def _get_sub_pathes(self, segments):
pathes = []
for i in range(len(segments)):
if i == 0:
continue
p = []
if i == 1:
p.extend(segments[0])
else:
half = len(segments[i - 1]) / 2
p.extend(segments[i - 1][half - 1:])
if i == len(segments) - 1:
p.extend(segments[i])
else:
half = len(segments[i]) / 2
p.extend(segments[i][:half - 1])
pathes.append(p)
for i, p in enumerate(pathes):
basic_io.points_to_pdb("path." + str(i) + ".pdb", p)
f = open("path." + str(i) + ".str", "w")
f.write(basic_io.points_to_str(p))
f.close()
return pathes
def _get_sub_pathes(self, segments):
pathes = []
for i in range(len(segments)):
if i == 0:
continue
p = []
if i == 1:
p.extend(segments[0])
else:
half = len(segments[i - 1]) / 2
p.extend(segments[i - 1][half - 1 :])
if i == len(segments) - 1:
p.extend(segments[i])
else:
half = len(segments[i]) / 2
p.extend(segments[i][: half - 1])
pathes.append(p)
for i, p in enumerate(pathes):
basic_io.points_to_pdb("path." + str(i) + ".pdb", p)
f = open("path." + str(i) + ".str", "w")
f.write(basic_io.points_to_str(p))
f.close()
return pathes
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 listen_for_keys(self, state):
if state.key == 'u':
if len(self.previous_points) > 0:
pos = self.previous_points.pop()
for i, p in enumerate(self.points):
p.pos = pos[i]
self._update_path()
if state.key == 'd':
if len(self.points) == 0:
return
if len(self.highlighted_ends) == 2:
dist = util.distance(self.points[-1].pos,
self.highlighted_ends[1][1].d)
if dist < 0.1:
self.highlighted_ends.pop()
for i in range(2):
last = self.points.pop()
last.visible = False
del last
for i in range(3):
last = self.lines.pop()
last.visible = False
del last
return
last = self.points.pop()
last.visible = False
del last
if len(self.lines) != 0:
last_l = self.lines.pop()
last_l.visible = False
del last_l
if len(self.lines) != 0:
last_l = self.lines.pop()
last_l.visible = False
del last_l
if len(self.points) == 1:
last = self.points.pop()
last.visible = False
del last
if state.key == 'r':
self._run_path_finding(state)
if state.key == 's':
print "saving session: rnamake.save"
f = open("rnamake.save", "w")
f.write(state.vmg.mg.topology_to_str() + "\n")
for n in state.vmg.mg.graph.nodes:
f.write(str(n.level) + " ")
f.write("\n")
point_pos = []
for p in self.points:
point_pos.append([p.pos.x, p.pos.y, p.pos.z])
f.write(basic_io.points_to_str(point_pos) + "\n")
f.write(
str(self.highlighted_ends[0][0]) + " " +
self.highlighted_ends[0][1].name() + "\n")
if len(self.highlighted_ends) > 1:
f.write(
str(self.highlighted_ends[1][0]) + " " +
self.highlighted_ends[1][1].name() + "\n")
f.close()
if state.key == 'f':
pass
if state.key == 'p':
print "printing structure: rnamake.pdb"
state.vmg.mg.to_pdb("rnamake.pdb", close_chain=1, renumber=1)
def listen_for_keys(self, state):
if state.key == 'u':
if len(self.previous_points) > 0:
pos = self.previous_points.pop()
for i, p in enumerate(self.points):
p.pos = pos[i]
self._update_path()
if state.key == 'd':
if len(self.points) == 0:
return
if len(self.highlighted_ends) == 2:
dist = util.distance(self.points[-1].pos, self.highlighted_ends[1][1].d)
if dist < 0.1:
self.highlighted_ends.pop()
for i in range(2):
last = self.points.pop()
last.visible = False
del last
for i in range(3):
last = self.lines.pop()
last.visible = False
del last
return
last = self.points.pop()
last.visible = False
del last
if len(self.lines) != 0:
last_l = self.lines.pop()
last_l.visible = False
del last_l
if len(self.lines) != 0:
last_l = self.lines.pop()
last_l.visible = False
del last_l
if len(self.points) == 1:
last = self.points.pop()
last.visible = False
del last
if state.key == 'r':
self._run_path_finding(state)
if state.key == 's':
print "saving session: rnamake.save"
f = open("rnamake.save", "w")
f.write(state.vmg.mg.topology_to_str() + "\n")
for n in state.vmg.mg.graph.nodes:
f.write(str(n.level) + " ")
f.write("\n")
point_pos = []
for p in self.points:
point_pos.append([p.pos.x, p.pos.y, p.pos.z])
f.write(basic_io.points_to_str(point_pos) + "\n")
f.write(str(self.highlighted_ends[0][0]) + " " +
self.highlighted_ends[0][1].name() + "\n")
if len(self.highlighted_ends) > 1:
f.write(str(self.highlighted_ends[1][0]) + " " +
self.highlighted_ends[1][1].name() + "\n")
f.close()
if state.key == 'f':
pass
if state.key == 'p':
print "printing structure: rnamake.pdb"
state.vmg.mg.to_pdb("rnamake.pdb", close_chain=1,renumber=1)