def __init__(self, interaction_file, desolv_file, background_file):
self.protein_complex = ProteinComplex()
self.ingest_interaction_file(interaction_file)
self.ingest_desolv_or_background_file(desolv_file)
self.ingest_desolv_or_background_file(background_file)
self.protein_complex.simplify()
self.protein_complex.normalize(0.0)
def __init__(self, interaction_file, desolv_file, background_file):
self.protein_complex = ProteinComplex()
self.ingest_interaction_file(interaction_file)
self.ingest_desolv_or_background_file(desolv_file)
self.ingest_desolv_or_background_file(background_file)
self.protein_complex.simplify()
self.protein_complex.normalize(0.0)
class Protein(object):
def __init__(self, interaction_file, desolv_file, background_file):
self.protein_complex = ProteinComplex()
self.ingest_interaction_file(interaction_file)
self.ingest_desolv_or_background_file(desolv_file)
self.ingest_desolv_or_background_file(background_file)
self.protein_complex.simplify()
self.protein_complex.normalize(0.0)
def ingest_interaction_file(self, interaction_file):
interaction_file.seek(0)
#Get and ditch header
interaction_file.readline()
interaction_file.readline()
for line in interaction_file:
self.process_interaction_line(line)
def process_interaction_line(self, line):
split_line = line.split()
group1, group2, group1_state, group2_state, _, _, inter_avg = split_line
_, group1_chain, group1_loc, _, group1_type = re.split('[_:]', group1)
_, group2_chain, group2_loc, _, group2_type = re.split('[_:]', group2)
inter_avg = float(inter_avg)
pc = self.protein_complex
pc.add_residue(group1_type, group1_chain, group1_loc)
pc.add_residue(group2_type, group2_chain, group2_loc)
#We skip all interactions with self. They should always be 0.
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
#All interaction files SHOULD be symmetric. PDB2PKA makes them that way.
#This just makes sure that is true, especially if we tweak stuff by hand.
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
print "Difference:", diff
else:
#This makes it easier to make test files and does not prevent
# the sanity checking above.
pc.interaction_energies[instance2, instance1] = inter_avg
elif inter_avg != 0:
print "Non-zero interaction energy with self:", inter_avg
print group1_type, group1_chain, group1_loc, group1_state, group2_state
def ingest_desolv_or_background_file(self, file_obj):
file_obj.seek(0)
for line in file_obj:
self.process_desolv_or_background_line(line)
def process_desolv_or_background_line(self, line):
split_line = line.split()
type_chain_loc, state_name, energy_str = split_line
energy = float(energy_str)
res_type, chain, location = type_chain_loc.split('_')
instance = self.protein_complex.get_instance(res_type, chain, location,
state_name)
instance.energy += energy
class Protein(object):
def __init__(self, interaction_file, desolv_file, background_file):
self.protein_complex = ProteinComplex()
self.ingest_interaction_file(interaction_file)
self.ingest_desolv_or_background_file(desolv_file)
self.ingest_desolv_or_background_file(background_file)
self.protein_complex.simplify()
self.protein_complex.normalize(0.0)
def ingest_interaction_file(self, interaction_file):
interaction_file.seek(0)
#Get and ditch header
interaction_file.readline()
interaction_file.readline()
for line in interaction_file:
self.process_interaction_line(line)
def process_interaction_line(self, line):
split_line = line.split()
group1, group2, group1_state, group2_state, _, _, inter_avg = split_line
_, group1_chain, group1_loc, _, group1_type = re.split('[_:]', group1)
_, group2_chain, group2_loc, _, group2_type = re.split('[_:]', group2)
inter_avg = float(inter_avg)
pc = self.protein_complex
pc.add_residue(group1_type, group1_chain, group1_loc)
pc.add_residue(group2_type, group2_chain, group2_loc)
#We skip all interactions with self. They should always be 0.
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
#All interaction files SHOULD be symmetric. PDB2PKA makes them that way.
#This just makes sure that is true, especially if we tweak stuff by hand.
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
print "Difference:", diff
else:
#This makes it easier to make test files and does not prevent
# the sanity checking above.
pc.interaction_energies[instance2, instance1] = inter_avg
elif inter_avg != 0:
print "Non-zero interaction energy with self:", inter_avg
print group1_type, group1_chain, group1_loc, group1_state, group2_state
def ingest_desolv_or_background_file(self, file_obj):
file_obj.seek(0)
for line in file_obj:
self.process_desolv_or_background_line(line)
def process_desolv_or_background_line(self, line):
split_line = line.split()
type_chain_loc, state_name, energy_str = split_line
energy = float(energy_str)
res_type, chain, location = type_chain_loc.split('_')
instance = self.protein_complex.get_instance(res_type, chain, location, state_name)
instance.energy += energy
