def fastcontact(pdb_f, fastcontact_exe):
felecv = .0
fdesolv = .0
freee = .0
prot_dic = PDB.load_structure(pdb_f)
for segid_x, segid_y in itertools.combinations(prot_dic, 2):
prot_x = '{}.pdb'.format(segid_x)
prot_x_str = ''.join(prot_dic[segid_x])
with open(prot_x, 'w') as fh_prot_x:
fh_prot_x.write(prot_x_str)
fh_prot_x.close()
prot_y = '{}.pdb'.format(segid_y)
prot_y_str = ''.join(prot_dic[segid_y])
with open(prot_y, 'w') as fh_prot_y:
fh_prot_y.write(prot_y_str)
fh_prot_y.close()
p = subprocess.Popen([fastcontact_exe, prot_x, prot_y],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
out = p.communicate()
returncode = p.wait()
if returncode != 0:
print('+ ERROR: Something wrong with fastcontact')
exit()
i, j, k = map(float, str(out[0]).split('\\n')[1].split())
felecv += i
fdesolv += j
freee += k
os.remove(prot_x)
os.remove(prot_y)
return felecv, fdesolv
def dfire(pdb_f, dcomplex_exe):
fixed_pdb = PDB.fix_id(pdb_f)
prot_dic = PDB.load_structure(fixed_pdb)
dfire_regex = r'-?\d*?\.\d\d*'
dfire_dic = {'binding': [], 'score': []}
for segid_x, segid_y in itertools.combinations(prot_dic, 2):
input_str = str.encode(f'{fixed_pdb}\n1\n{segid_x}\n1\n{segid_y}')
p = subprocess.run(dcomplex_exe,
input=input_str,
stdout=subprocess.PIPE)
try:
result = p.stdout.decode('utf-8')
score, binding = re.findall(dfire_regex, result)
score = float(score)
binding = float(binding)
except ValueError:
binding = .0
score = .0
dfire_dic['binding'].append(binding)
dfire_dic['score'].append(score)
binding_l = [float(e) for e in dfire_dic['binding']]
score_l = [float(e) for e in dfire_dic['score']]
mean_binding = sum(binding_l) / len(binding_l)
mean_score = sum(score_l) / len(score_l)
return mean_binding, mean_score
class TestPDB(unittest.TestCase):
def setUp(self):
self.PDB = PDB()
def test_treat_ensemble(self):
copyfile(f'{data_path}/mini_ens.pdb', f'{data_path}/temp_ens.pdb')
input_pdb_dic = {'mol1': f'{data_path}/temp_ens.pdb'}
treated_dic = self.PDB.treat_ensemble(input_pdb_dic)
expected_treated_dic = {'mol1': [f'{data_path}/temp_1.pdb', f'{data_path}/temp_2.pdb']}
self.assertEqual(treated_dic, expected_treated_dic)
self.assertTrue(filecmp.cmp(f'{data_path}/temp_1.pdb', f'{data_path}/mini_ens1.pdb'))
self.assertTrue(filecmp.cmp(f'{data_path}/temp_2.pdb', f'{data_path}/mini_ens2.pdb'))
os.remove(f'{data_path}/temp_1.pdb')
os.remove(f'{data_path}/temp_2.pdb')
os.remove(f'{data_path}/temp_ens.pdb')
def test_load_structure(self):
pdb_f = f'{data_path}/miniA.pdb'
pdb_dic = self.PDB.load_structure(pdb_f)
expected_pdb_dic = {'A': ['ATOM 2 CA MET A 1 16.967 12.784 4.338 1.00 10.80 A C \n',
'ATOM 9 CA ARG A 2 13.856 11.469 6.066 1.00 8.31 A C \n',
'ATOM 16 CA CYS A 3 13.660 10.707 9.787 1.00 5.39 A C \n']}
self.assertEqual(pdb_dic, expected_pdb_dic)
def test_identify_chains(self):
pdb_f = f'{data_path}/mini.pdb'
chain_l = self.PDB.identify_chains(pdb_f)
expected_chain_l = ['A', 'B','C']
self.assertEqual(chain_l, expected_chain_l)
def test_identify_segids(self):
pdb_f = f'{data_path}/miniA.pdb'
segid_l = self.PDB.identify_segids(pdb_f)
expected_segid_l = ['A']
self.assertEqual(segid_l, expected_segid_l)
def test_split_models(self):
ensamble_f = f'{data_path}/mini_ens.pdb'
model_list = self.PDB.split_models(ensamble_f)
expected_list = [f'{data_path}/mini_1.pdb', f'{data_path}/mini_2.pdb']
self.assertEqual(model_list, expected_list, 'Name of list elements differ')
self.assertTrue(filecmp.cmp(f'{data_path}/mini_1.pdb', f'{data_path}/mini_1.gold'))
self.assertTrue(filecmp.cmp(f'{data_path}/mini_2.pdb', f'{data_path}/mini_2.gold'))
for f in model_list:
os.remove(f)
def test_fix_id(self):
nosegid_pdb_f = f'{data_path}/mini.pdb'
nochain_pdb_f = f'{data_path}/mini_nochain.pdb'
segid_pdb = self.PDB.fix_id(nosegid_pdb_f, priority='chain', overwrite=False)
chain_pdb = self.PDB.fix_id(nochain_pdb_f, priority='seg', overwrite=False)
self.assertTrue(filecmp.cmp(segid_pdb, f'{data_path}/mini_segid.pdb'))
self.assertTrue(filecmp.cmp(chain_pdb, f'{data_path}/mini_segid.pdb'))
os.remove(f'{data_path}/mini.pdb_')
os.remove(f'{data_path}/mini_nochain.pdb_')
def test_add_chainseg(self):
copyfile(f'{data_path}/mini.pdb', f'{data_path}/temp.pdb')
check = self.PDB.add_chainseg(f'{data_path}/temp.pdb', 'A')
self.assertTrue(check)
self.assertTrue(filecmp.cmp(f'{data_path}/temp.pdb', f'{data_path}/miniA.pdb'))
os.remove(f'{data_path}/temp.pdb')
def test_identify_chainseg(self):
pdbf = f'{data_path}/miniA.pdb'
chainseg = self.PDB.identify_chainseg(pdbf)
self.assertEqual(chainseg, ['A'])
def test_fix_chainseg(self):
copyfile(f'{data_path}/mini_1.gold', f'{data_path}/mol1.pdb')
copyfile(f'{data_path}/mini_2.gold', f'{data_path}/mol2.pdb')
input_pdb_dic = {'mol1': f'{data_path}/mol1.pdb', 'segid1': 'X', 'mol2': f'{data_path}/mol2.pdb'}
return_pdb_dic = self.PDB.fix_chainseg(input_pdb_dic)
expected_return_dic = {'mol1': f'{data_path}/mol1.pdb', 'mol2': f'{data_path}/mol2.pdb'}
self.assertEqual(return_pdb_dic, expected_return_dic)
self.assertTrue(filecmp.cmp(f'{data_path}/mol1.pdb', f'{data_path}/miniX.pdb'))
os.remove(f'{data_path}/mol1.pdb')
os.remove(f'{data_path}/mol2.pdb')
def test_sanitize(self):
copyfile(f'{data_path}/mini.dirty.pdb', f'{data_path}/temp.pdb')
input_pdb_dic = {'mol1': [f'{data_path}/temp.pdb']}
model_list = self.PDB.sanitize(input_pdb_dic)
expected_model_list = [f'{data_path}/temp.pdb']
self.assertEqual(model_list, expected_model_list)
self.assertTrue(filecmp.cmp(f'{data_path}/temp.pdb', f'{data_path}/mini.clean.pdb'))
os.remove(f'{data_path}/temp.pdb')
def test_count_atoms(self):
pdb_f = f'{data_path}/mini.pdb'
atom_count = self.PDB.count_atoms(pdb_f)
self.assertEqual(atom_count, 3)
def test_organize_chains(self):
pass
def test_replace_chain(self):
pdb_f = f'{data_path}/mini.pdb'
newchain_pdb = self.PDB.replace_chain(pdb_f, 'A', 'X', overwrite=False)
self.assertTrue(filecmp.cmp(newchain_pdb, f'{data_path}/mini_A-X.pdb'))
os.remove(f'{data_path}/mini.pdb_')
def test_renumber(self):
pass
def test_load_seq(self):
pass
def tearDown(self):
pass