def setUpClass(cls):
cls.pdb_structure = Bio.PDB.PDBParser(QUIET=True).get_structure(
cls.name, data_dir + '%s.pdb' % cls.name)
cls.converter = numberconverter.NumberConverter(cls.pdb_structure)
cls.model = random.choice(cls.pdb_structure)
with warnings.catch_warnings(record=True):
cls.struct = structure.Structure(cls.model, cls.converter)
def test_init(self):
pdb_structure = Bio.PDB.PDBParser(QUIET=True).get_structure(
self.name, data_dir + '%s.pdb' % self.name)
converter = numberconverter.NumberConverter(pdb_structure)
for model in pdb_structure:
with warnings.catch_warnings(record=True) as wlist:
warnings.simplefilter("always")
structure.Structure(model, converter)
syntax_check.warning_message(self, wlist)
def setUpClass(cls):
cls.pdb_structure = Bio.PDB.PDBParser(QUIET=True).get_structure(
cls.name, data_dir + '%s.pdb' % cls.name)
cls.converter = numberconverter.NumberConverter(cls.pdb_structure)
cls.model = random.choice(cls.pdb_structure)
with warnings.catch_warnings(record=True):
cls.struct = structure.Structure(cls.model, cls.converter)
#~ crit = contacts.ContactsAlternative(contacts.CaContact(), contacts.CbxContact(), contacts.RaContact())
#~ cls.struct.set_contact_map(crit)
cls.struct.set_contact_map()
def setUpClass(cls):
cls.basic_sel_cls = [
random_selection_set, random_selection_range,
random_selection_chain, random_selection_monomername,
random_selection_monomertype, random_selection_everything,
random_selection_nothing
]
cls.pdb_structure = Bio.PDB.PDBParser(QUIET=True).get_structure(
cls.name, data_dir + '%s.pdb' % cls.name)
cls.converter = numberconverter.NumberConverter(cls.pdb_structure)
cls.model = random.choice(cls.pdb_structure)
with warnings.catch_warnings(record=True):
cls.struct = structure.Structure(cls.model, cls.converter)
def load_structure_to_class(cls, strname):
if strname in struct_dict:
cls.pdb_structure, cls.converter, cls.model, cls.struct = struct_dict[
strname]
else:
cls.pdb_structure = Bio.PDB.PDBParser(QUIET=True).get_structure(
strname, data_dir + '%s.pdb' % strname)
cls.converter = numberconverter.NumberConverter(cls.pdb_structure)
cls.model = random.choice(cls.pdb_structure)
with warnings.catch_warnings(record=True):
cls.struct = structure.Structure(cls.model, cls.converter)
struct_dict[strname] = (cls.pdb_structure, cls.converter, cls.model,
cls.struct)
def test_select(self):
nc = numcon.NumberConverter(self.pdb_structure)
class S:
converter = nc
for i in self.ress:
for res in i.values():
res.structure = S
pid = res.pdb_residue.get_full_id()
pids = numcon.PDB_id.from_string(pid[2] + str(pid[3][1]) +
pid[3][2])
res.ind = nc.get_ind(pids)
s = res.select()
self.assertEquals(len(s.ids), 1)
self.assertEquals(pids, s.ids[0])
def setUpClass(cls):
cls.structs = []
if not skip_slow:
for strname in cls.struct_names:
pdb_structure = Bio.PDB.PDBParser(QUIET=True).get_structure(
strname, data_dir + '%s.pdb' % strname)
converter = numberconverter.NumberConverter(pdb_structure)
model = random.choice(pdb_structure)
with warnings.catch_warnings(record=True):
try:
cls.structs.append(
structure.Structure(model, converter))
except:
print "Failed to load %s" % strname
if len(cls.structs) == 0:
print "All structures failed to load!!!"
cls.points1 = [syntax_check.randomcoord() for dummy in range(100)]
cls.points2 = [syntax_check.randomcoord() for dummy in range(100)]
