def __init__(self, model, pdb_file = None,
naccess_binary = 'naccess', tmp_directory = '/tmp'):
res_data, atm_data = run_naccess(model, pdb_file, naccess = naccess_binary,
temp_path = tmp_directory)
self.naccess_atom_dict = process_asa_data(atm_data)
atom_list = []
property_dict={}
property_keys=[]
property_list=[]
# Now create a dictionary that maps Atom objects to accessibility
for chain in model:
chain_id = chain.get_id()
for residue in chain:
res_id = residue.get_id()
for atom in residue:
atom_id = atom.get_id()
full_id=(chain_id, res_id, atom_id)
if full_id in self.naccess_atom_dict:
asa = self.naccess_atom_dict[full_id]
property_dict[full_id]=asa
property_keys.append((full_id))
property_list.append((atom, asa))
atom.xtra['EXP_NACCESS']=asa
AbstractAtomPropertyMap.__init__(self, property_dict, property_keys,
property_list)
def __init__(self,
model,
pdb_file=None,
naccess_binary='naccess',
tmp_directory='/tmp'):
res_data, atm_data = run_naccess(model,
pdb_file,
naccess=naccess_binary,
temp_path=tmp_directory)
self.naccess_atom_dict = process_asa_data(atm_data)
atom_list = []
property_dict = {}
property_keys = []
property_list = []
# Now create a dictionary that maps Atom objects to accessibility
for chain in model:
chain_id = chain.get_id()
for residue in chain:
res_id = residue.get_id()
for atom in residue:
atom_id = atom.get_id()
full_id = (chain_id, res_id, atom_id)
if full_id in self.naccess_atom_dict:
asa = self.naccess_atom_dict[full_id]
property_dict[full_id] = asa
property_keys.append((full_id))
property_list.append((atom, asa))
atom.xtra['EXP_NACCESS'] = asa
AbstractAtomPropertyMap.__init__(self, property_dict, property_keys,
property_list)