def test_1(self):
"""Formatlib: second test"""
pdb_file = PDBFile(pdb_path=os.path.join(DIRNAME, 'test1.in'))
pdb_file.pedantic_pdb()
result = pdb_file.pdb_string
f = open(os.path.join(DIRNAME, 'test1.out'))
correct = f.read()
f.close()
self.assertEqual(correct, result)
def test_0(self):
"""Formatlib: first test"""
tmpfile = os.path.join(tempdir or '/tmp/', str(uuid.uuid4()))
shutil.copyfile(os.path.join(DIRNAME, 'test0.in'), tmpfile)
pdb_file = PDBFile(pdb_path=tmpfile)
pdb_file.pedantic_pdb()
result = pdb_file.pdb_string
os.remove(tmpfile)
f = open(os.path.join(DIRNAME, 'test0.out'))
correct = f.read()
f.close()
self.assertEqual(correct, result)
def rebuild_full_atom(input_pdb, output_pdb):
"""Make all atom PDB file from 3 atom PDB file
Arguments:
* input_pdb = path to input PDB
* output_pdb = path to output PDB
"""
try:
old_pwd = os.getcwd()
print old_pwd
except:
old_pwd = None
tempdir = mkdtemp()
os.chdir(tempdir)
try:
os.symlink(REBUILDRNA_PATH + os.sep + 'histograms', 'histograms')
os.symlink(REBUILDRNA_PATH + os.sep + 'pdb', 'pdb')
except OSError:
pass
# remove strange residue names
pdb_file = PDBFile(pdb_path=os.path.join(old_pwd, input_pdb))
pdb_file._resname_3to1()
pdb_file.save(os.path.join(tempdir, input_pdb))
cmd = Popen([REBUILDRNA_PATH + os.sep + 'RebuildRNA',
'-t', os.path.join(tempdir, input_pdb), '-o', tempdir])
returncode = cmd.wait()
out_name = tempdir + os.sep +\
'.'.join(os.path.basename(input_pdb).split('.')[:-1]) + '_beforeCorrecting.pdb'
os.rename(out_name, output_pdb)
try:
if old_pwd:
os.chdir(old_pwd)
rmtree(tempdir)
except OSError:
pass
return returncode
else:
print("\nNeed to provide at least an output type.\n")
sys.exit(0)
except:
print("\nFailed to process input\n")
printhelp()
sys.exit(0)
########################################################################
##PARSE
pdb = PDBFile(filepath=filename)
pdb.parametersParse()
############################################################################
def remove_model_tags(filepath):
#remove model references
print("Removing MODEL references for Coot....")
file = open(outputfile,"r")
lines = file.readlines()
newlines = []
for line in lines:
if ("MODEL" not in line) and ("ENDMDL" not in line) :
newlines.append(line)
else:
print("Removing MODEL entry "+line)
file.close()
def test_resname_check_and_1to3(self):
pdb_file = PDBFile(pdb_path=os.path.join(DIRNAME, 'test0.in'))
pdb_file.resname_check_and_3to1()
with open(os.path.join(DIRNAME, 'test0_3to1.out')) as f:
correct = f.read()
self.assertEqual(pdb_file.pdb_string, correct)
def test_remove_non_atoms(self):
pdb_file = PDBFile(pdb_path=os.path.join(DIRNAME, 'test_nmr.in'))
pdb_file.remove_non_atoms()
with open(os.path.join(DIRNAME, 'test_nmr_atom.out')) as f:
correct = f.read()
self.assertEqual(pdb_file.pdb_string, correct)
def test_get_fasta(self):
pdb_file = PDBFile(pdb_path=os.path.join(DIRNAME, 'test0.in'))
self.assertEqual(pdb_file.get_fasta(name='test'), '>test\nGAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC\n')
def test_seq_from_pdb(self):
pdb_file = PDBFile(pdb_path=os.path.join(DIRNAME, 'test0.in'))
self.assertEqual(pdb_file.seq_from_pdb(), 'GAGCCGUAUGCGAUGAAAGUCGCACGUACGGUUC')
def test_detect_proteins(self):
pdb_file = PDBFile(pdb_path=os.path.join(DIRNAME, 'protein.pdb'))
self.assertTrue(pdb_file.detect_proteins())
def test_validate_pdb_false(self):
pdb_file = PDBFile(pdb_path=os.path.join(DIRNAME, 'test.py'))
self.assertFalse(pdb_file.validate_pdb())
def test_validate_pdb_true(self):
pdb_file = PDBFile(pdb_path=os.path.join(DIRNAME, 'test0.in'))
self.assertTrue(pdb_file.validate_pdb())
def test_check_and_get_first_model(self):
pdb_file = PDBFile(pdb_path=os.path.join(DIRNAME, 'test_nmr.in'))
pdb_file.check_and_get_first_model()
with open(os.path.join(DIRNAME, 'test_nmr.out')) as f:
correct = f.read()
self.assertEqual(pdb_file.pdb_string, correct)
def test_count_models(self):
pdb_file = PDBFile(pdb_path=os.path.join(DIRNAME, 'test_nmr.in'))
self.assertEqual(pdb_file.count_models(), 10)