def addtoDeterminantList(residue1, residue2, distance, iterative_interactions,
version):
"""
Adds 'iterative determinants' to list ..., [[R1, R2], [side-chain, coulomb], [A1, A2]], ...
Note, the sign is determined when the interaction is added to the iterative object!
Note, distance < coulomb_cutoff here
"""
add_interaction = False
hbond_value = 0.00
coulomb_value = 0.00
# Side-chain interactions
if True:
atoms1 = residue1.makeDeterminantAtomList(residue2.resName,
version=version)
atoms2 = residue2.makeDeterminantAtomList(residue1.resName,
version=version)
atom_distance = 999.
for atom1 in atoms1:
for atom2 in atoms2:
# select the smallest inter-atom distance
atom_distance = min(calculate.InterAtomDistance(atom1, atom2),
atom_distance)
dpka_max, cutoff = version.SideChainParameters[residue1.resType][
residue2.resType]
weight = version.calculatePairWeight(residue1.Nmass, residue2.Nmass)
if atom_distance < cutoff[1]:
add_interaction = True
exception, hbond_value = version.checkExceptions(
residue1, residue2)
if residue1.resType == "COO" and residue2.resType == "COO":
""" do nothing """
#print("xxx %6.2lf" % (atom_distance))
#exception = False # circumventing exception
if exception == True:
""" do nothing, value should have been assigned """
#print(" exception for %s %s (I)" % (residue1.label, residue2.label))
else:
f_angle = 1.0
hbond_value = version.calculateSideChainEnergy(
atom_distance, dpka_max, cutoff, weight, f_angle)
# Back-bone interactions
""" Not done, never iterative """
# Coulomb interactions
do_coulomb = version.checkCoulombPair(residue1, residue2, distance)
if do_coulomb == True:
add_interaction = True
weight = version.calculatePairWeight(residue1.Nmass, residue2.Nmass)
coulomb_value = version.calculateCoulombEnergy(distance, weight)
# adding the interaction to 'iterative_interactions'
if add_interaction == True:
interaction = []
pair = [residue1, residue2]
values = [hbond_value, coulomb_value]
annihilation = [0., 0.]
interaction = [pair, values, annihilation]
iterative_interactions.append(interaction)
def setBackBoneBaseDeterminants(data_clump, version=None):
"""
adding back-bone determinants/perturbations for bases:
Angle: atom1 -- atom2-atom3, i.e. C=O -- H-N(HIS)
data_clump = [bases, CO]
"""
residues, interactions = data_clump
for residue in residues:
if residue.location != "BONDED":
dpKa_max, cutoff = version.BackBoneParameters[residue.resType]
for interaction in interactions:
distance = 999.
atom1 = interaction[1]
atoms = residue.makeDeterminantAtomList("back-bone", version=version)
for atom in atoms:
current_distance = calculate.InterAtomDistance(atom1, atom)
if current_distance < distance:
atom2 = atom
distance = current_distance
if distance < cutoff[1]:
if residue.resType in version.angularDependentSideChainInteractions:
atom3 = residue.getThirdAtomInAngle(atom2)
distance, f_angle, nada = calculate.AngleFactorX(atom1, atom2, atom3)
else:
f_angle = 1.0
if f_angle > 0.001:
# add determinant
label = "%s%4d%2s" % (atom2.resName, atom2.resNumb, atom2.chainID)
value = residue.Q * calculate.HydrogenBondEnergy(distance, dpKa_max, cutoff, f_angle)
newDeterminant = Determinant(label, value)
residue.determinants[1].append(newDeterminant)
def setBackBoneAcidDeterminants(data_clump, version=None):
"""
adding back-bone determinants/perturbations for acids:
Angle: atom1 -- atom2-atom3, i.e. COO -- H-N
data_clump = [acids, NH]
"""
residues, interactions = data_clump
for residue in residues:
if residue.location != "BONDED":
dpKa_max, cutoff = version.BackBoneParameters[residue.resType]
for interaction in interactions:
atom2 = interaction[1]
atom3 = interaction[0]
atoms = residue.makeDeterminantAtomList("back-bone", version=version)
shortest_distance = 999.
for atom in atoms:
distance = calculate.InterAtomDistance(atom, atom2)
if distance < shortest_distance:
shortest_distance = distance
atom1 = atom
distance, f_angle, nada = calculate.AngleFactorX(atom1, atom2, atom3)
if distance < cutoff[1] and f_angle > 0.001:
label = "%s%4d%2s" % (atom2.resName, atom2.resNumb, atom2.chainID)
value = residue.Q * calculate.HydrogenBondEnergy(distance, dpKa_max, cutoff, f_angle)
newDeterminant = Determinant(label, value)
residue.determinants[1].append(newDeterminant)
def addSidechainDeterminants(residue1, residue2, version=None):
"""
adding side-chain determinants/perturbations
Note, resNumb1 > resNumb2
"""
distance = 999.0
closest_atom1 = None
closest_atom2 = None
atoms1 = residue1.makeDeterminantAtomList(residue2.resName,
version=version)
atoms2 = residue2.makeDeterminantAtomList(residue1.resName,
version=version)
for atom1 in atoms1:
for atom2 in atoms2:
# select the smallest inter-atom distance
current_distance = calculate.InterAtomDistance(atom1, atom2)
if current_distance < distance:
closest_atom1 = atom1
closest_atom2 = atom2
distance = current_distance
dpka_max, cutoff = version.SideChainParameters[residue1.resType][
residue2.resType]
if distance < cutoff[1]:
if residue2.resType in version.angularDependentSideChainInteractions:
atom3 = residue2.getThirdAtomInAngle(closest_atom2)
distance, f_angle, nada = calculate.AngleFactorX(
closest_atom1, closest_atom2, atom3)
elif residue1.resType in version.angularDependentSideChainInteractions:
atom3 = residue1.getThirdAtomInAngle(closest_atom1)
distance, f_angle, nada = calculate.AngleFactorX(
closest_atom2, closest_atom1, atom3)
else:
# i.e. no angular dependence
f_angle = 1.0
weight = version.calculatePairWeight(residue1.Nmass, residue2.Nmass)
exception, value = version.checkExceptions(residue1, residue2)
#exception = False # circumventing exception
if exception == True:
""" do nothing, value should have been assigned """
#pka_print(" exception for %s %s %6.2lf" % (residue1.label, residue2.label, value))
else:
value = version.calculateSideChainEnergy(distance, dpka_max,
cutoff, weight, f_angle)
if residue1.Q == residue2.Q:
# acid pair or base pair
if residue1.pKa_mod < residue2.pKa_mod:
newDeterminant1 = Determinant(residue2.label, -value)
newDeterminant2 = Determinant(residue1.label, value)
else:
newDeterminant1 = Determinant(residue2.label, value)
newDeterminant2 = Determinant(residue1.label, -value)
else:
newDeterminant1 = Determinant(residue2.label, value * residue1.Q)
newDeterminant2 = Determinant(residue1.label, value * residue2.Q)
if residue1.resName not in version.exclude_sidechain_interactions:
residue1.determinants[0].append(newDeterminant1)
if residue2.resName not in version.exclude_sidechain_interactions:
residue2.determinants[0].append(newDeterminant2)
def findSSbonds(self):
"""
Finds all SS-pairs and sets location to 'BONDED' if distance < 2.50
"""
# create CYS-list if not on protein object
if self.residue_dictionary == None:
CYSlist = []
for chain in self.chains:
for residue in chain.residues:
if residue.resName == "CYS":
CYSlist.append(residue)
else:
CYSlist = self.residue_dictionary["CYS"]
# Searching all CYS pairs
for residue1 in CYSlist:
S1 = residue1.getAtom("SG")
for residue2 in CYSlist:
if residue1 == residue2:
break
else:
S2 = residue2.getAtom("SG")
distance = calculate.InterAtomDistance(S1, S2)
if distance < 2.50:
residue1.location = "BONDED"
residue2.location = "BONDED"
residue1.pKa_mod = 99.99
residue2.pKa_mod = 99.99
# cleaning out 'bonded' CYS from dictionary
self.cleanBondedResiduesFromList(self.residue_dictionary["CYS"])
return
def printCooArgAtomDistances(residue_coo, residue_arg):
"""
printing out all COO and ARG distances for debugging, picking closest + runner-up
"""
for atom_coo in residue_coo.makeDeterminantAtomList(residue_arg.resName):
for atom_arg in residue_arg.makeDeterminantAtomList(
residue_coo.resName):
distance = calculate.InterAtomDistance(atom_coo, atom_arg)
print("%3s %3s %6.2lf" % (atom_coo.name, atom_arg.name, distance))
