def gn_comparer(self, gn1, gn2, protein_conformation):
'''
'''
res1 = Residue.objects.get(protein_conformation=protein_conformation,
display_generic_number__label=dgn(
gn1, protein_conformation))
res2 = Residue.objects.get(protein_conformation=protein_conformation,
display_generic_number__label=dgn(
gn2, protein_conformation))
return res1.sequence_number - res2.sequence_number
def fetch_residues_from_pdb(self, structure, generic_numbers, modify_bulges=False, just_nums=False):
''' Fetches specific lines from pdb file by generic number (if generic number is
not available then by residue number). Returns nested OrderedDict()
with generic numbers as keys in the outer dictionary, and atom names as keys
in the inner dictionary.
@param structure: Structure, Structure object where residues should be fetched from \n
@param generic_numbers: list, list of generic numbers to be fetched \n
@param modify_bulges: boolean, set it to true when used for bulge switching. E.g. you want a 5x461
residue to be considered a 5x46 residue.
'''
output = OrderedDict()
atoms_list = []
for gn in generic_numbers:
rotamer=None
if 'x' in str(gn):
rotamer = list(Rotamer.objects.filter(structure__protein_conformation=structure.protein_conformation,
residue__display_generic_number__label=dgn(gn,structure.protein_conformation),
structure__preferred_chain=structure.preferred_chain))
else:
rotamer = list(Rotamer.objects.filter(structure__protein_conformation=structure.protein_conformation,
residue__sequence_number=gn, structure__preferred_chain=structure.preferred_chain))
if just_nums==False:
try:
gn = ggn(Residue.objects.get(protein_conformation=structure.protein_conformation,
sequence_number=gn).display_generic_number.label)
except:
pass
if len(rotamer)>1:
for i in rotamer:
if i.pdbdata.pdb.startswith('COMPND')==False:
if i.pdbdata.pdb[21] in structure.preferred_chain:
rotamer = i
break
else:
rotamer = rotamer[0]
io = StringIO(rotamer.pdbdata.pdb)
rota_struct = PDB.PDBParser(QUIET=True).get_structure('structure', io)[0]
for chain in rota_struct:
for residue in chain:
for atom in residue:
atoms_list.append(atom)
if modify_bulges==True and len(gn)==5:
output[gn.replace('x','.')[:-1]] = atoms_list
else:
try:
output[gn.replace('x','.')] = atoms_list
except:
output[str(gn)] = atoms_list
atoms_list = []
return output
def fetch_residues_from_pdb(self, structure, generic_numbers, modify_bulges=False, just_nums=False):
''' Fetches specific lines from pdb file by generic number (if generic number is
not available then by residue number). Returns nested OrderedDict()
with generic numbers as keys in the outer dictionary, and atom names as keys
in the inner dictionary.
@param structure: Structure, Structure object where residues should be fetched from \n
@param generic_numbers: list, list of generic numbers to be fetched \n
@param modify_bulges: boolean, set it to true when used for bulge switching. E.g. you want a 5x461
residue to be considered a 5x46 residue.
'''
output = OrderedDict()
atoms_list = []
for gn in generic_numbers:
rotamer=None
if 'x' in str(gn):
rotamer = list(Rotamer.objects.filter(structure__protein_conformation=structure.protein_conformation,
residue__display_generic_number__label=dgn(gn,structure.protein_conformation),
structure__preferred_chain=structure.preferred_chain))
else:
rotamer = list(Rotamer.objects.filter(structure__protein_conformation=structure.protein_conformation,
residue__sequence_number=gn, structure__preferred_chain=structure.preferred_chain))
if just_nums==False:
try:
gn = ggn(Residue.objects.get(protein_conformation=structure.protein_conformation,
sequence_number=gn).display_generic_number.label)
except:
pass
if len(rotamer)>1:
for i in rotamer:
if i.pdbdata.pdb.startswith('COMPND')==False:
if i.pdbdata.pdb[21] in structure.preferred_chain:
rotamer = i
break
else:
rotamer = rotamer[0]
io = StringIO(rotamer.pdbdata.pdb)
rota_struct = PDB.PDBParser(QUIET=True).get_structure('structure', io)[0]
for chain in rota_struct:
for residue in chain:
for atom in residue:
atoms_list.append(atom)
if modify_bulges==True and len(gn)==5:
output[gn.replace('x','.')[:-1]] = atoms_list
else:
try:
output[gn.replace('x','.')] = atoms_list
except:
output[str(gn)] = atoms_list
atoms_list = []
return output
def get_residue_distance(self, residue1, residue2):
try:
res1 = Residue.objects.get(protein_conformation__protein=self.structure.protein_conformation.protein.parent, display_generic_number__label=dgn(residue1, self.parent_prot_conf))
res2 = Residue.objects.get(protein_conformation__protein=self.structure.protein_conformation.protein.parent, display_generic_number__label=dgn(residue2, self.parent_prot_conf))
print(res1, res1.id, res2, res2.id)
try:
rota1 = Rotamer.objects.filter(structure=self.structure, residue__sequence_number=res1.sequence_number)
if len(rota1)==0:
raise Exception
except:
rota1 = Rotamer.objects.filter(structure=self.structure, residue__display_generic_number__label=dgn(residue1, self.structure.protein_conformation))
rota1 = right_rotamer_select(rota1, self.structure.preferred_chain[0])
try:
rota2 = Rotamer.objects.filter(structure=self.structure, residue__sequence_number=res2.sequence_number)
if len(rota2)==0:
raise Exception
except:
rota2 = Rotamer.objects.filter(structure=self.structure, residue__display_generic_number__label=dgn(residue2, self.structure.protein_conformation))
rota2 = right_rotamer_select(rota2, self.structure.preferred_chain[0])
rotas = [rota1, rota2]
io1 = StringIO(rotas[0].pdbdata.pdb)
rota_struct1 = PDB.PDBParser(QUIET=True).get_structure('structure', io1)[0]
io2 = StringIO(rotas[1].pdbdata.pdb)
rota_struct2 = PDB.PDBParser(QUIET=True).get_structure('structure', io2)[0]
for chain1, chain2 in zip(rota_struct1, rota_struct2):
for r1, r2 in zip(chain1, chain2):
# print(self.structure, r1.get_id()[1], r2.get_id()[1], self.calculate_CA_distance(r1, r2), self.structure.state.name)
line = '{},{},{},{},{}\n'.format(self.structure, self.structure.state.name, round(self.calculate_CA_distance(r1, r2), 2), r1.get_id()[1], r2.get_id()[1])
self.line = line
return self.calculate_CA_distance(r1, r2)
except:
try:
res1 = Residue.objects.get(protein_conformation=self.parent_prot_conf, display_generic_number__label=dgn(residue1, self.parent_prot_conf))
res2 = Residue.objects.get(protein_conformation=self.parent_prot_conf, display_generic_number__label=dgn(residue2, self.parent_prot_conf))
if self.structure_type=='refined':
pdb_data = self.structure.pdb_data.pdb
elif self.structure_type=='hommod':
pdb_data = self.structure.pdb_data.pdb
io = StringIO(pdb_data)
struct = PDB.PDBParser(QUIET=True).get_structure('structure', io)[0]
for chain in struct:
r1 = chain[res1.sequence_number]
r2 = chain[res2.sequence_number]
print(self.structure, r1.get_id()[1], r2.get_id()[1], self.calculate_CA_distance(r1, r2), self.structure.state.name)
line = '{},{},{},{},{}\n'.format(self.structure, self.structure.state.name, round(self.calculate_CA_distance(r1, r2), 2), r1.get_id()[1], r2.get_id()[1])
self.line = line
return self.calculate_CA_distance(r1, r2)
except:
print('Error: {} no matching rotamers ({}, {})'.format(self.structure.pdb_code.index, residue1, residue2))
return False
def get_residue_distance(self, residue1, residue2):
try:
res1 = Residue.objects.get(protein_conformation__protein=self.structure.protein_conformation.protein.parent, display_generic_number__label=dgn(residue1, self.parent_prot_conf))
res2 = Residue.objects.get(protein_conformation__protein=self.structure.protein_conformation.protein.parent, display_generic_number__label=dgn(residue2, self.parent_prot_conf))
print(res1, res1.id, res2, res2.id)
try:
rota1 = Rotamer.objects.filter(structure=self.structure, residue__sequence_number=res1.sequence_number)
if len(rota1)==0:
raise Exception
except:
rota1 = Rotamer.objects.filter(structure=self.structure, residue__display_generic_number__label=dgn(residue1, self.structure.protein_conformation))
rota1 = right_rotamer_select(rota1, self.structure.preferred_chain[0])
try:
rota2 = Rotamer.objects.filter(structure=self.structure, residue__sequence_number=res2.sequence_number)
if len(rota2)==0:
raise Exception
except:
rota2 = Rotamer.objects.filter(structure=self.structure, residue__display_generic_number__label=dgn(residue2, self.structure.protein_conformation))
rota2 = right_rotamer_select(rota2, self.structure.preferred_chain[0])
rotas = [rota1, rota2]
io1 = StringIO(rotas[0].pdbdata.pdb)
rota_struct1 = PDB.PDBParser(QUIET=True).get_structure('structure', io1)[0]
io2 = StringIO(rotas[1].pdbdata.pdb)
rota_struct2 = PDB.PDBParser(QUIET=True).get_structure('structure', io2)[0]
for chain1, chain2 in zip(rota_struct1, rota_struct2):
for r1, r2 in zip(chain1, chain2):
# print(self.structure, r1.get_id()[1], r2.get_id()[1], self.calculate_CA_distance(r1, r2), self.structure.state.name)
line = '{},{},{},{},{}\n'.format(self.structure, self.structure.state.name, round(self.calculate_CA_distance(r1, r2), 2), r1.get_id()[1], r2.get_id()[1])
self.line = line
return self.calculate_CA_distance(r1, r2)
except:
try:
res1 = Residue.objects.get(protein_conformation=self.parent_prot_conf, display_generic_number__label=dgn(residue1, self.parent_prot_conf))
res2 = Residue.objects.get(protein_conformation=self.parent_prot_conf, display_generic_number__label=dgn(residue2, self.parent_prot_conf))
if self.structure_type=='refined':
pdb_data = self.structure.pdb_data.pdb
elif self.structure_type=='hommod':
pdb_data = self.structure.pdb_data.pdb
io = StringIO(pdb_data)
struct = PDB.PDBParser(QUIET=True).get_structure('structure', io)[0]
for chain in struct:
r1 = chain[res1.sequence_number]
r2 = chain[res2.sequence_number]
print(self.structure, r1.get_id()[1], r2.get_id()[1], self.calculate_CA_distance(r1, r2), self.structure.state.name)
line = '{},{},{},{},{}\n'.format(self.structure, self.structure.state.name, round(self.calculate_CA_distance(r1, r2), 2), r1.get_id()[1], r2.get_id()[1])
self.line = line
return self.calculate_CA_distance(r1, r2)
except:
print('Error: {} no matching rotamers ({}, {})'.format(self.structure.pdb_code.index, residue1, residue2))
return False
def run_recog(self):
chain = self.pdb_struct[self.structure.preferred_chain[0]]
constrictions, bulges, values = OrderedDict(),OrderedDict(),OrderedDict()
for r in chain:
skip = True
for ran in self.range:
if ran[0]-1<r.get_id()[1]<ran[1]:
skip=False
if skip:
continue
try:
ca = r['CA'].get_coord()
ca2 = chain[r.get_id()[1]+2]['CA'].get_coord()
ca3 = chain[r.get_id()[1]+3]['CA'].get_coord()
ca5 = chain[r.get_id()[1]+5]['CA'].get_coord()
b0 = -1.0*(ca2-ca)
b1 = ca3-ca2
b2 = ca5-ca3
b0xb1 = np.cross(b0,b1)
b1xb2 = np.cross(b2,b1)
b0xb1_x_b1xb2 = np.cross(b0xb1, b1xb2)
y = np.dot(b0xb1_x_b1xb2, b1)*(1.0/np.linalg.norm(b1))
x = np.dot(b0xb1, b1xb2)
if self.verbose:
print(chain[r.get_id()[1]+2].get_id()[1],'-',chain[r.get_id()[1]+3].get_id()[1],np.degrees(np.arctan2(y, x)))
values[r.get_id()[1]] = np.degrees(np.arctan2(y, x))
except:
pass
for num, val in values.items():
if abs(val)>150:
count = 1
for i in range(1,4):
try:
if abs(values[num+i])>150:
count+=1
else:
raise Exception
except:
break
if count==3:
constrictions[num+2] = [val]
if abs(val)<100:
count = 1
for i in range(1,3):
try:
if abs(values[num+i])<100:
count+=1
else:
raise Exception
except:
break
if count==3:
bulges[num+2] = [val]
found_c, missed_c, found_b, missed_b = OrderedDict(),OrderedDict(),OrderedDict(),OrderedDict()
remove_c = []
db_constrictions = self.structure.protein_anomalies.filter(anomaly_type__slug='constriction')
db_constrictions_dict = OrderedDict()
for c in db_constrictions:
gn = c.generic_number.label
prev_gn = gn[:-1]+str(int(gn[-1])-1)
prev_resi = Residue.objects.get(protein_conformation=self.parent_prot_conf,
display_generic_number__label=dgn(prev_gn, self.parent_prot_conf))
db_constrictions_dict[gn] = prev_resi.sequence_number
for ca2 in constrictions:
if ca2-2<=prev_resi.sequence_number<=ca2+3:
if gn not in found_c:
found_c[gn] = prev_resi.sequence_number
remove_c.append(ca2)
else:
remove_c.append(ca2)
if gn not in found_c:
missed_c[gn] = ''
for r in remove_c:
del constrictions[r]
for ca2 in constrictions:
ca2_found = False
for key, value in found_c.items():
if ca2-2<=value<=ca2+3:
ca2_found = True
break
if not ca2_found:
missed_c[ca2] = ca2
remove_b = []
db_bulges = self.structure.protein_anomalies.filter(anomaly_type__slug='bulge')
db_bulges_dict = OrderedDict()
for b in db_bulges:
gn = b.generic_number.label
resi = Residue.objects.get(protein_conformation=self.parent_prot_conf,
display_generic_number__label=dgn(b.generic_number.label, self.parent_prot_conf))
db_bulges_dict[gn] = resi.sequence_number
for ca2 in bulges:
if ca2-2<=resi.sequence_number<=ca2+2:
if gn not in found_b:
found_b[gn] = resi.sequence_number
remove_b.append(ca2)
else:
remove_b.append(ca2)
if gn not in found_b:
missed_b[gn] = ''
for r in remove_b:
del bulges[r]
for ca2 in bulges:
ca2_found = False
for key, value in found_b.items():
if ca2-2<=value<=ca2+3:
ca2_found = True
break
if not ca2_found:
missed_b[ca2] = ca2
print('#################')
print(self.structure)
print('DB constrictions: {}'.format(db_constrictions_dict))
print('DB bulges: {}'.format(db_bulges_dict))
print('Found constrictions: {}'.format(found_c))
print('Missed constrictions: {}'.format(missed_c))
print('Found bulges: {}'.format(found_b))
print('Missed bulges: {}'.format(missed_b))
for c in missed_c:
if type(c)==type(0):
for i in range(c-3,c+3):
try:
print(i,values[i])
except:
pass
for b in missed_b:
if type(b)==type(0):
for i in range(b-3,b+3):
try:
print(i,values[i])
except:
pass
def run_recog(self):
chain = self.pdb_struct[self.structure.preferred_chain[0]]
constrictions, bulges, values = OrderedDict(), OrderedDict(
), OrderedDict()
for r in chain:
skip = True
for ran in self.range:
if ran[0] - 1 < r.get_id()[1] < ran[1]:
skip = False
if skip:
continue
try:
ca = r['CA'].get_coord()
ca2 = chain[r.get_id()[1] + 2]['CA'].get_coord()
ca3 = chain[r.get_id()[1] + 3]['CA'].get_coord()
ca5 = chain[r.get_id()[1] + 5]['CA'].get_coord()
b0 = -1.0 * (ca2 - ca)
b1 = ca3 - ca2
b2 = ca5 - ca3
b0xb1 = np.cross(b0, b1)
b1xb2 = np.cross(b2, b1)
b0xb1_x_b1xb2 = np.cross(b0xb1, b1xb2)
y = np.dot(b0xb1_x_b1xb2, b1) * (1.0 / np.linalg.norm(b1))
x = np.dot(b0xb1, b1xb2)
if self.verbose:
print(chain[r.get_id()[1] + 2].get_id()[1], '-',
chain[r.get_id()[1] + 3].get_id()[1],
np.degrees(np.arctan2(y, x)))
values[r.get_id()[1]] = np.degrees(np.arctan2(y, x))
except:
pass
for num, val in values.items():
if abs(val) > 150:
count = 1
for i in range(1, 4):
try:
if abs(values[num + i]) > 150:
count += 1
else:
raise Exception
except:
break
if count == 3:
constrictions[num + 2] = [val]
if abs(val) < 100:
count = 1
for i in range(1, 3):
try:
if abs(values[num + i]) < 100:
count += 1
else:
raise Exception
except:
break
if count == 3:
bulges[num + 2] = [val]
found_c, missed_c, found_b, missed_b = OrderedDict(), OrderedDict(
), OrderedDict(), OrderedDict()
remove_c = []
db_constrictions = self.structure.protein_anomalies.filter(
anomaly_type__slug='constriction')
db_constrictions_dict = OrderedDict()
for c in db_constrictions:
gn = c.generic_number.label
prev_gn = gn[:-1] + str(int(gn[-1]) - 1)
prev_resi = Residue.objects.get(
protein_conformation=self.parent_prot_conf,
display_generic_number__label=dgn(prev_gn,
self.parent_prot_conf))
db_constrictions_dict[gn] = prev_resi.sequence_number
for ca2 in constrictions:
if ca2 - 2 <= prev_resi.sequence_number <= ca2 + 3:
if gn not in found_c:
found_c[gn] = prev_resi.sequence_number
remove_c.append(ca2)
else:
remove_c.append(ca2)
if gn not in found_c:
missed_c[gn] = ''
for r in remove_c:
del constrictions[r]
for ca2 in constrictions:
ca2_found = False
for key, value in found_c.items():
if ca2 - 2 <= value <= ca2 + 3:
ca2_found = True
break
if not ca2_found:
missed_c[ca2] = ca2
remove_b = []
db_bulges = self.structure.protein_anomalies.filter(
anomaly_type__slug='bulge')
db_bulges_dict = OrderedDict()
for b in db_bulges:
gn = b.generic_number.label
try:
resi = Residue.objects.get(
protein_conformation=self.parent_prot_conf,
display_generic_number__label=dgn(b.generic_number.label,
self.parent_prot_conf))
except ResidueGenericNumberEquivalent.DoesNotExist:
print(
'Warning: {} ResidueGenericNumberEquivalent object missing from db'
.format(gn))
continue
db_bulges_dict[gn] = resi.sequence_number
for ca2 in bulges:
if ca2 - 2 <= resi.sequence_number <= ca2 + 2:
if gn not in found_b:
found_b[gn] = resi.sequence_number
remove_b.append(ca2)
else:
remove_b.append(ca2)
if gn not in found_b:
missed_b[gn] = ''
for r in remove_b:
del bulges[r]
for ca2 in bulges:
ca2_found = False
for key, value in found_b.items():
if ca2 - 2 <= value <= ca2 + 3:
ca2_found = True
break
if not ca2_found:
missed_b[ca2] = ca2
print('#################')
print(self.structure)
print('DB constrictions: {}'.format(db_constrictions_dict))
print('DB bulges: {}'.format(db_bulges_dict))
print('Found constrictions: {}'.format(found_c))
print('Missed constrictions: {}'.format(missed_c))
print('Found bulges: {}'.format(found_b))
print('Missed bulges: {}'.format(missed_b))
for c in missed_c:
if type(c) == type(0):
for i in range(c - 3, c + 3):
try:
print(i, values[i])
except:
pass
for b in missed_b:
if type(b) == type(0):
for i in range(b - 3, b + 3):
try:
print(i, values[i])
except:
pass
def gn_comparer(self, gn1, gn2, protein_conformation):
'''
'''
res1 = Residue.objects.get(protein_conformation=protein_conformation, display_generic_number__label=dgn(gn1,protein_conformation))
res2 = Residue.objects.get(protein_conformation=protein_conformation, display_generic_number__label=dgn(gn2,protein_conformation))
return res1.sequence_number-res2.sequence_number
