def test_basic(self):
"""
nothing is specified
"""
path1 = DIRNAME + '/data/sample1.pdb'
path2 = DIRNAME + '/data/sample2.pdb'
p = PDBParser(PERMISSIVE=1)
query_struct = p.get_structure(os.path.basename(path1), path1)
against_struct = p.get_structure(os.path.basename(path2), path2)
query_complex = Complex(query_struct)
against_complex = Complex(against_struct)
query_complex.get_fp()
against_complex.get_fp()
query_fp_string = query_complex.fp2str()
against_fp_string = against_complex.fp2str()
query = FPWithComplex(query_complex, query_fp_string)
against = FPWithComplex(against_complex, against_fp_string)
score1, score2, score3 = similarity_between(query, against)
expected = {"score1": 118.00269647021572, "score3": 20, "score2": -8}
actual = {"score1": score1, "score3": score2, "score2": score3}
self.assertEqual(actual, expected)
def test_basic_with_another_spinimage(self):
"""
non-default spinimage
"""
path1 = DIRNAME + '/data/sample1.pdb'
path2 = DIRNAME + '/data/sample2.pdb'
p = PDBParser(PERMISSIVE=1)
query_struct = p.get_structure(os.path.basename(path1), path1)
against_struct = p.get_structure(os.path.basename(path2), path2)
query_complex = Complex(query_struct)
against_complex = Complex(against_struct)
query_complex.get_fp(spin_image_radius_step=2,
spin_image_height_step=2,
sphere_radius_step=2)
against_complex.get_fp(spin_image_radius_step=2,
spin_image_height_step=2,
sphere_radius_step=2)
query_fp_string = query_complex.fp2str()
against_fp_string = against_complex.fp2str()
query = FPWithComplex(query_complex, query_fp_string)
against = FPWithComplex(against_complex, against_fp_string)
score1, score2, score3 = similarity_between(query, against)
expected = {'score1': 129.68169758476202, 'score3': 5, 'score2': 20}
actual = {"score1": score1, "score2": score2, "score3": score3}
self.assertEqual(actual, expected)
def test_basic_with_epitope(self):
"""
epitope is specified
"""
path1 = DIRNAME + '/data/sample1.pdb'
path2 = DIRNAME + '/data/sample2.pdb'
p = PDBParser(PERMISSIVE=1)
query_struct = p.get_structure(os.path.basename(path1), path1)
against_struct = p.get_structure(os.path.basename(path2), path2)
query_complex = Complex(
query_struct,
epitope=[211, 213, 214, 224, 225, 226, 227, 228, 229])
against_complex = Complex(against_struct,
epitope=[216, 217, 218, 219, 220, 221])
query_complex.get_fp()
against_complex.get_fp()
query_fp_string = query_complex.fp2str()
against_fp_string = against_complex.fp2str()
query = FPWithComplex(query_complex, query_fp_string)
against = FPWithComplex(against_complex, against_fp_string)
score1, score2, score3 = similarity_between(query, against)
expected = {'score1': 34.705754203703862, 'score3': 0, 'score2': 6}
actual = {"score1": score1, "score2": score2, "score3": score3}
self.assertEqual(actual, expected)
def test_with_epitope_another_cutoff(self):
"""
the similarity calculation cutoff is set to 5
"""
path1 = DIRNAME + '/data/sample1.pdb'
path2 = DIRNAME + '/data/sample2.pdb'
p = PDBParser(PERMISSIVE=1)
query_struct = p.get_structure(os.path.basename(path1), path1)
against_struct = p.get_structure(os.path.basename(path2), path2)
query_complex = Complex(query_struct)
against_complex = Complex(against_struct)
query_complex.get_fp()
against_complex.get_fp()
query_fp_string = query_complex.fp2str()
against_fp_string = against_complex.fp2str()
query = FPWithComplex(query_complex, query_fp_string)
against = FPWithComplex(against_complex, against_fp_string)
score1, score2, score3 = similarity_between(query, against, cutoff=5)
expected = {"score1": 119.75339423551459, "score3": -8, "score2": 20}
actual = {"score1": score1, "score2": score2, "score3": score3}
self.assertEqual(actual, expected)
def score(query_pdb_path,
against_pdb_path,
query_fp_path=None,
against_fp_path=None,
query_epitope=[],
against_epitope=[],
spin_image_height_step=5,
spin_image_radius_step=2,
sphere_radius_step=2,
cutoff=20.0,
spin_image_radius_range=(0, 20),
spin_image_height_range=(-30, 10),
sphere_radius_range=(0, 20),
callback=write_score_to_file,
cbargs=[]):
p = PDBParser(PERMISSIVE=1)
query_struct = p.get_structure(os.path.basename(query_pdb_path),
query_pdb_path)
against_struct = p.get_structure(os.path.basename(against_pdb_path),
against_pdb_path)
query_complex = Complex(query_struct, query_epitope)
against_complex = Complex(against_struct, against_epitope)
if query_fp_path is None or against_fp_path is None: #if fp is not given
query_complex.get_fp(spin_image_radius_step=spin_image_radius_step,
spin_image_height_step=spin_image_height_step,
sphere_radius_step=sphere_radius_step)
against_complex.get_fp(spin_image_radius_step=spin_image_radius_step,
spin_image_height_step=spin_image_height_step,
sphere_radius_step=sphere_radius_step)
query_fp_string = query_complex.fp2str()
against_fp_string = against_complex.fp2str()
else:
#if fp is given, read them
with open(query_fp_path, 'r') as f1, open(against_fp_path, 'r') as f2:
query_fp_string = f1.read()
against_fp_string = f2.read()
query = FPWithComplex(query_complex, query_fp_string)
against = FPWithComplex(against_complex, against_fp_string)
score1, score2, score3 = similarity_between(query, against, cutoff=cutoff)
#z1, z2, z3 = similarity_between (query, query, cutoff = cutoff) #the normalization constant
#print score1, score2, score3
if callback is not None:
callback((score1, score2, score3), *cbargs)
return score1, score2, score3
def score (query_pdb_path,
against_pdb_path,
query_fp_path = None,
against_fp_path = None,
query_epitope = [],
against_epitope = [],
spin_image_height_step = 5,
spin_image_radius_step = 2,
sphere_radius_step = 2,
cutoff = 20.0,
spin_image_radius_range = (0, 20),
spin_image_height_range = (-30, 10),
sphere_radius_range = (0, 20),
callback = write_score_to_file, cbargs=[]):
p = PDBParser(PERMISSIVE=1)
query_struct = p.get_structure(os.path.basename (query_pdb_path), query_pdb_path)
against_struct = p.get_structure(os.path.basename (against_pdb_path), against_pdb_path)
query_complex = Complex (query_struct, query_epitope)
against_complex = Complex (against_struct, against_epitope)
if query_fp_path is None or against_fp_path is None:#if fp is not given
query_complex.get_fp(spin_image_radius_step = spin_image_radius_step, spin_image_height_step = spin_image_height_step, sphere_radius_step = sphere_radius_step)
against_complex.get_fp(spin_image_radius_step = spin_image_radius_step, spin_image_height_step = spin_image_height_step, sphere_radius_step = sphere_radius_step)
query_fp_string = query_complex.fp2str ()
against_fp_string = against_complex.fp2str ()
else:
#if fp is given, read them
with open (query_fp_path, 'r') as f1, open(against_fp_path, 'r') as f2:
query_fp_string = f1.read ()
against_fp_string = f2.read ()
query = FPWithComplex (query_complex, query_fp_string)
against = FPWithComplex (against_complex, against_fp_string)
score1, score2, score3 = similarity_between (query, against, cutoff = cutoff)
#z1, z2, z3 = similarity_between (query, query, cutoff = cutoff) #the normalization constant
#print score1, score2, score3
if callback is not None:
callback ((score1, score2, score3), *cbargs)
return score1, score2, score3
def test_with_epitope_another_spinimage(self):
"""
Epitope is specified and non-default spinimage
"""
path1 = DIRNAME + '/data/sample1.pdb'
path2 = DIRNAME + '/data/sample2.pdb'
p = PDBParser(PERMISSIVE=1)
query_struct = p.get_structure(os.path.basename(path1), path1)
against_struct = p.get_structure(os.path.basename(path2), path2)
query_complex = Complex(
query_struct,
epitope=[211, 213, 214, 224, 225, 226, 227, 228, 229])
against_complex = Complex(against_struct,
epitope=[216, 217, 218, 219, 220, 221])
query_complex.get_fp(spin_image_radius_step=2,
spin_image_height_step=2,
sphere_radius_step=2)
against_complex.get_fp(spin_image_radius_step=2,
spin_image_height_step=2,
sphere_radius_step=2)
query_fp_string = query_complex.fp2str()
against_fp_string = against_complex.fp2str()
query = FPWithComplex(query_complex, query_fp_string)
against = FPWithComplex(against_complex, against_fp_string)
score1, score2, score3 = similarity_between(query, against)
expected = {'score1': 35.771598481467343, 'score3': 2, 'score2': 6}
actual = {"score1": score1, "score2": score2, "score3": score3}
self.assertEqual(actual, expected)