [-0.59, -0.51, -0.67, -0.67, -0.74, -0.65, -0.2, -0.02, 0.08, -0.07, -0.09, 0.1, 0.16, 0.15, 0.25, 0.27, 0.41, 0.19, 0.22, 0.22], [-0.66, -0.73, -0.68, -0.6, -0.62, -0.51, -0.64, -0.11, 0.01, 0.01, -0.03, 0.19, 0.15, 0.09, 0.06, 0.05, 0.15, -0.08, -0.03, 0.05], [-0.39, -0.56, -0.58, -0.49, -0.55, -0.38, -0.49, -0.45, 0.0, 0.05, -0.03, 0.08, 0.04, -0.06, 0.02, -0.07, -0.03, -0.05, -0.1, -0.12], [-0.33, -0.27, -0.36, -0.37, -0.38, -0.32, -0.27, -0.2, -0.12, -0.09, -0.05, 0.0, 0.0, 0.08, 0.07, 0.18, 0.1, 0.1, 0.18, 0.13], [-0.31, -0.17, -0.19, -0.13, -0.16, -0.15, -0.25, -0.22, -0.08, -0.29, -0.26, -0.08, -0.1, -0.01, -0.1, 0.13, -0.06, 0.04, 0.02, 0.01], [-0.15, -0.11, -0.15, -0.15, -0.15, -0.07, -0.02, -0.09, 0.04, -0.04, -0.03, -0.08, -0.13, -0.09, -0.12, -0.11, -0.13, -0.06, -0.03, -0.02], [-0.13, 0.05, -0.12, 0.03, -0.02, 0.04, -0.01, -0.08, 0.1, -0.01, -0.04, 0.05, -0.17, -0.04, -0.12, -0.14, -0.2, -0.06, -0.04, -0.05], [-0.07, -0.06, -0.11, -0.01, -0.04, 0.08, -0.02, -0.14, 0.22, 0.13, -0.12, 0.22, 0.2, -0.1, -0.2, -0.1, -0.1, 0.02, -0.14, -0.17], [-0.01, 0.04, -0.01, 0.14, 0.04, 0.12, -0.1, -0.11, 0.15, -0.01, -0.04, 0.09, 0.06, -0.06, -0.27, -0.19, -0.27, -0.08, -0.08, -0.18], [0.2, 0.12, 0.14, 0.17, 0.17, 0.26, 0.0, -0.08, 0.38, 0.32, -0.16, 0.18, 0.27, 0.12, 0.46, 0.03, 0.04, -0.19, -0.52, -0.58], [0.12, 0.3, 0.18, 0.22, 0.27, 0.36, 0.07, -0.07, 0.27, 0.11, -0.11, 0.1, 0.24, 0.02, 0.44, 0.29, -0.08, -0.26, -0.51, -0.49], [-0.36, -0.29, -0.34, -0.13, -0.18, -0.06, -0.37, -0.3, 0.07, 0.0, -0.03, 0.04, 0.15, 0.0, 0.0, -0.1, -0.4, -0.36, -0.02, 0.1], [0.08, 0.03, -0.05, 0.0, -0.04, 0.08, -0.21, -0.25, 0.24, 0.09, -0.11, 0.16, 0.09, 0.1, -0.22, -0.24, 0.05, 0.19, 0.03, 0.28], [0.33, 0.29, 0.19, 0.24, 0.22, 0.29, 0.09, -0.05, 0.41, 0.29, -0.33, 0.36, 0.28, 0.22, -0.06, -0.01, 0.38, 0.66, 0.76, 0.16], [-0.18, -0.13, -0.19, -0.05, -0.12, -0.05, -0.37, -0.25, 0.15, 0.02, -0.13, 0.2, 0.17, 0.18, 0.37, 0.33, 0.01, 0.17, 0.47, 0.11]]
potentials = {'Miyazawa': [[-1.19, -0.54, -0.03, -0.02, -0.03, 0.0, -0.03, -0.06, 0.16, 0.01, -0.03, 0.12, 0.08, 0.1, 0.21, 0.31, 0.26, -0.01, 0.33, 0.35], [-0.61, -0.7, -0.19, -0.24, -0.13, -0.12, -0.03, -0.21, -0.08, 0.0, -0.1, 0.09, 0.19, 0.04, 0.19, 0.16, 0.37, -0.02, 0.21, 0.24], [-0.67, -0.83, -0.88, -0.22, -0.11, -0.14, -0.11, -0.08, -0.02, -0.02, -0.16, 0.13, 0.1, 0.07, 0.22, 0.26, 0.33, 0.0, 0.2, 0.22], [-0.64, -0.66, -0.73, -0.74, -0.18, -0.2, -0.16, -0.05, 0.02, -0.07, -0.17, 0.08, 0.2, 0.12, 0.32, 0.24, 0.32, 0.18, 0.21, 0.23], [-0.65, -0.7, -0.8, -0.81, -0.84, -0.19, -0.19, -0.03, 0.0, -0.04, -0.18, 0.13, 0.2, 0.14, 0.26, 0.28, 0.41, 0.17, 0.21, 0.24], [-0.59, -0.51, -0.67, -0.67, -0.74, -0.65, -0.2, -0.02, 0.08, -0.07, -0.09, 0.1, 0.16, 0.15, 0.25, 0.27, 0.41, 0.19, 0.22, 0.22], [-0.66, -0.73, -0.68, -0.6, -0.62, -0.51, -0.64, -0.11, 0.01, 0.01, -0.03, 0.19, 0.15, 0.09, 0.06, 0.05, 0.15, -0.08, -0.03, 0.05], [-0.39, -0.56, -0.58, -0.49, -0.55, -0.38, -0.49, -0.45, 0.0, 0.05, -0.03, 0.08, 0.04, -0.06, 0.02, -0.07, -0.03, -0.05, -0.1, -0.12], [-0.33, -0.27, -0.36, -0.37, -0.38, -0.32, -0.27, -0.2, -0.12, -0.09, -0.05, 0.0, 0.0, 0.08, 0.07, 0.18, 0.1, 0.1, 0.18, 0.13], [-0.31, -0.17, -0.19, -0.13, -0.16, -0.15, -0.25, -0.22, -0.08, -0.29, -0.26, -0.08, -0.1, -0.01, -0.1, 0.13, -0.06, 0.04, 0.02, 0.01], [-0.15, -0.11, -0.15, -0.15, -0.15, -0.07, -0.02, -0.09, 0.04, -0.04, -0.03, -0.08, -0.13, -0.09, -0.12, -0.11, -0.13, -0.06, -0.03, -0.02], [-0.13, 0.05, -0.12, 0.03, -0.02, 0.04, -0.01, -0.08, 0.1, -0.01, -0.04, 0.05, -0.17, -0.04, -0.12, -0.14, -0.2, -0.06, -0.04, -0.05], [-0.07, -0.06, -0.11, -0.01, -0.04, 0.08, -0.02, -0.14, 0.22, 0.13, -0.12, 0.22, 0.2, -0.1, -0.2, -0.1, -0.1, 0.02, -0.14, -0.17], [-0.01, 0.04, -0.01, 0.14, 0.04, 0.12, -0.1, -0.11, 0.15, -0.01, -0.04, 0.09, 0.06, -0.06, -0.27, -0.19, -0.27, -0.08, -0.08, -0.18], [0.2, 0.12, 0.14, 0.17, 0.17, 0.26, 0.0, -0.08, 0.38, 0.32, -0.16, 0.18, 0.27, 0.12, 0.46, 0.03, 0.04, -0.19, -0.52, -0.58], [0.12, 0.3, 0.18, 0.22, 0.27, 0.36, 0.07, -0.07, 0.27, 0.11, -0.11, 0.1, 0.24, 0.02, 0.44, 0.29, -0.08, -0.26, -0.51, -0.49], [-0.36, -0.29, -0.34, -0.13, -0.18, -0.06, -0.37, -0.3, 0.07, 0.0, -0.03, 0.04, 0.15, 0.0, 0.0, -0.1, -0.4, -0.36, -0.02, 0.1], [0.08, 0.03, -0.05, 0.0, -0.04, 0.08, -0.21, -0.25, 0.24, 0.09, -0.11, 0.16, 0.09, 0.1, -0.22, -0.24, 0.05, 0.19, 0.03, 0.28], [0.33, 0.29, 0.19, 0.24, 0.22, 0.29, 0.09, -0.05, 0.41, 0.29, -0.33, 0.36, 0.28, 0.22, -0.06, -0.01, 0.38, 0.66, 0.76, 0.16], [-0.18, -0.13, -0.19, -0.05, -0.12, -0.05, -0.37, -0.25, 0.15, 0.02, -0.13, 0.2, 0.17, 0.18, 0.37, 0.33, 0.01, 0.17, 0.47, 0.11]], 'Thomas': [[-0.65], [0.04, 0.05], [-0.68, -0.26, -3.25], [0.32, 0.12, 1.42, 0.61], [-0.17, 0.17, -0.09, -0.43, 1.91]]}
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), ...}}