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from pdb2pka.graph_cut.protein_complex import ProteinComplex
from pdb2pka.graph_cut.titration_curve import get_titration_curves
def _add_state_pair(pc, inter_avg,
group1_type, group1_chain, group1_loc, group1_state,
group2_type, group2_chain, group2_loc, group2_state):
pc.add_residue(group1_type, group1_chain, group1_loc)
pc.add_residue(group2_type, group2_chain, group2_loc)
if (group1_type, group1_chain, group1_loc) != (group2_type, group2_chain, group2_loc):
instance1 = pc.get_instance(group1_type, group1_chain, group1_loc, group1_state)
instance2 = pc.get_instance(group2_type, group2_chain, group2_loc, group2_state)
pc.interaction_energies[instance1, instance2] = inter_avg
flipped_inter_avg = pc.interaction_energies.get((instance2, instance1))
if flipped_inter_avg is not None:
diff = abs(inter_avg - flipped_inter_avg)
if diff > 0.0:
print(group1_type, group1_chain, group1_loc, group1_state)
print(group2_type, group2_chain, group2_loc, group2_state)
def create_protein_complex_from_matrix(correct_matrix):
"""Builds a protein complex from a matrix returned from pKaRoutines.correct_matrix"""
protein_complex = ProteinComplex()
for pKa1 in correct_matrix:
for titration1 in correct_matrix[pKa1]:
for state1 in correct_matrix[pKa1][titration1]:
for pKa2 in correct_matrix[pKa1][titration1][state1]:
for titration2 in correct_matrix[pKa1][titration1][state1][pKa2]:
for state2 in correct_matrix[pKa1][titration1][state1][pKa2][titration2]:
inter_avg = correct_matrix[pKa1][titration1][state1][pKa2][titration2][state2]
res1 = pKa1.residue
res2 = pKa2.residue
_add_state_pair(protein_complex, inter_avg,
pKa1.pKaGroup.name, res1.chainID, str(res1.resSeq), state1,
pKa2.pKaGroup.name, res2.chainID, str(res2.resSeq), state2)
return protein_complex
def process_desolv_and_background(protein_complex, pKa):
"""Applies the background and desolvation energies from a pKa to a protein complex"""
res_type = pKa.pKaGroup.name
chain = pKa.residue.chainID
location = str(pKa.residue.resSeq)
for state, energy in pKa.desolvation.items():
_process_desolv_or_background_line(protein_complex, res_type, chain, location, state, energy)
for state, energy in pKa.background.items():
_process_desolv_or_background_line(protein_complex, res_type, chain, location, state, energy)
def _process_desolv_or_background_line(protein_complex, res_type, chain, location, state_name, energy):
instance = protein_complex.get_instance(res_type, chain, location, state_name)
instance.energy += energy
def _create_protein_complex_from_pKa(pKa):
protein_complex = ProteinComplex()
res = pKa.residue
group = pKa.pKaGroup
#Grab all of the states
states = []
for titration1 in group.DefTitrations:
states.extend(titration1.allstates)
states.sort()
for state1 in states:
for state2 in states:
_add_state_pair(protein_complex, 0.0,
group.name, res.chainID, str(res.resSeq), state1,
group.name, res.chainID, str(res.resSeq), state2)
return protein_complex
def curve_for_one_group(pKa):
"""Roughly equivalent to pka_help.titrate_one_group
Titrate a single group and return the titration curve for it.
"""
protein_complex = _create_protein_complex_from_pKa(pKa)
process_desolv_and_background(protein_complex, pKa)
protein_complex.simplify()
curve = get_titration_curves(protein_complex)
return curve
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