def pdb_contacts(pdb, chain, dist):
i = 0
# Get chain code from 6th letter in pdb name
pdb_chain = pdb_getchain(pdb, chain)
ppb = CaPPBuilder()
# Initialise building of a polypeptide and its sequence
# If a mutated residue is present in a chain it is classed as a hetatm
# However, not all hetatms in a chain are part of the sequence. The CaPPBuilder
# makes sequences by requiring CA-CA distances to be <4.3A. Common hetatms are
# identified such that an MSE hetatm will be replaced by an M in the sequence
polypepTot = ppb.build_peptides(pdb_chain, aa_only=False)[0]
sequen = polypepTot.get_sequence()
# Add to the polypeptide
for polypep_raw in ppb.build_peptides(pdb_chain, aa_only=False)[1:]:
sequen += (polypep_raw.get_sequence())
polypepTot += polypep_raw
i = 0
# Sometimes the terminal residue in a protein isn't fully resolved
last_res = polypepTot[-1]
if last_res.has_id("CA") or last_res.has_id("CB"):
polypep = polypepTot # If resolved take whole AA
file_seq.write(">sequence\n%s\n" % sequen)
file_seq.write("%s" % sequen)
else:
polypep = polypepTot[:-1] # Otherwise take all but the last AA
file_seq.write(">sequence\n%s\n" % sequen[:-1])
file_seq.write("%s" % sequen[:-1])
file_map.write(str(len(polypep)) + "\n")
# sys.stderr.write(pdb+'\n')
for residue1 in polypep:
# Quite frequently residues do not have resolved CB, in which case use CA
# If no CA exists, print ERROR. Grep the output if running unsupervised.
try:
if residue1.has_id("CB"): #get_resname() == "GLY":
c_alpha = residue1["CB"]
else:
c_alpha = residue1["CA"]
except:
sys.stdout.write("ERROR")
raise
i += 1
j = 0
for residue2 in polypep:
try:
if residue2.has_id("CB"): #get_resname() == "GLY":
c_alpha2 = residue2["CB"]
else:
c_alpha2 = residue2["CA"]
except:
file_map.write("ERROR")
raise
j += 1
if (norm(c_alpha.get_coord(), c_alpha2.get_coord()) <
dist): # 3.5 ):
file_map.write("%d %d\n" % (i - 1, j - 1))
def pdb_polypep(pdb, chain, trim):
i = 0
# Get chain code from 6th letter in pdb name
pdb_chain = pdb_getchain(pdb, chain)
ppb = CaPPBuilder()
# Initialise building of a polypeptide and its sequence
# If a mutated residue is present in a chain it is classed as a hetatm
# However, not all hetatms in a chain are part of the sequence. The CaPPBuilder
# makes sequences by requiring CA-CA distances to be <4.3A. Common hetatms are
# identified such that an MSE hetatm will be replaced by an M in the sequence
polypepTot = ppb.build_peptides(pdb_chain, aa_only=False)[0]
sequen = polypepTot.get_sequence()
# Add to the polypeptide
for polypep_raw in ppb.build_peptides(pdb_chain, aa_only=False)[1:]:
sequen += (polypep_raw.get_sequence())
polypepTot += polypep_raw
# Remove unstructured terminal ends
if trim:
polypepTot = pp_trim(polypepTot)
# Sometimes the terminal residue in a protein isn't fully resolved
last_res = polypepTot[-1]
if last_res.has_id("CA") or last_res.has_id("CB"):
polypep = polypepTot # If resolved take whole AA
# file_seq.write(">sequence\n%s\n" %sequen)
## file_seq.write("%s" %sequen)
else:
polypep = polypepTot[:-1] # Otherwise take all but the last AA
# file_seq.write(">sequence\n%s\n" %sequen[:-1])
## file_seq.write("%s" %sequen[:-1])
# file_map.write( str(len(polypep)) +"\n" )
# sys.stderr.write(pdb+'\n')
return polypep
def test_ca_ca(self):
"""Extract polypeptides using CA-CA."""
ppbuild = CaPPBuilder()
polypeptides = ppbuild.build_peptides(self.structure[1])
self.assertEqual(len(polypeptides), 1)
pp = polypeptides[0]
# Check the start and end positions
self.assertEqual(pp[0].get_id()[1], 2)
self.assertEqual(pp[-1].get_id()[1], 86)
def test_cappbuilder_tau(self):
"""Test tau angles calculated with CaPPBuilder."""
ppb = CaPPBuilder()
pp = ppb.build_peptides(self.structure)
taus = pp[1].get_tau_list()
self.assertAlmostEqual(taus[0], 0.3597907225123525, places=3)
self.assertAlmostEqual(taus[1], 0.43239284636769254, places=3)
self.assertAlmostEqual(taus[2], 0.99820157492712114, places=3)
thetas = pp[2].get_theta_list()
self.assertAlmostEqual(thetas[0], 1.6610069445335354, places=3)
self.assertAlmostEqual(thetas[1], 1.7491703334817772, places=3)
self.assertAlmostEqual(thetas[2], 2.0702447422720143, places=3)
def test_cappbuilder_real(self):
"""Test CaPPBuilder on real PDB file."""
ppb = CaPPBuilder()
pp = ppb.build_peptides(self.structure)
pp0_seq = pp[0].get_sequence()
pp1_seq = pp[1].get_sequence()
pp2_seq = pp[2].get_sequence()
self.assertEqual(pp0_seq, "DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW")
self.assertEqual(pp1_seq, "TETLLVQNANPDCKTILKALGPGATLEE")
self.assertEqual(pp2_seq, "TACQG")
self.assertEqual(
[ca.serial_number for ca in pp[0].get_ca_list()],
[
10,
18,
26,
37,
46,
50,
57,
66,
75,
82,
93,
104,
112,
124,
131,
139,
150,
161,
173,
182,
189,
197,
208,
213,
222,
231,
236,
242,
251,
260,
267,
276,
284,
],
)
def test_ca_ca(self):
"""Extract polypeptides using CA-CA."""
ppbuild = CaPPBuilder()
polypeptides = ppbuild.build_peptides(self.structure[1])
self.assertEqual(len(polypeptides), 1)
pp = polypeptides[0]
# Check the start and end positions
self.assertEqual(pp[0].get_id()[1], 2)
self.assertEqual(pp[-1].get_id()[1], 86)
# Check the sequence
s = pp.get_sequence()
self.assertTrue(isinstance(s, Seq))
self.assertEqual(s.alphabet, generic_protein)
self.assertEqual("RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGER"
"SDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYRC",
str(s))
def test_ca_ca(self):
"""Extract polypeptides using CA-CA."""
ppbuild = CaPPBuilder()
polypeptides = ppbuild.build_peptides(self.structure[1])
self.assertEqual(len(polypeptides), 1)
pp = polypeptides[0]
# Check the start and end positions
self.assertEqual(pp[0].get_id()[1], 2)
self.assertEqual(pp[-1].get_id()[1], 86)
# Check the sequence
s = pp.get_sequence()
self.assertTrue(isinstance(s, Seq))
self.assertEqual(s.alphabet, generic_protein)
self.assertEqual("RCGSQGGGSTCPGLRCCSIWGWCGDSEPYCGRTCENKCWSGER"
"SDHRCGAAVGNPPCGQDRCCSVHGWCGGGNDYCSGGNCQYRC",
str(s))
def test_cappbuilder_real_nonstd(self):
"""Test CaPPBuilder on real PDB file allowing non-standard amino acids."""
ppb = CaPPBuilder()
pp = ppb.build_peptides(self.structure, False)
self.assertEqual(len(pp), 1)
# Check the start and end positions
self.assertEqual(pp[0][0].get_id()[1], 151)
self.assertEqual(pp[0][-1].get_id()[1], 220)
# Check the sequence
s = pp[0].get_sequence()
self.assertIsInstance(s, Seq)
# Here non-standard MSE are shown as M
self.assertEqual(
"MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQG",
s)
def pdb_sequence(pdb_file, id=None, method="order"):
from Bio.PDB import PDBParser, CaPPBuilder
from Bio.PDB.Polypeptide import three_to_one
if id is None:
id = util.make_id_from_file_name(pdb_file)
parser = PDBParser()
structure = parser.get_structure(id, pdb_file)
seq_chains = []
for chain in structure.get_chains():
id_chain = chain.get_id()
if method == "distance":
ppb = CaPPBuilder()
seq = sum((pp.get_sequence() for pp in ppb.build_peptides(chain)),
Seq("", IUPAC.protein))
seq_spec = None #TODO: implement
elif method == "order":
seq = []
seq_spec = []
for res in chain.get_residues():
seq.append(three_to_one(res.get_resname()))
## from Bio docs, res.get_full_id() returns: ("1abc", 0, "A", (" ", 10, "A"))
fid = res.get_full_id()
seq_spec.append(
pdb_seq_spec(chain=fid[-2].strip(),
resn=res.get_resname(),
resi=fid[-1][-2],
ins=fid[-1][-1].strip()))
seq = Seq("".join(seq), IUPAC.protein)
else:
raise ValueError("Unknown method: {}".format(method))
seq_chains.append(
dict(id_chain=id_chain,
seq_rec=SeqRecord(seq,
id="{}_{}".format(id, id_chain),
description=""),
seq_spec=seq_spec))
chains_map = dict(((x["id_chain"], x) for x in seq_chains))
return pdb_seqs(id=id, chains=seq_chains, chains_map=chains_map)
#from TCRmodeller_functions import *
from subprocess import Popen, PIPE
script, filename, tag, chainid = argv
tmpdir = os.getcwd()
hmmscan_program = '/TCRmodeller/programs/hmmer/hmmscan'
profit_program = '/Users/ragul/profit/ProFitV3.1/src/profit'
f2 = open('temp.fa','w+')
pdbfile = parser.get_structure("PDB", filename)
mychain = pdbfile[0][chainid]
f2.write(">"+filename+"\n")
for ppe in ppb.build_peptides(mychain):
f2.write(str(ppe.get_sequence())+"\n")
f2.close()
def find_CDRs(tcr_seq, hmmscan_program, tmpdir, tag):
CDR1_start_pos = 0
CDR1_end_pos = 0
CDR2_start_pos = 0
CDR2_end_pos = 0
CDR3_start_pos = 0
CDR3_end_pos = 0
HV4_start_pos = 0
class nonHetSelect(Select):
def accept_residue(self,residue):
if residue.id[0] == ' ':
return 1
else:
return 0
gzpdbfile_path = "/TCRmodeller/PDB_RELEASE/pdb_structures" + '/%s/pdb%s.ent.gz' %(pdbcode[1:3], pdbcode)
gzpdbfile = gzip.open(gzpdbfile_path, 'rb')
pdbfile = parser.get_structure("PDB", gzpdbfile)
mychaina = pdbfile[0][chainida]
io.set_structure(mychaina)
io.save('tmpa.pdb', nonHetSelect())
faseqa = ""
for ppe in ppb.build_peptides(mychaina):
faseqa += str(ppe.get_sequence())
print "faseqa : ", faseqa
mychainb = pdbfile[0][chainidb]
io.set_structure(mychainb)
io.save('tmpb.pdb', nonHetSelect())
faseqb = ""
for ppe in ppb.build_peptides(mychainb):
faseqb += str(ppe.get_sequence())
print "faseqb : ", faseqb
regexa = "[A-Z]{0,23}C[A-Z]([A-Z]{8,12}W)[YF][A-Z]{13}([A-Z]{6,11})[A-Z]{15,30}[DL][A-Z]{2,3}Y[A-Z][CW][A-Z]([A-Z]{7,16}[FW])G[A-Z]G[A-Z]{0,7}[PA]*"
regexb = "[A-Z]{0,23}C[A-Z]([A-Z]{8,12}W)[Y][A-Z]{13}([A-Z]{6,11})[A-Z]{15,40}[YLF][A-Z][CW][A-Z]([A-Z]{7,17}[F])G[A-Z]G[A-Z]{0,7}[E]*"
