def run_naccess(model, pdb_file, probe_size=None, z_slice=None, naccess="naccess", temp_path="/tmp/"):
# make temp directory;
tmp_path = tempfile.mkdtemp(dir=temp_path)
# file name must end with '.pdb' to work with NACCESS
# -> create temp file of existing pdb
# or write model to temp file
handle, tmp_pdb_file = tempfile.mkstemp(".pdb", dir=tmp_path)
os.close(handle)
if pdb_file:
pdb_file = os.path.abspath(pdb_file)
shutil.copy(pdb_file, tmp_pdb_file)
else:
writer = PDBIO()
writer.set_structure(model.get_parent())
writer.save(tmp_pdb_file)
# chdir to temp directory, as NACCESS writes to current working directory
old_dir = os.getcwd()
os.chdir(tmp_path)
# create the command line and run
# catch standard out & err
command = [naccess, tmp_pdb_file]
if probe_size:
command.extend(["-p", probe_size])
if z_slice:
command.extend(["-z", z_slice])
p = subprocess.Popen(command, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
out, err = p.communicate()
os.chdir(old_dir)
# get the output, then delete the temp directory
rsa_file = tmp_pdb_file[:-4] + ".rsa"
with open(rsa_file) as rf:
rsa_data = rf.readlines()
asa_file = tmp_pdb_file[:-4] + ".asa"
with open(asa_file) as af:
asa_data = af.readlines()
shutil.rmtree(tmp_path, ignore_errors=True)
return rsa_data, asa_data
def extract(structure, chain_id, start, end, filename):
"""
Write out selected portion to filename.
"""
sel=ChainSelector(chain_id, start, end)
io=PDBIO()
io.set_structure(structure)
io.save(filename, sel)
def run_naccess(model,
pdb_file,
probe_size=None,
z_slice=None,
naccess='naccess',
temp_path='/tmp/'):
# make temp directory;
tmp_path = tempfile.mkdtemp(dir=temp_path)
# file name must end with '.pdb' to work with NACCESS
# -> create temp file of existing pdb
# or write model to temp file
handle, tmp_pdb_file = tempfile.mkstemp('.pdb', dir=tmp_path)
os.close(handle)
if pdb_file:
pdb_file = os.path.abspath(pdb_file)
shutil.copy(pdb_file, tmp_pdb_file)
else:
writer = PDBIO()
writer.set_structure(model.get_parent())
writer.save(tmp_pdb_file)
# chdir to temp directory, as NACCESS writes to current working directory
old_dir = os.getcwd()
os.chdir(tmp_path)
# create the command line and run
# catch standard out & err
command = [naccess, tmp_pdb_file]
if probe_size:
command.extend(['-p', probe_size])
if z_slice:
command.extend(['-z', z_slice])
p = subprocess.Popen(command,
universal_newlines=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
out, err = p.communicate()
os.chdir(old_dir)
# get the output, then delete the temp directory
rsa_file = tmp_pdb_file[:-4] + '.rsa'
with open(rsa_file) as rf:
rsa_data = rf.readlines()
asa_file = tmp_pdb_file[:-4] + '.asa'
with open(asa_file) as af:
asa_data = af.readlines()
shutil.rmtree(tmp_path, ignore_errors=True)
return rsa_data, asa_data