def exercise_fixed_vertices(n_trials=10):
cm = cluster_manager(n_vertices=2, fixed_vertex_lists=[[0]])
assert cm.clusters == [[0], [1]]
cm = cluster_manager(n_vertices=2, fixed_vertex_lists=[[1]])
assert cm.clusters == [[1], [0]]
edge_list = [(0,1),(1,2),(2,3),(1,3)]
edge_sets = construct_edge_sets(n_vertices=4, edge_list=edge_list)
for fixed_vertex in [0,1]:
for optimize in [False, True]:
for connects in [[(1,2),(2,3)], [(2,3),(1,2)], [(2,1),(3,2)]]:
cm = cluster_manager(n_vertices=4, fixed_vertex_lists=[[fixed_vertex]])
for i,j in connects:
cm.connect_vertices(i=i, j=j, optimize=optimize)
if (fixed_vertex == 0):
if (connects[0] == (2,1)):
if (not optimize):
assert cm.clusters == [[0], [], [], [3, 2, 1]]
else:
assert cm.clusters == [[0], [], [2, 1, 3], []]
else:
if (not optimize or connects[0][0] == 1):
assert cm.clusters == [[0], [1,2,3], [], []]
else:
assert cm.clusters == [[0], [], [2,3,1], []]
cm.tidy()
assert cm.clusters == [[0], [1,2,3]]
else:
assert cm.clusters == [[1,2,3], [0], [], []]
cm.tidy()
assert cm.clusters == [[1,2,3], [0]]
cm.construct_spanning_trees(edge_sets=edge_sets)
assert cm.clusters == [[0,1,2,3]]
assert cm.hinge_edges == [(-1,1)]
assert cm.loop_edges == []
#
from scitbx.graph import test_cases_tardy_pdb
tc = test_cases_tardy_pdb.test_cases[5]
assert tc.tag == "tyr_with_h"
tt = tc.tardy_tree_construct(fixed_vertex_lists=[[0,16,17]])
assert tt.cluster_manager.clusters == [
[0,1,2,3,4,5,6,7,8,9,10,12,13,14,15,16,17,18,19],
[11], [20]]
try:
tc.tardy_tree_construct(fixed_vertex_lists=[[0],[1]])
except RuntimeError, e:
assert str(e) == \
"connect_clusters(): fixed vertex lists in same connected tree."
def exercise_cluster_manager():
cm = cluster_manager(n_vertices=0)
assert cm.cluster_indices == []
assert cm.clusters == []
cm = cluster_manager(n_vertices=5)
for p in xrange(2):
assert cm.cluster_indices == [0,1,2,3,4]
assert cm.clusters == [[0],[1],[2],[3],[4]]
cm.connect_vertices(i=0, j=0, optimize=True)
for p in xrange(2):
cm.connect_vertices(i=1, j=3, optimize=True)
assert cm.cluster_indices == [0,1,2,1,4]
assert cm.clusters == [[0],[1,3],[2],[],[4]]
for p in xrange(2):
cm.connect_vertices(i=0, j=3, optimize=True)
assert cm.cluster_indices == [1,1,2,1,4]
for q in xrange(2):
assert cm.clusters == [[],[1,3,0],[2],[],[4]]
cm.refresh_indices()
cm.connect_vertices(i=2, j=4, optimize=True)
assert cm.clusters == [[],[1,3,0],[2,4],[],[]]
assert cm.cluster_indices == [1,1,2,1,2]
cm.connect_vertices(i=2, j=3, optimize=True)
assert cm.clusters == [[],[1,3,0,2,4],[],[],[]]
assert cm.cluster_indices == [1,1,1,1,1]
cm.tidy()
assert cm.clusters == [[0,1,2,3,4]]
assert cm.cluster_indices == [0,0,0,0,0]
#
cm = cluster_manager(n_vertices=6)
cm.connect_vertices(i=3, j=0, optimize=True)
cm.connect_vertices(i=2, j=4, optimize=True)
cm.connect_vertices(i=1, j=2, optimize=True)
cm.tidy()
assert cm.clusters == [[1,2,4],[0,3],[5]]
assert cm.cluster_indices == [1,0,0,1,0,2]
edges = [(0,1), (0,2), (3,4), (4,5)]
cm.connect_vertices(i=4, j=5, optimize=True)
cm.tidy()
assert cm.clusters == [[1,2,4,5],[0,3]]
assert cm.cluster_indices == [1,0,0,1,0,0]
es = construct_edge_sets(n_vertices=6, edge_list=edges)
cm.construct_spanning_trees(edge_sets=es)
assert cm.clusters == [[0,1,2,4,5],[3]]
assert cm.cluster_indices == [0,0,0,1,0,0]
assert cm.hinge_edges == [(-1,1), (1,0)]
assert cm.loop_edges == [(2,0), (4,3)]
assert cm.roots() == [0]
assert cm.tree_ids() == [0,0]
cm.find_loop_edge_bendings(edge_sets=es)
assert cm.loop_edge_bendings == [(1,2), (3,5)]
#
cm.cluster_indices = [1,0,0,1,0,0]
cm.clusters = [[1,2,4,5],[0,3]]
cm.hinge_edges = None
cm.loop_edges = None
cm.loop_edge_bendings = None
cm.merge_clusters_with_multiple_connections(edge_sets=es)
assert cm.clusters == [[0,1,2,3,4,5]]
assert cm.cluster_indices == [0,0,0,0,0,0]
#
sio = StringIO()
assert cm.show_summary(out=sio, prefix=">") is cm
assert not show_diff(sio.getvalue(), """\
>number of fixed vertex lists: 0
>number of fixed vertices: 0
>number of clusters: 1
>merge clusters with multiple connections: 2 passes
>number of hinge edges: None
>number of loop edges: None
>number of loop edge bendings: None
>number of fixed hinges: None
""")
#
cm = cluster_manager(n_vertices=3, all_in_one_rigid_body=True)
assert cm.clusters == [[0,1,2]]
assert cm.cluster_indices == [0,0,0]
cm.tidy()
cm.construct_spanning_trees(edge_sets=None)
assert cm.clusters == [[0,1,2]]
assert cm.cluster_indices == [0,0,0]
assert cm.hinge_edges == [(-1,0)]
assert cm.loop_edges == []
assert cm.roots() == [0]
assert cm.tree_ids() == [0]
cm.find_loop_edge_bendings(edge_sets=None)
assert cm.loop_edge_bendings == []
def run(args):
assert args in [[], ["python"], ["c++"]]
#
sgno_list_by_index_list_by_cs = {}
from cctbx import sgtbx
from cctbx import miller
for symbols in sgtbx.space_group_symbol_iterator():
psgi = sgtbx.space_group_info(symbols.universal_hermann_mauguin()) \
.primitive_setting()
p_indices = miller.index_generator(
space_group_type=psgi.type(),
anomalous_flag=False,
max_index=[4]*3).to_array()
# 4 is the smallest value leading to correct results; any larger
# value will work, too, but will make this procedure slower
p1_indices = miller.expand_to_p1_iselection(
space_group=psgi.group(),
anomalous_flag=False,
indices=p_indices,
build_iselection=False).indices
from cctbx.array_family import flex
sort_perm = flex.sort_permutation(
data=miller.index_span(p1_indices).pack(p1_indices))
p1_indices = p1_indices.select(sort_perm)
index_list = tuple(p1_indices)
sgno = psgi.type().number()
sgno_list_by_index_list = sgno_list_by_index_list_by_cs \
.setdefault(symbols.crystal_system(), {})
sgno_list_by_index_list.setdefault(index_list, []).append(sgno)
from scitbx.graph import tardy_tree
cluster_manager = tardy_tree.cluster_manager(n_vertices=231)
for cs,sgno_list_by_index_list in sgno_list_by_index_list_by_cs.items():
for sgno_list in sgno_list_by_index_list.values():
i = sgno_list[0]
for j in sgno_list[1:]:
cluster_manager.connect_vertices(i=i, j=j, optimize=True)
cluster_manager.tidy()
#
# everything below is just to format the results
#
if (args == []):
for cluster in cluster_manager.clusters:
if (len(cluster) == 1): break
print cluster
else:
note = ("""\
Output of: cctbx/examples/find_sys_abs_equiv_space_groups.py %s
If you have to edit this table, please send email to: [email protected]
""" % args[0]).splitlines()
#
if (args == ["python"]):
print "space_group_numbers = ["
for line in note:
print " #", line
ci = cluster_manager.cluster_indices
cl = cluster_manager.clusters
for sgno in xrange(231):
cluster = list(cl[ci[sgno]])
cluster.remove(sgno)
if (len(cluster) == 0): s = "None"
else: s = str(tuple(cluster))
if (sgno == 230): comma = ""
else: comma = ","
print " %s%s" % (s, comma)
print "]"
else:
print """\
#ifndef CCTBX_SGTBX_SYS_ABS_EQUIV_H
#define CCTBX_SGTBX_SYS_ABS_EQUIV_H
namespace cctbx { namespace sgtbx { namespace sys_abs_equiv {
"""
data = []
ci = cluster_manager.cluster_indices
cl = cluster_manager.clusters
for line in note:
print " //", line
for sgno in xrange(231):
cluster = list(cl[ci[sgno]])
cluster.remove(sgno)
if (len(cluster) == 0):
data.append("0")
else:
cid = "data_%03d" % sgno
data.append(cid)
print " static const unsigned %s[] = {%d, %s};" % (
cid, len(cluster), ", ".join([str(i) for i in cluster]))
print ""
print " static const unsigned* space_group_numbers[] = {"
print " ", ",\n ".join(data)
print """\
def run(args):
assert args in [[], ["python"], ["c++"]]
#
sgno_list_by_index_list_by_cs = {}
from cctbx import sgtbx
from cctbx import miller
for symbols in sgtbx.space_group_symbol_iterator():
psgi = sgtbx.space_group_info(symbols.universal_hermann_mauguin()) \
.primitive_setting()
p_indices = miller.index_generator(space_group_type=psgi.type(),
anomalous_flag=False,
max_index=[4] * 3).to_array()
# 4 is the smallest value leading to correct results; any larger
# value will work, too, but will make this procedure slower
p1_indices = miller.expand_to_p1_iselection(
space_group=psgi.group(),
anomalous_flag=False,
indices=p_indices,
build_iselection=False).indices
from cctbx.array_family import flex
sort_perm = flex.sort_permutation(
data=miller.index_span(p1_indices).pack(p1_indices))
p1_indices = p1_indices.select(sort_perm)
index_list = tuple(p1_indices)
sgno = psgi.type().number()
sgno_list_by_index_list = sgno_list_by_index_list_by_cs \
.setdefault(symbols.crystal_system(), {})
sgno_list_by_index_list.setdefault(index_list, []).append(sgno)
from scitbx.graph import tardy_tree
cluster_manager = tardy_tree.cluster_manager(n_vertices=231)
for cs, sgno_list_by_index_list in sgno_list_by_index_list_by_cs.items():
for sgno_list in sgno_list_by_index_list.values():
i = sgno_list[0]
for j in sgno_list[1:]:
cluster_manager.connect_vertices(i=i, j=j, optimize=True)
cluster_manager.tidy()
#
# everything below is just to format the results
#
if (args == []):
for cluster in cluster_manager.clusters:
if (len(cluster) == 1): break
print(cluster)
else:
note = ("""\
Output of: cctbx/examples/find_sys_abs_equiv_space_groups.py %s
If you have to edit this table, please send email to: [email protected]
""" % args[0]).splitlines()
#
if (args == ["python"]):
print("space_group_numbers = [")
for line in note:
print(" #", line)
ci = cluster_manager.cluster_indices
cl = cluster_manager.clusters
for sgno in range(231):
cluster = list(cl[ci[sgno]])
cluster.remove(sgno)
if (len(cluster) == 0): s = "None"
else: s = str(tuple(cluster))
if (sgno == 230): comma = ""
else: comma = ","
print(" %s%s" % (s, comma))
print("]")
else:
print("""\
#ifndef CCTBX_SGTBX_SYS_ABS_EQUIV_H
#define CCTBX_SGTBX_SYS_ABS_EQUIV_H
namespace cctbx { namespace sgtbx { namespace sys_abs_equiv {
""")
data = []
ci = cluster_manager.cluster_indices
cl = cluster_manager.clusters
for line in note:
print(" //", line)
for sgno in range(231):
cluster = list(cl[ci[sgno]])
cluster.remove(sgno)
if (len(cluster) == 0):
data.append("0")
else:
cid = "data_%03d" % sgno
data.append(cid)
print(" static const unsigned %s[] = {%d, %s};" %
(cid, len(cluster), ", ".join(
[str(i) for i in cluster])))
print("")
print(" static const unsigned* space_group_numbers[] = {")
print(" ", ",\n ".join(data))
print("""\
};
}}}
#endif // GUARD""")
def exercise_fixed_vertices(n_trials=10):
cm = cluster_manager(n_vertices=2, fixed_vertex_lists=[[0]])
assert cm.clusters == [[0], [1]]
cm = cluster_manager(n_vertices=2, fixed_vertex_lists=[[1]])
assert cm.clusters == [[1], [0]]
edge_list = [(0, 1), (1, 2), (2, 3), (1, 3)]
edge_sets = construct_edge_sets(n_vertices=4, edge_list=edge_list)
for fixed_vertex in [0, 1]:
for optimize in [False, True]:
for connects in [[(1, 2), (2, 3)], [(2, 3), (1, 2)],
[(2, 1), (3, 2)]]:
cm = cluster_manager(n_vertices=4,
fixed_vertex_lists=[[fixed_vertex]])
for i, j in connects:
cm.connect_vertices(i=i, j=j, optimize=optimize)
if (fixed_vertex == 0):
if (connects[0] == (2, 1)):
if (not optimize):
assert cm.clusters == [[0], [], [], [3, 2, 1]]
else:
assert cm.clusters == [[0], [], [2, 1, 3], []]
else:
if (not optimize or connects[0][0] == 1):
assert cm.clusters == [[0], [1, 2, 3], [], []]
else:
assert cm.clusters == [[0], [], [2, 3, 1], []]
cm.tidy()
assert cm.clusters == [[0], [1, 2, 3]]
else:
assert cm.clusters == [[1, 2, 3], [0], [], []]
cm.tidy()
assert cm.clusters == [[1, 2, 3], [0]]
cm.construct_spanning_trees(edge_sets=edge_sets)
assert cm.clusters == [[0, 1, 2, 3]]
assert cm.hinge_edges == [(-1, 1)]
assert cm.loop_edges == []
#
from scitbx.graph import test_cases_tardy_pdb
tc = test_cases_tardy_pdb.test_cases[5]
assert tc.tag == "tyr_with_h"
tt = tc.tardy_tree_construct(fixed_vertex_lists=[[0, 16, 17]])
assert tt.cluster_manager.clusters == [[
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19
], [11], [20]]
try:
tc.tardy_tree_construct(fixed_vertex_lists=[[0], [1]])
except RuntimeError as e:
assert str(e) == \
"connect_clusters(): fixed vertex lists in same connected tree."
else:
raise Exception_expected
try:
tc.tardy_tree_construct(fixed_vertex_lists=[[0], [10]])
except RuntimeError as e:
assert str(e) == \
"determine_weighted_order_for_construct_spanning_tree():" \
" fixed vertex lists in same connected tree."
else:
raise Exception_expected
try:
tc.tardy_tree_construct(fixed_vertex_lists=[[0], [11]])
except RuntimeError as e:
assert str(e) == \
"construct_spanning_trees():" \
" fixed vertex lists in same connected tree."
else:
raise Exception_expected
#
for tc in test_cases:
if (max(tc.tree_ids1) == 0): continue
tt = construct(n_vertices=tc.n_vertices, edge_list=tc.edge_list)
tt.build_tree()
cm = tt.cluster_manager
cl = cm.clusters
ti = cm.tree_ids()
assert ti[0] != ti[-1]
for lfvl0 in range(1, len(cl[0]) + 1):
for lfvl1 in range(1, len(cl[-1]) + 1):
for i_trial in range(n_trials):
fvl0 = random_permutation(cl[0])[:lfvl0]
fvl1 = random_permutation(cl[-1])[:lfvl1]
ttf = construct(n_vertices=tc.n_vertices,
edge_list=tc.edge_list,
fixed_vertex_lists=[fvl0,
fvl1]).build_tree()
cmf = ttf.cluster_manager
cif = cmf.cluster_indices
fvgci = cmf.fixed_vertices_given_cluster_index_dict()
assert len(fvgci) == len(cmf.fixed_vertex_lists)
for fixed_vertices in cmf.fixed_vertex_lists:
assert len(set([cif[i] for i in fixed_vertices])) == 1
assert fvgci[cif[fixed_vertices[0]]] is fixed_vertices
#
for fixed_vertex in [0, 1]:
tt = construct(n_vertices=2,
edge_list=[(0, 1)],
fixed_vertex_lists=[[fixed_vertex]]).build_tree()
assert tt.cluster_manager.clusters == [[0, 1]]
#
for fixed_vertex in [0, 1, 2]:
tt = construct(n_vertices=3,
edge_list=[(0, 1), (1, 2)],
fixed_vertex_lists=[[fixed_vertex]]).build_tree()
assert tt.cluster_manager.clusters == [[0, 1, 2]]
#
el = [(8, 9), (7, 9), (3, 7), (8, 11), (8, 12), (12, 14), (13, 15),
(7, 13), (1, 6), (4, 6), (0, 5)]
tt = construct(n_vertices=16, edge_list=el, fixed_vertices=())
assert tt.cluster_manager.fixed_vertex_lists == ()
tt = construct(n_vertices=16,
edge_list=el,
fixed_vertices=(12, 6, 4, 7, 9, 5))
assert tt.cluster_manager.fixed_vertex_lists == [[12, 7, 9], [6, 4], [5]]
