def points_from_str(self, s):
point_pos = basic_io.str_to_points(s)
for i, pos in enumerate(point_pos):
if i == 0:
p = sphere(pos=pos, radius=0.5, color=color.cyan)
else:
p = sphere(pos=pos, radius=7.5, color=color.cyan)
self.points.append(p)
count = 0
if len(pos) > 0:
count = 1 + (len(self.points) - 2) * 2
for i in range(count):
line = cylinder(pos=[0, 0, 0],
axis=[0, 0, 0],
color=color.cyan,
radius=7)
self.lines.append(line)
self._update_path()
for p in self.points:
p.opacity = 0.5
for l in self.lines:
l.opacity = 0.5
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 points_from_str(self, s):
point_pos = basic_io.str_to_points(s)
for i, pos in enumerate(point_pos):
if i == 0:
p = sphere(pos=pos, radius=0.5, color=color.cyan)
else:
p = sphere(pos=pos, radius=7.5, color=color.cyan)
self.points.append(p)
count = 0
if len(pos) > 0:
count = 1 + (len(self.points)-2)*2
for i in range(count):
line = cylinder(pos=[0,0,0], axis=[0,0,0],
color=color.cyan, radius = 7)
self.lines.append(line)
self._update_path()
for p in self.points:
p.opacity = 0.5
for l in self.lines:
l.opacity = 0.5
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()