def exercise_show_summary():
from scitbx.graph import test_cases_tardy_pdb
tcs = test_cases_tardy_pdb.select_test_cases(
tags_or_indices=["ZINC03847120"])
assert len(tcs) == 1
tt = tcs[0].tardy_tree_construct()
for vl,cb in [(None, ("10", "11")),
(list("ABCDEFGHIKLMNO"), ("L", "M"))]:
sio = StringIO()
assert tt.show_summary(vertex_labels=vl, out=sio, prefix="&") is tt
assert not show_diff(sio.getvalue(), """\
&number of vertices: 14
&number of edges: 15
&find cluster loops: 0 repeats
&number of fixed vertex lists: 0
&number of fixed vertices: 0
&number of clusters: 1
&merge clusters with multiple connections: 1 pass
&number of hinge edges: 1
&number of loop edges: 0
&number of loop edge bendings: 0
&number of fixed hinges: 1
&tardy fixed hinge: %s
& %s
""" % cb)
def get(tag):
from scitbx.graph import test_cases_tardy_pdb
tcs = test_cases_tardy_pdb.select_test_cases(tags_or_indices=[tag])
assert len(tcs) == 1
tt = tcs[0].tardy_tree_construct()
ec = tt.cluster_manager.edge_classifier()
edge_classes = {
"base": [],
"hinge": [],
"intra": [],
"loop": [],
"fixed": []}
for e in tt.edge_list:
edge_classes[ec(edge=e)].append(e)
return tt, edge_classes
def exercise_pickle():
from scitbx.graph import test_cases_tardy_pdb
tcs = test_cases_tardy_pdb.select_test_cases(
tags_or_indices=["ZINC03847120"])
assert len(tcs) == 1
tt = tcs[0].tardy_tree_construct()
try:
tt.arbitrary = 0
except AttributeError: pass # make sure __slots__ work
else: raise Exception_expected
ts = StringIO()
tt.show_summary(vertex_labels=None, out=ts)
for protocol in xrange(pickle.HIGHEST_PROTOCOL):
s = pickle.dumps(tt, protocol)
l = pickle.loads(s)
ls = StringIO()
l.show_summary(vertex_labels=None, out=ls)
assert not show_diff(ls.getvalue(), ts.getvalue())
def run(args):
if (1):
random.seed(0)
flex.set_random_seed(0)
out = null_out()
remaining_args = []
for arg in args:
if (arg == "--verbose"): out = sys.stdout
else: remaining_args.append(arg)
test_cases = test_cases_tardy_pdb.select_test_cases(
tags_or_indices=remaining_args)
for test_case in test_cases:
print >> out, "test case %d: %s" % (test_case.index, test_case.tag)
minimized = []
for use_geo in [False, True]:
minimized.append(exercise_lbfgs(test_case, use_geo=use_geo, out=out))
m0, m1 = minimized
assert m0.real_space_target_weight == 1
assert m1.real_space_target_weight == 1
assert m1.f_final < m0.f_start * 0.98
print format_cpu_times()
def run(args):
if (1):
random.seed(0)
flex.set_random_seed(0)
out = null_out()
remaining_args = []
for arg in args:
if (arg == "--verbose"): out = sys.stdout
else: remaining_args.append(arg)
test_cases = test_cases_tardy_pdb.select_test_cases(
tags_or_indices=remaining_args)
for test_case in test_cases:
print("test case %d: %s" % (test_case.index, test_case.tag), file=out)
minimized = []
for use_geo in [False, True]:
minimized.append(
exercise_lbfgs(test_case, use_geo=use_geo, out=out))
m0, m1 = minimized
assert m0.real_space_target_weight == 1
assert m1.real_space_target_weight == 1
assert m1.f_final < m0.f_start * 0.98
print(format_cpu_times())