def build(self):
f = open("all_points.str")
line = f.readline()
f.close()
path = basic_io.str_to_points(line)
mg = None
f = open("mg.top")
line = f.readline()
f.close()
mg = motif_graph.motif_graph_from_topology(line)
segments = self._get_segments(path)
pathes = self._get_sub_pathes(segments)
if mg == None:
mg = motif_graph.MotifGraph()
w = wrapper.FollowPathWrapper()
w.run(path="path.0.str", mg="mg.top")
f = open("mt_out.top")
line = f.readline()
f.close()
mt_all = motif_tree.motif_tree_from_topology_str(line)
mg.add_motif_tree(mt_all)
print "building:"
for i in range(1, len(pathes)):
print "path: ", i
last_node = mg.last_node()
s = mg.topology_to_str()
f = open("mg_input.top", "w")
f.write(s + "\n")
f.write(str(last_node.index) + " " + last_node.data.ends[1].name() + "\n")
f.close()
w = wrapper.FollowPathWrapper()
w.run(path="path." + str(i) + ".str", mg="mg_input.top")
f = open("mt_out.top")
line = f.readline()
f.close()
mt = motif_tree.motif_tree_from_topology_str(line)
mg.add_motif_tree(mt)
mt_all.add_motif_tree(mt)
mg.to_pdb("final_rna_path.pdb")
f = open("mt_out.top", "w")
f.write(mt_all.topology_to_str() + "\n")
f.close()
def _run_path_finding(self, state):
if self.built:
state.vmg.remove_node_level(1)
state.vmg.mg.decrease_level()
all_points = []
reg_points = []
for p in self.points:
reg_points.append(np.array(p.pos))
for i in range(len(reg_points) - 1):
all_points.append(reg_points[i])
diff = reg_points[i + 1] - reg_points[i]
unit_vector = util.normalize(diff)
current = reg_points[i] + unit_vector * 5.0
while util.distance(reg_points[i + 1], current) > 5.0:
all_points.append(current)
current = current + unit_vector * 5.0
s = basic_io.points_to_str(all_points)
f = open("all_points.str", "w")
f.write(s)
f.close()
basic_io.points_to_pdb("all_points.pdb", all_points)
f = open("mg.top", "w")
f.write(state.vmg.mg.topology_to_str() + "\n")
f.write(
str(self.highlighted_ends[0][0]) + " " +
self.highlighted_ends[0][1].name())
f.close()
self.path_builder.build()
f = open("mt_out.top")
lines = f.readlines()
f.close()
mt = motif_tree.motif_tree_from_topology_str(lines[0])
state.vmg.mg.increase_level()
state.vmg.add_motif_tree(mt, self.highlighted_ends[0][0],
self.highlighted_ends[0][1].name())
for p in self.points:
p.opacity = 0.5
for l in self.lines:
l.opacity = 0.5
self.built = 1
state.update_center = 1
def _run_path_finding(self, state):
if self.built:
state.vmg.remove_node_level(1)
state.vmg.mg.decrease_level()
all_points = []
reg_points = []
for p in self.points:
reg_points.append(np.array(p.pos))
for i in range(len(reg_points)-1):
all_points.append(reg_points[i])
diff = reg_points[i+1] - reg_points[i]
unit_vector = util.normalize(diff)
current = reg_points[i] + unit_vector*5.0
while util.distance(reg_points[i+1], current) > 5.0:
all_points.append(current)
current = current + unit_vector*5.0
s = basic_io.points_to_str(all_points)
f = open("all_points.str", "w")
f.write(s)
f.close()
basic_io.points_to_pdb("all_points.pdb", all_points)
f = open("mg.top", "w")
f.write(state.vmg.mg.topology_to_str() + "\n")
f.write(str(self.highlighted_ends[0][0]) + " " + self.highlighted_ends[0][1].name())
f.close()
self.path_builder.build()
f = open("mt_out.top")
lines = f.readlines()
f.close()
mt = motif_tree.motif_tree_from_topology_str(lines[0])
state.vmg.mg.increase_level()
state.vmg.add_motif_tree(mt,
self.highlighted_ends[0][0],
self.highlighted_ends[0][1].name())
for p in self.points:
p.opacity = 0.5
for l in self.lines:
l.opacity = 0.5
self.built = 1
state.update_center = 1
def build(self):
f = open("all_points.str")
line = f.readline()
f.close()
path = basic_io.str_to_points(line)
mg = None
f = open("mg.top")
line = f.readline()
f.close()
mg = motif_graph.motif_graph_from_topology(line)
segments = self._get_segments(path)
pathes = self._get_sub_pathes(segments)
if mg == None:
mg = motif_graph.MotifGraph()
w = wrapper.FollowPathWrapper()
w.run(path="path.0.str", mg="mg.top")
f = open("mt_out.top")
line = f.readline()
f.close()
mt_all = motif_tree.motif_tree_from_topology_str(line)
mg.add_motif_tree(mt_all)
print "building:"
for i in range(1, len(pathes)):
print "path: ", i
last_node = mg.last_node()
s = mg.topology_to_str()
f = open("mg_input.top", "w")
f.write(s + "\n")
f.write(
str(last_node.index) + " " + last_node.data.ends[1].name() +
"\n")
f.close()
w = wrapper.FollowPathWrapper()
w.run(path="path." + str(i) + ".str", mg="mg_input.top")
f = open("mt_out.top")
line = f.readline()
f.close()
mt = motif_tree.motif_tree_from_topology_str(line)
mg.add_motif_tree(mt)
mt_all.add_motif_tree(mt)
mg.to_pdb("final_rna_path.pdb")
f = open("mt_out.top", "w")
f.write(mt_all.topology_to_str() + "\n")
f.close()
