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 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 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_insertions(self):
"""Test file with residue insertion codes."""
parser = MMCIFParser(QUIET=1)
with warnings.catch_warnings():
warnings.simplefilter("ignore", PDBConstructionWarning)
structure = parser.get_structure("example", "PDB/4ZHL.cif")
for ppbuild in [PPBuilder(), CaPPBuilder()]:
# First try allowing non-standard amino acids,
polypeptides = ppbuild.build_peptides(structure[0], False)
self.assertEqual(len(polypeptides), 2)
pp = polypeptides[0]
# Check the start and end positions (first segment only)
self.assertEqual(pp[0].get_id()[1], 16)
self.assertEqual(pp[-1].get_id()[1], 244)
# Check the sequence
refseq = (
"IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGR"
"SRLNSNTQGEMKFEVENLILHKDYSADTLAYHNDIALLKIRSKEGRCAQPSRTIQTIALPSMY"
"NDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQW"
"KTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKE"
)
s = pp.get_sequence()
self.assertIsInstance(s, Seq)
self.assertEqual(s.alphabet, generic_protein)
self.assertEqual(refseq, 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_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 read_pdb_file(file_name, name=None):
"""
Extract info from a PDB file
file_name: path of pdb file
name: name of the structure (default name of the file without extension)
return:: (structure,R,polypeptides,sequence,seq_res_dict)
structure: structure object
residues: list of residues
polypeptides: list of polypeptides in the structure
sequence: combined sequence (for all polypeptides)
seq_res_dict: Sequence to residues mapping index list, sequence[i] corresponds to
residues[seq_res_dict[i]]
"""
if name is None:
name = splitext(file_name)[0]
structure = PDBParser().get_structure(name, file_name)
if len(structure) != 1:
raise ValueError("Unexpected number of structures in " + name)
# residues = Selection.unfold_entities(structure, 'R')
atoms = Selection.unfold_entities(structure, 'A')
polypeptides = PPBuilder().build_peptides(structure)
if len(polypeptides) == 0:
polypeptides = CaPPBuilder().build_peptides(structure)
sequence = ''.join([str(p.get_sequence()) for p in polypeptides])
residues = [
residue for polypeptide in polypeptides for residue in polypeptide
]
protein_name = os.path.basename(file_name).replace(".pdb", "")
return protein_name, structure, residues, sequence, atoms
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 test_parser(self):
"""Extract polypeptides from 1A80."""
parser = MMCIFParser()
structure = parser.get_structure("example", "PDB/1A8O.cif")
self.assertEqual(len(structure), 1)
for ppbuild in [PPBuilder(), CaPPBuilder()]:
# ==========================================================
# Check that serial_num (model column) is stored properly
self.assertEqual(structure[0].serial_num, 1)
# First try allowing non-standard amino acids,
polypeptides = ppbuild.build_peptides(structure[0], False)
self.assertEqual(len(polypeptides), 1)
pp = polypeptides[0]
# Check the start and end positions
self.assertEqual(pp[0].get_id()[1], 151)
self.assertEqual(pp[-1].get_id()[1], 220)
# Check the sequence
s = pp.get_sequence()
self.assertTrue(isinstance(s, Seq))
self.assertEqual(s.alphabet, generic_protein)
# Here non-standard MSE are shown as M
self.assertEqual(
"MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQ"
"NANPDCKTILKALGPGATLEEMMTACQG", str(s))
# ==========================================================
# Now try strict version with only standard amino acids
# Should ignore MSE 151 at start, and then break the chain
# at MSE 185, and MSE 214,215
polypeptides = ppbuild.build_peptides(structure[0], True)
self.assertEqual(len(polypeptides), 3)
# First fragment
pp = polypeptides[0]
self.assertEqual(pp[0].get_id()[1], 152)
self.assertEqual(pp[-1].get_id()[1], 184)
s = pp.get_sequence()
self.assertTrue(isinstance(s, Seq))
self.assertEqual(s.alphabet, generic_protein)
self.assertEqual("DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW", str(s))
# Second fragment
pp = polypeptides[1]
self.assertEqual(pp[0].get_id()[1], 186)
self.assertEqual(pp[-1].get_id()[1], 213)
s = pp.get_sequence()
self.assertTrue(isinstance(s, Seq))
self.assertEqual(s.alphabet, generic_protein)
self.assertEqual("TETLLVQNANPDCKTILKALGPGATLEE", str(s))
# Third fragment
pp = polypeptides[2]
self.assertEqual(pp[0].get_id()[1], 216)
self.assertEqual(pp[-1].get_id()[1], 220)
s = pp.get_sequence()
self.assertTrue(isinstance(s, Seq))
self.assertEqual(s.alphabet, generic_protein)
self.assertEqual("TACQG", str(s))
def testModels(self):
"""Test file with multiple models."""
parser = MMCIFParser(QUIET=1)
f_parser = FastMMCIFParser(QUIET=1)
with warnings.catch_warnings():
warnings.simplefilter("ignore", PDBConstructionWarning)
structure = parser.get_structure("example", "PDB/1LCD.cif")
f_structure = f_parser.get_structure("example", "PDB/1LCD.cif")
self.assertEqual(len(structure), 3)
self.assertEqual(len(f_structure), 3)
for ppbuild in [PPBuilder(), CaPPBuilder()]:
# ==========================================================
# Check that serial_num (model column) is stored properly
self.assertEqual(structure[0].serial_num, 1)
self.assertEqual(structure[1].serial_num, 2)
self.assertEqual(structure[2].serial_num, 3)
# First try allowing non-standard amino acids,
polypeptides = ppbuild.build_peptides(structure[0], False)
self.assertEqual(len(polypeptides), 1)
pp = polypeptides[0]
# Check the start and end positions
self.assertEqual(pp[0].get_id()[1], 1)
self.assertEqual(pp[-1].get_id()[1], 51)
# Check the sequence
s = pp.get_sequence()
self.assertIsInstance(s, Seq)
self.assertEqual(s.alphabet, generic_protein)
# Here non-standard MSE are shown as M
self.assertEqual(
"MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR", str(s)
)
# ==========================================================
# Now try strict version with only standard amino acids
polypeptides = ppbuild.build_peptides(structure[0], True)
self.assertEqual(len(polypeptides), 1)
pp = polypeptides[0]
# Check the start and end positions
self.assertEqual(pp[0].get_id()[1], 1)
self.assertEqual(pp[-1].get_id()[1], 51)
# Check the sequence
s = pp.get_sequence()
self.assertIsInstance(s, Seq)
self.assertEqual(s.alphabet, generic_protein)
self.assertEqual(
"MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR", str(s)
)
# This structure contains several models with multiple lengths.
# The tests were failing.
structure = parser.get_structure("example", "PDB/2OFG.cif")
self.assertEqual(len(structure), 3)
def test_polypeptide(self):
"""Tests on polypetide class and methods."""
p = PDBParser(PERMISSIVE=True)
pdb1 = "PDB/1A8O.pdb"
s = p.get_structure("scr", pdb1)
ppb = PPBuilder()
pp = ppb.build_peptides(s)
self.assertEqual(str(pp[0].get_sequence()),
"DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW")
self.assertEqual(str(pp[1].get_sequence()),
"TETLLVQNANPDCKTILKALGPGATLEE")
self.assertEqual(str(pp[2].get_sequence()), "TACQG")
phi_psi = pp[0].get_phi_psi_list()
self.assertEqual(phi_psi[0][0], None)
self.assertAlmostEqual(phi_psi[0][1], -0.46297171497725553, places=3)
self.assertAlmostEqual(phi_psi[1][0], -1.0873937604007962, places=3)
self.assertAlmostEqual(phi_psi[1][1], 2.1337707832637109, places=3)
self.assertAlmostEqual(phi_psi[2][0], -2.4052232743651878, places=3)
self.assertAlmostEqual(phi_psi[2][1], 2.3807316946081554, places=3)
phi_psi = pp[1].get_phi_psi_list()
self.assertEqual(phi_psi[0][0], None)
self.assertAlmostEqual(phi_psi[0][1], -0.6810077089092923, places=3)
self.assertAlmostEqual(phi_psi[1][0], -1.2654003477656888, places=3)
self.assertAlmostEqual(phi_psi[1][1], -0.58689987042756309, places=3)
self.assertAlmostEqual(phi_psi[2][0], -1.7467679151684763, places=3)
self.assertAlmostEqual(phi_psi[2][1], -1.5655066256698336, places=3)
phi_psi = pp[2].get_phi_psi_list()
self.assertEqual(phi_psi[0][0], None)
self.assertAlmostEqual(phi_psi[0][1], -0.73222884210889716, places=3)
self.assertAlmostEqual(phi_psi[1][0], -1.1044740234566259, places=3)
self.assertAlmostEqual(phi_psi[1][1], -0.69681334592782884, places=3)
self.assertAlmostEqual(phi_psi[2][0], -1.8497413300164958, places=3)
self.assertAlmostEqual(phi_psi[2][1], 0.34762889834809058, places=3)
ppb = CaPPBuilder()
pp = ppb.build_peptides(s)
self.assertEqual(str(pp[0].get_sequence()),
"DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW")
self.assertEqual(str(pp[1].get_sequence()),
"TETLLVQNANPDCKTILKALGPGATLEE")
self.assertEqual(str(pp[2].get_sequence()), "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
])
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 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)
def run_test():
from Bio.PDB import PDBParser, PPBuilder, CaPPBuilder
# first make a PDB parser object
p = PDBParser(PERMISSIVE=1)
# get the structure, call it "example"
structure = p.get_structure("example", "PDB/a_structure.pdb")
# now loop over content and print some info
for model in structure.get_list():
model_id = model.get_id()
print "Model %i contains %i chains." % (model_id, len(model))
for chain in model.get_list():
chain_id = chain.get_id()
print "\tChain '%s' contains %i residues." % (chain_id, len(chain))
for residue in chain.get_list():
residue_id = residue.get_id()
hetfield, resseq, icode = residue_id
print "\t\tResidue ('%s', %i, '%s') contains %i atoms." % (
hetfield, resseq, icode, len(residue))
# check if there is disorder due to a point mutation --- this is rare
if residue.is_disordered() == 2:
print "\t\t\tThere is a point mutation present in the crystal at this position."
s = "\t\t\tResidues at this position are "
for resname in residue.disordered_get_id_list():
s = s + resname + " "
print s[:-1] + "."
# count the number of disordered atoms
if residue.is_disordered() == 1:
disordered_count = 0
for atom in residue.get_list():
if atom.is_disordered():
disordered_count = disordered_count + 1
if disordered_count > 0:
print "\t\t\tThe residue contains %i disordered atoms." % disordered_count
print "Polypeptides using C-N"
ppb = PPBuilder()
for pp in ppb.build_peptides(structure[1]):
print pp
print "Polypeptides using CA-CA"
ppb = CaPPBuilder()
for pp in ppb.build_peptides(structure[1]):
print pp
print "NeighborSearch test"
quick_neighbor_search_test()
def testModels(self):
"""Test file with multiple models"""
parser = MMCIFParser()
structure = parser.get_structure("example", "PDB/1LCD.cif")
self.assertEqual(len(structure), 3)
for ppbuild in [PPBuilder(), CaPPBuilder()]:
#==========================================================
# Check that serial_num (model column) is stored properly
self.assertEqual(structure[0].serial_num, 1)
self.assertEqual(structure[1].serial_num, 2)
self.assertEqual(structure[2].serial_num, 3)
#First try allowing non-standard amino acids,
polypeptides = ppbuild.build_peptides(structure[0], False)
self.assertEqual(len(polypeptides), 1)
pp = polypeptides[0]
# Check the start and end positions
self.assertEqual(pp[0].get_id()[1], 1)
self.assertEqual(pp[-1].get_id()[1], 51)
# Check the sequence
s = pp.get_sequence()
self.assertTrue(isinstance(s, Seq))
self.assertEqual(s.alphabet, generic_protein)
#Here non-standard MSE are shown as M
self.assertEqual(
"MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR", str(s))
#==========================================================
#Now try strict version with only standard amino acids
polypeptides = ppbuild.build_peptides(structure[0], True)
self.assertEqual(len(polypeptides), 1)
pp = polypeptides[0]
# Check the start and end positions
self.assertEqual(pp[0].get_id()[1], 1)
self.assertEqual(pp[-1].get_id()[1], 51)
# Check the sequence
s = pp.get_sequence()
self.assertTrue(isinstance(s, Seq))
self.assertEqual(s.alphabet, generic_protein)
self.assertEqual(
"MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR", str(s))
def _remove_missing_res(self, record: SeqRecord, pdb: Path):
structure = PDBParser().get_structure(record.id, pdb)
sequence = ''.join([
str(_.get_sequence())
for _ in CaPPBuilder().build_peptides(structure, aa_only=False)
])
path = PairwiseAligner().align(record.seq.ungap('-'), sequence)[0].path
gaps = []
for i, _ in enumerate(path[:-1]):
if path[i][1] == path[i + 1][1]:
gaps.append((path[i][0], path[i + 1][0]))
gaps = list(reversed(gaps))
mut = record.seq.tomutable()
for gap in gaps:
i = 0
for k, res in enumerate(mut):
if res == '-':
continue
if gap[0] <= i < gap[1]:
mut[k] = '-'
i += 1
record.seq = mut.toseq()
return record
#!/usr/bin/env python
import os, sys
from sys import argv
from Bio import SearchIO
from Bio.PDB import PDBParser, CaPPBuilder
parser = PDBParser(PERMISSIVE=1,QUIET=True)
ppb = CaPPBuilder()
#sys.path.append('/Users/ragul/Rosetta/tools/antibody/tcr')
#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()
#!/usr/bin/env python
import sys, os, re
import gzip
from sys import argv
from Bio.PDB import PDBParser, Selection, PDBIO, CaPPBuilder, Select
parser = PDBParser(PERMISSIVE=1,QUIET=True)
io = PDBIO()
ppb = CaPPBuilder()
import rosetta
rosetta.init(extra_options = "-database /TCRmodeller/programs/PyRosetta/database -mute basic -mute core -mute protocols -renumber_pdb -ignore_unrecognized_res -ignore_zero_occupancy false")
import rosetta.protocols.grafting as graft
script, pdbcode, chainida, chainidb = argv
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 = ""
def test_parsers(self):
"""Extract polypeptides from 1A80."""
parser = MMCIFParser()
fast_parser = FastMMCIFParser()
structure = parser.get_structure("example", "PDB/1A8O.cif")
f_structure = fast_parser.get_structure("example", "PDB/1A8O.cif")
self.assertEqual(len(structure), 1)
self.assertEqual(len(f_structure), 1)
for ppbuild in [PPBuilder(), CaPPBuilder()]:
# ==========================================================
# Check that serial_num (model column) is stored properly
self.assertEqual(structure[0].serial_num, 1)
self.assertEqual(f_structure[0].serial_num, structure[0].serial_num)
# First try allowing non-standard amino acids,
polypeptides = ppbuild.build_peptides(structure[0], False)
f_polypeptides = ppbuild.build_peptides(f_structure[0], False)
self.assertEqual(len(polypeptides), 1)
self.assertEqual(len(f_polypeptides), 1)
pp = polypeptides[0]
f_pp = f_polypeptides[0]
# Check the start and end positions
self.assertEqual(pp[0].get_id()[1], 151)
self.assertEqual(pp[-1].get_id()[1], 220)
self.assertEqual(f_pp[0].get_id()[1], 151)
self.assertEqual(f_pp[-1].get_id()[1], 220)
# Check the sequence
s = pp.get_sequence()
f_s = f_pp.get_sequence()
self.assertEqual(s, f_s) # enough to test this
self.assertIsInstance(s, Seq)
self.assertEqual(s.alphabet, generic_protein)
# Here non-standard MSE are shown as M
self.assertEqual(
"MDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQ"
"NANPDCKTILKALGPGATLEEMMTACQG",
str(s),
)
# ==========================================================
# Now try strict version with only standard amino acids
# Should ignore MSE 151 at start, and then break the chain
# at MSE 185, and MSE 214,215
polypeptides = ppbuild.build_peptides(structure[0], True)
self.assertEqual(len(polypeptides), 3)
# First fragment
pp = polypeptides[0]
self.assertEqual(pp[0].get_id()[1], 152)
self.assertEqual(pp[-1].get_id()[1], 184)
s = pp.get_sequence()
self.assertIsInstance(s, Seq)
self.assertEqual(s.alphabet, generic_protein)
self.assertEqual("DIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNW", str(s))
# Second fragment
pp = polypeptides[1]
self.assertEqual(pp[0].get_id()[1], 186)
self.assertEqual(pp[-1].get_id()[1], 213)
s = pp.get_sequence()
self.assertIsInstance(s, Seq)
self.assertEqual(s.alphabet, generic_protein)
self.assertEqual("TETLLVQNANPDCKTILKALGPGATLEE", str(s))
# Third fragment
pp = polypeptides[2]
self.assertEqual(pp[0].get_id()[1], 216)
self.assertEqual(pp[-1].get_id()[1], 220)
s = pp.get_sequence()
self.assertIsInstance(s, Seq)
self.assertEqual(s.alphabet, generic_protein)
self.assertEqual("TACQG", str(s))
s_atoms = list(structure.get_atoms())
f_atoms = list(f_structure.get_atoms())
for atoms in [s_atoms, f_atoms]:
self.assertEqual(len(atoms), 644)
atom_names = ["N", "CA", "C", "O", "CB"]
self.assertSequenceEqual([a.get_name() for a in atoms[:5]], atom_names)
self.assertSequenceEqual([a.get_id() for a in atoms[:5]], atom_names)
self.assertSequenceEqual([a.get_fullname() for a in atoms[:5]], atom_names)
self.assertSequenceEqual(
[a.get_occupancy() for a in atoms[:5]], [1.0, 1.0, 1.0, 1.0, 1.0]
)
self.assertIsInstance(atoms[0].get_coord(), numpy.ndarray)
coord = numpy.array([19.594, 32.367, 28.012], dtype=numpy.float32)
numpy.testing.assert_array_equal(atoms[0].get_coord(), coord)
self.assertEqual(atoms[0].get_bfactor(), 18.03)
for atom in atoms:
self.assertIsNone(atom.get_anisou())
