def setUp(self):
super().setUp()
populate_cutoff()
populate_atlas(graph_list=AtlasHandler().atlas_graphs)
self.codes = ['2ebo', '10gs']
self.cta = UpdateCodes(codes=self.codes, store_files=False)
self.cta.run_update(mode=_mode)
def setUp(self):
super().setUp()
populate_cutoff()
populate_atlas(graph_list=AtlasHandler().atlas_graphs)
self.code = '2ebo'
# add pdb code
UpdateCodes(codes=[self.code], store_files=False).run_update(mode=_mode)
remove_pdb_code(code=self.code)
class AtlasHandlerTestCase(unittest.TestCase):
def setUp(self):
self.atlas_handler = AtlasHandler(mode=mode)
self.g1 = complete_graph(8)
self.g2 = complete_graph(9)
self.g1_name = 'U1'
self.g2_name = 'jack_test_graph'
def clear_unknown_graphs(self):
with open(unknown_graphs, 'wb') as foo:
pickle.dump([], foo)
def tearDown(self):
self.clear_unknown_graphs()
def test_atlas_graphs(self):
self.assertEqual(len(self.atlas_handler.atlas_graphs), 1253)
def test_cyclic_graphs(self):
self.assertEqual(len(self.atlas_handler.cyclic_graphs(max_nodes=88)),
81)
def test_path_graphs(self):
self.assertEqual(len(self.atlas_handler.path_graphs(max_nodes=88)), 81)
def name_against_unknowns(knob_graphs):
""" Checks each unnamed graph for isomorphism against list of 'unknown' (large) graphs.
Parameters
----------
knob_graphs: list(networkx.Graph)
Returns
-------
None
"""
large_graph_list = AtlasHandler().get_graph_list(atlas=False,
cyclics=False,
paths=False,
unknowns=True)
for g in knob_graphs:
if g.graph['name'] is None:
name = isomorphism_checker(g, graph_list=large_graph_list)
if name is not None:
g.graph['name'] = name
return
def add_unknowns(knob_graphs, mode):
""" Name all new unknown graphs, add them to unknown_pickle and to database.
Parameters
----------
knob_graphs: list(networkx.Graph)
mode: str
Allowed values: 'production' or 'testing'.
Returns
-------
None
"""
large_graph_list = AtlasHandler().get_graph_list(atlas=False,
cyclics=False,
paths=False,
unknowns=True)
assert not all_graphs_named(knob_graphs=knob_graphs)
assert all(
isomorphism_checker(x, graph_list=large_graph_list)
for x in knob_graphs)
next_number_to_add = max([int(x.name[1:]) for x in large_graph_list]) + 1
to_add_to_atlas = []
for i, g in enumerate(knob_graphs):
n = isomorphism_checker(g, graph_list=knob_graphs[:i])
if n is None:
h = graph_to_plain_graph(g)
n = 'U{}'.format(next_number_to_add)
h.name = n
to_add_to_atlas.append(h)
next_number_to_add += 1
g.graph['name'] = n
large_graph_list += to_add_to_atlas
unknown_pickle = global_settings["unknown_graphs"][mode]
with open(unknown_pickle, 'wb') as foo:
pickle.dump(large_graph_list, foo)
populate_atlas(graph_list=to_add_to_atlas)
return
def setUp(self):
super().setUp()
self.graph_list = AtlasHandler().atlas_graphs
import networkx
import numpy
from isambard.add_ons.filesystem import FileSystem, preferred_mmol, get_cif, get_mmol
from isambard.add_ons.knobs_into_holes import KnobGroup
from isambard.add_ons.parmed_to_ampal import convert_cif_to_ampal
from isambard.ampal.pdb_parser import convert_pdb_to_ampal
from isocket.graph_theory import graph_to_plain_graph, AtlasHandler, isomorphism_checker
from isocket_settings import global_settings
try:
data_dir = global_settings['structural_database']['path']
except KeyError:
data_dir = None
_graph_list = AtlasHandler().get_graph_list(atlas=True,
paths=True,
cyclics=True,
unknowns=False)
class StructureHandler:
""" Class for parsing pdb/cif files into KIH graphs """
def __init__(self, assembly):
self.assembly = assembly
self.is_preferred = False
self.code = self.assembly.id
self.mmol = None
def __repr__(self):
return '<StructureHandler(code={0}, mmol={1})>'.format(
self.code, self.mmol)
def setUp(self):
self.graph_list = AtlasHandler(mode=mode).get_graph_list()
def setUp(self):
self.atlas_handler = AtlasHandler(mode=mode)
self.g1 = complete_graph(8)
self.g2 = complete_graph(9)
self.g1_name = 'U1'
self.g2_name = 'jack_test_graph'