def to_motif_tree(self):
mt = motif_tree.MotifTree(sterics=self.option('sterics'))
for i, n in enumerate(self.tree.nodes):
m = rm.manager.get_motif(name=n.data.ref_state.name,
end_name=n.data.ref_state.end_names[0])
if i == 0:
motif.align_motif(n.data.cur_state.end_states[0], m.ends[0], m)
j = mt.add_motif(m)
else:
parent_index = n.parent_index()
parent_end_index = n.parent_end_index()
j = mt.add_motif(m, parent_index, parent_end_index)
if j == -1:
raise ValueError("cannot convert mst to mt in to_motif_tree")
for c in self.connections:
mt.add_connection(c.i, c.j, c.name_i, c.name_j)
return mt
def __init__(self):
self.pdb_str = ""
self.i = 1
self.mt = motif_tree.MotifTree(sterics=0)
def __init__(self, m=None, error_on_add=1, **options):
self.error_on_add = error_on_add
self.mt = motif_tree.MotifTree(m, **options)
def convert(self, mg, start=None, start_end_index=None, last_node=None):
self.mt = motif_tree.MotifTree()
self.mt.option('sterics', 0)
start_n = self._get_start_node(mg, start, start_end_index)
open_nodes = [start_n]
last_node_to_add = None
while len(open_nodes) > 0:
current = open_nodes.pop(0)
if last_node == current.node:
last_node_to_add = current
continue
if current.parent is None:
self.mt.add_motif(current.motif)
else:
new_parent_index = self.mt.get_node_by_id(
current.parent.data.id).index
self.mt.add_motif(current.motif,
parent_index=new_parent_index,
parent_end_index=current.parent_end_index)
new_nodes = self._get_new_nodes(current)
# check for duplicates
for n1 in new_nodes:
found = 0
for n2 in open_nodes:
if n2.node.index == n1.node.index:
found = 1
break
if last_node_to_add is not None:
if last_node_to_add.node.index == n1.index:
found = 1
break
if not found:
open_nodes.append(n1)
if last_node_to_add is not None:
new_parent_index = self.mt.get_node_by_id(
last_node_to_add.parent.data.id).index
self.mt.add_motif(
last_node_to_add.motif,
parent_index=new_parent_index,
parent_end_index=last_node_to_add.parent_end_index)
# add missing connections
for n in mg:
for c in n.connections:
if c is None:
continue
n_id = n.data.id
partner = c.partner(n.index)
pn_id = partner.data.id
try:
mt_n1 = self.mt.get_node_by_id(n_id)
mt_n2 = self.mt.get_node_by_id(pn_id)
except exceptions.MotifTreeException:
continue
if mt_n1.parent == mt_n2:
continue
if mt_n2.parent == mt_n1:
continue
n1_ei = c.end_index(n.index)
if n.data.mtype == motif_type.HELIX:
n1_ei = 1
n1_end_name = n.data.ends[n1_ei].name()
if self.mt.connections.in_connection(mt_n1.index, n1_end_name):
continue
n2_ei = c.end_index(partner.index)
if partner.data.mtype == motif_type.HELIX:
n2_ei = 1
n2_end_name = partner.data.ends[n2_ei].name()
self.mt.add_connection(mt_n1.index, mt_n2.index, n1_end_name,
n2_end_name)
self.mt.option('sterics', 1)
return self.mt
def graph_to_tree(mg, start=None, last_end=None):
if start is None:
start = mg.graph.oldest_node()
seen = []
open = [start]
mt = motif_tree.MotifTree()
mt.option('sterics', 0)
ss = mg.secondary_structure()
seen_nodes = {}
seen_connections = {}
index = 0
pos = 0
while len(open) > 0:
current = open.pop(0)
ss_m = ss.motif(current.data.id)
if index == 0:
free_end = -1
for i, c in enumerate(current.connections):
if c is None:
free_end = i
name = ss_m.name
if ss_m.name[2] == "=":
m = rm.manager.get_motif(name=name)
else:
m = rm.manager.get_motif(name=name,
end_name=ss_m.ends[free_end].name())
mt.add_motif(m)
else:
highest = -1
p = None
p_index = None
p_end_index = None
p_end_name = None
c_end_index = -1
c_end_name = None
for c in current.connections:
if c is None:
continue
p_new = c.partner(current.index)
if p_new in seen_nodes:
p_index = seen_nodes[p_new]
if highest < p_index:
highest = p_index
else:
continue
p = p_new
p_end_index = c.end_index(p_new.index)
p_end_name = p.data.ends[p_end_index].name()
c_end_index = c.end_index(current.index)
c_end_name = current.data.ends[c_end_index].name()
if p.data.name[2] == "=":
act_parent = mt.get_node(p_index)
p_end_index = 1
p_end_name = act_parent.data.ends[1].name()
if last_end is not None:
if last_end.name(
) == p_end_name and len(seen_nodes) != len(mg) - 1:
open.append(current)
continue
if ss_m.name[2] == "=":
name = ss_m.name
if c_end_index == 1:
spl = name.split("=")
name = spl[1] + "=" + spl[0]
m = rm.manager.get_motif(name=name)
else:
m = rm.manager.get_motif(name=ss_m.name, end_name=c_end_name)
#print m.name, p.data.name, p_index, p_end_index, p_end_name
seen_connections[str(p_index) + " " + str(index)] = 1
pos = mt.add_motif(m,
parent_index=p_index,
parent_end_name=p_end_name)
if pos == -1:
raise ValueError("could not convert graph to tree")
seen_nodes[current] = index
index += 1
for c in current.connections:
if c is not None:
p = c.partner(current.index)
if p not in seen_nodes and p not in open:
open.append(p)
for n in mg.graph:
for c in n.connections:
if c is None:
continue
key1 = str(seen_nodes[c.node_1]) + " " + str(seen_nodes[c.node_2])
key2 = str(seen_nodes[c.node_2]) + " " + str(seen_nodes[c.node_1])
if key1 not in seen_connections and key2 not in seen_connections:
mt.add_connection(seen_nodes[c.node_1], seen_nodes[c.node_2])
seen_connections[key1] = 1
return mt
def __init__(self):
self.mt = motif_tree.MotifTree()