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())