def _get_segments(self, path):
direction = [0, 0, 0]
new_direction = None
segments = []
segment = []
for i, p in enumerate(path):
if i < 2:
segment.append(p)
if i == 1:
direction = util.normalize(segment[0] - segment[1])
continue
new_direction = util.normalize(segment[-1] - p)
if util.distance(new_direction, direction) > 0.1:
segments.append(segment)
segment = [p]
direction = new_direction
else:
segment.append(p)
if len(segment) > 0:
segments.append(segment)
return segments
def _get_segments(self, path):
direction = [0, 0, 0]
new_direction = None
segments = []
segment = []
for i, p in enumerate(path):
if i < 2:
segment.append(p)
if i == 1:
direction = util.normalize(segment[0] - segment[1])
continue
new_direction = util.normalize(segment[-1] - p)
if util.distance(new_direction, direction) > 0.1:
segments.append(segment)
segment = [p]
direction = new_direction
else:
segment.append(p)
if len(segment) > 0:
segments.append(segment)
return segments
def listen(self):
self.state.key = self.listen_for_keys()
self.state.m_event = self.listen_for_mouse()
if self.state.update_center:
self._center_view()
self.state.update_center = 0
if self.dragging:
vec1 = util.normalize(self.scene.mouse.pos - self.lastpos)
if util.distance(vec1, [0, 0, 0]) > 0.1:
vec2 = self.scene.forward
rotation = cross(vec1, vec2)
mag = util.distance(self.scene.mouse.pos - self.lastpos,
[0, 0, 0])
self.scene.forward = self.scene.forward.rotate(angle=0.0007 *
mag,
axis=rotation)
if self.scene.forward.y > 0.90:
self.scene.forward.y = 0.90
if self.scene.forward.y < -0.90:
self.scene.forward.y = -0.90
if self.zooming:
vec1 = util.normalize(self.scene.mouse.pos - self.lastpos)
if util.distance(vec1, [0, 0, 0]) > 0.1:
mag = util.distance(self.scene.mouse.pos - self.lastpos,
[0, 0, 0])
if vec1[1] > 0:
self.scene.range = self.range / (1.000 + 0.0005 * mag)
self.range = self.range / (1.000 + 0.0005 * mag)
if vec1[1] < 0:
self.scene.range = self.range / (1.000 - 0.0005 * mag)
self.range = self.range / (1.000 - 0.0005 * mag)
val = self.tc.GetValue()
spl = val.split("\n")
if len(spl) > 1:
self._parse_commands(spl[0])
self.tc.SetValue("")
for f in self.functions:
if not f.activated:
continue
f.listen(self.state)
def listen(self):
self.state.key = self.listen_for_keys()
self.state.m_event = self.listen_for_mouse()
if self.state.update_center:
self._center_view()
self.state.update_center = 0
if self.dragging:
vec1 = util.normalize(self.scene.mouse.pos - self.lastpos)
if util.distance(vec1, [0, 0, 0]) > 0.1:
vec2 = self.scene.forward
rotation = cross(vec1, vec2)
mag = util.distance(self.scene.mouse.pos - self.lastpos, [0,0,0])
self.scene.forward = self.scene.forward.rotate(angle=0.0007*mag,
axis=rotation)
if self.scene.forward.y > 0.90:
self.scene.forward.y = 0.90
if self.scene.forward.y < -0.90:
self.scene.forward.y = -0.90
if self.zooming:
vec1 = util.normalize(self.scene.mouse.pos - self.lastpos)
if util.distance(vec1, [0, 0, 0]) > 0.1:
mag = util.distance(self.scene.mouse.pos - self.lastpos, [0,0,0])
if vec1[1] > 0:
self.scene.range = self.range/(1.000 + 0.0005*mag)
self.range = self.range/(1.000 + 0.0005*mag)
if vec1[1] < 0:
self.scene.range = self.range/(1.000 - 0.0005*mag)
self.range = self.range/(1.000 - 0.0005*mag)
val = self.tc.GetValue()
spl = val.split("\n")
if len(spl) > 1:
self._parse_commands(spl[0])
self.tc.SetValue("")
for f in self.functions:
if not f.activated:
continue
f.listen(self.state)
def draw_base_cartoon(self, indices, pos1, pos2):
points = []
for i in indices:
points.append(self.atoms[i].coords)
dir1 = points[0] - points[pos1]
dir2 = points[0] - points[pos2]
norm = util.normalize(np.cross(dir1, dir2))*0.25
self.cartoons.append(self.draw_cartoon(points, norm))
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 draw(self, view_mode=0):
self.view_mode = view_mode
self.drawn = 1
for va in self.atoms:
if va is not None:
va.draw(view_mode)
if view_mode == 0:
self.draw_bonds()
if view_mode == 1:
beads = self.get_beads()
pos_i = beads[1].center
pos_j = beads[2].center
axis = pos_j - pos_i
self.rod = cylinder(pos=pos_i, axis=axis, radius=1.0,
color=color.blue)
if view_mode == 2:
sugar_points = []
sugar_points.append( self.atoms[5].coords)
sugar_points.append( self.atoms[6].coords)
sugar_points.append( self.atoms[9].coords)
sugar_points.append( self.atoms[10].coords)
sugar_points.append( self.atoms[7].coords)
dir1 = self.atoms[5].coords - self.atoms[9].coords
dir2 = self.atoms[5].coords - self.atoms[10].coords
norm = util.normalize(np.cross(dir1, dir2))*0.25
if len(self.cartoons) > 0:
return
self.cartoons = [ self.draw_cartoon(sugar_points, norm) ]
if self.rtype.name == "ADE":
self.draw_base_cartoon([21, 20, 19, 16, 15], 3, 2)
self.draw_base_cartoon([17, 16, 15, 14, 13, 12], 3, 2)
self.draw_bond(21, 9)
elif self.rtype.name == "GUA":
self.draw_base_cartoon([22, 21, 20, 17, 16], 3, 2)
self.draw_base_cartoon([17, 16, 18, 12, 13, 15], 3, 2)
self.draw_bond(22, 9)
else:
self.draw_base_cartoon([12, 13, 15, 16, 18, 19], 3, 2)
self.draw_bond(12, 9)