def setDeterminants(propka_residues, version=None, options=None):
"""
adding side-chain and coulomb determinants/perturbations to all residues - note, backbone determinants are set separately
"""
#debug.printResidues(propka_residues)
iterative_interactions = []
# --- NonIterative section ---#
for residue1 in propka_residues:
for residue2 in propka_residues:
if residue1 == residue2:
break
distance = calculate.InterResidueDistance(residue1, residue2)
if distance < version.sidechain_cutoff or distance < version.coulomb_cutoff[1]:
try:
do_pair, iterative_interaction = version.interaction[residue1.resType][residue2.resType]
except KeyError as e:
do_pair = False
if do_pair == True:
if iterative_interaction == True:
iterative.addtoDeterminantList(residue1, residue2, distance, iterative_interactions, version=version)
#print "%s - %s I" % (residue1.label, residue2.label)
else:
addDeterminants(residue1, residue2, distance, version=version)
#print "%s - %s" % (residue1.label, residue2.label)
else:
""" False - don't do this at home folks """
# --- Iterative section ---#
#debug.printIterativeDeterminants(iterative_interactions)
iterative.addDeterminants(iterative_interactions, version, options=options)
def setIonDeterminants(protein, version=None):
"""
adding ion determinants/perturbations
"""
ionizable_residues = lib.residueList("propka1")
for residue in protein.propka_residues:
if residue.resName in ionizable_residues:
for ion in protein.residue_dictionary["ION"]:
distance = calculate.InterResidueDistance(residue, ion)
if distance < version.coulomb_cutoff[1]:
label = "%s%4d%2s" % (ion.resName, ion.resNumb, ion.chainID)
weight = version.calculatePairWeight(residue.Nmass, ion.Nmass)
# the pKa of both acids and bases are shifted up by negative ions (and vice versa)
value = (-ion.Q) * version.calculateCoulombEnergy(distance, weight)
newDeterminant = Determinant(label, value)
residue.determinants[2].append(newDeterminant)