def listen_for_mouse(self, state):
if state.m_event:
m1 = state.m_event # get event
if m1.drop:
self.pick = None
self._update_path()
if m1.button == 'left' and m1.alt and m1.pick:
if m1.pick in self.points and m1.drag:
dist = util.distance(self.dragpos, m1.pickpos)
if dist < 1:
return
self.previous_points.append(
[vector(p.pos) for p in self.points])
self.dragpos = m1.pickpos
self.pick = m1.pick
else:
self._add_points_on_rna(m1, state)
elif m1.button == 'left' and m1.alt and not m1.drag:
pos = m1.pos
if len(self.points) > 0:
dist = util.distance(pos, self.points[-1].pos)
if dist < 1:
return
#need points on RNA first
if len(self.points) == 0:
return
#no points after reconnecting to RNA
if len(self.highlighted_ends) == 2:
dist = util.distance(self.points[-1].pos,
self.highlighted_ends[1][1].d)
if dist < 0.1:
return
p = sphere(pos=pos, radius=7.5, color=color.cyan)
self.points.append(p)
if len(self.points) > 1:
line = cylinder(pos=self.points[-2].pos,
axis=(p.pos - self.points[-2].pos) / 2,
color=color.cyan,
radius=7)
self.lines.append(line)
new_pos = self.points[-2].pos + (p.pos -
self.points[-2].pos) / 2
line = cylinder(pos=new_pos,
axis=(new_pos - self.points[-2].pos),
color=color.cyan,
radius=7)
self.lines.append(line)
def listen_for_mouse(self, state):
if state.m_event:
m1 = state.m_event# get event
if m1.drop:
self.pick = None
self._update_path()
if m1.button == 'left' and m1.alt and m1.pick:
if m1.pick in self.points and m1.drag:
dist = util.distance(self.dragpos, m1.pickpos)
if dist < 1:
return
self.previous_points.append([vector(p.pos) for p in self.points])
self.dragpos = m1.pickpos
self.pick = m1.pick
else:
self._add_points_on_rna(m1, state)
elif m1.button == 'left' and m1.alt and not m1.drag:
pos = m1.pos
if len(self.points) > 0:
dist = util.distance(pos, self.points[-1].pos)
if dist < 1:
return
#need points on RNA first
if len(self.points) == 0:
return
#no points after reconnecting to RNA
if len(self.highlighted_ends) == 2:
dist = util.distance(self.points[-1].pos, self.highlighted_ends[1][1].d)
if dist < 0.1:
return
p = sphere(pos=pos, radius=7.5, color=color.cyan)
self.points.append(p)
if len(self.points) > 1:
line = cylinder(pos=self.points[-2].pos,
axis=(p.pos - self.points[-2].pos)/2,
color=color.cyan,
radius = 7)
self.lines.append(line)
new_pos = self.points[-2].pos + (p.pos - self.points[-2].pos)/2
line = cylinder(pos=new_pos,
axis=(new_pos - self.points[-2].pos),
color=color.cyan,
radius = 7)
self.lines.append(line)
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 _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 _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 contact_map_from_pdbs(pdbs, res_seperation=8, max_dist=14, max=100000):
if len(pdbs) == 0:
raise ValueError("no pdbs supplied")
s = structure.structure_from_pdb(pdbs[0])
num_res = len(s.residues())
matrix = []
for i in range(num_res):
matrix.append([0 for j in range(num_res)])
for k, pdb in enumerate(pdbs):
if k > max:
break
s = structure.structure_from_pdb(pdb)
residues = s.residues()
for i, r1 in enumerate(residues):
try:
beads = r1.get_beads()
a1 = beads[-1]
except:
continue
for j, r2 in enumerate(residues):
if abs(i - j) < res_seperation:
continue
if i >= j:
continue
try:
beads = r2.get_beads()
a2 = beads[-1]
except:
continue
dist = util.distance(a1.center, a2.center)
if dist < max_dist:
matrix[i][j] += 1
return matrix
continue
m.name = r.side1 + "=" + r.side2
seqs = m.sequence().split("&")
flank1_5prime, flank1_3prime = get_final_flank_sequences(
r.flank1_5prime, r.flank1_3prime, seqs[0])
flank2_5prime, flank2_3prime = get_final_flank_sequences(
r.flank2_5prime, r.flank2_3prime, seqs[1])
front_bps = get_bp_steps_from_seqs(flank1_5prime, flank2_3prime)
end_bps = get_bp_steps_from_seqs(flank1_3prime, flank2_5prime)
rs = get_combined_structure(front_bps, end_bps, m)
#print rs.name + "." + r.side1_all + "." + r.side2_all
motifs[rs.name + "." + r.side1_all + "." + r.side2_all] = rs
dist_1 = util.distance(origin, rs.ends[0].d())
dist_2 = util.distance(origin, rs.ends[1].d())
if dist_1 > dist_2:
diff.append(basic_io.point_to_str(rs.ends[0].d()))
rot_diff.append(basic_io.matrix_to_str(rs.ends[0].r()))
else:
diff.append(basic_io.point_to_str(rs.ends[1].d()))
rot_diff.append(basic_io.matrix_to_str(rs.ends[1].r()))
#df['translation'] = diff
#df['rotation'] = rot_diff
#fname = util.filename(args.csv)
#df.to_csv(fname[:-4]+"_diff.csv", index=False)
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 _add_points_on_rna(self, m1, state):
for ni, v_end in state.vmg.open_bp_ends:
if not v_end.clicked(m1.pick):
continue
included = 0
for i, high_end in self.highlighted_ends:
if v_end == high_end:
included = 1
if included:
continue
self.highlighted_ends.append([ni, v_end])
if len(self.points) > 1:
"""pos = v_end.d
p = sphere(pos=pos, radius=0.1, color=color.cyan)
self.points.append(p)
line = cylinder(pos=self.points[-2].pos,
axis=(p.pos - self.points[-2].pos)/2,
color=color.cyan,
radius = 7)
self.lines.append(line)
new_pos = self.points[-2].pos + (p.pos - self.points[-2].pos)/2
line = cylinder(pos=new_pos,
axis=(new_pos - self.points[-2].pos),
color=color.cyan,
radius = 7)
self.lines.append(line)"""
pos = v_end.d
p1 = sphere(pos=pos, radius=0.1, color=color.cyan)
dir = v_end.r[2]
new_pos = pos - dir * 20
p2 = sphere(pos=new_pos, radius=7.5, color=color.cyan)
line = cylinder(pos=self.points[-1].pos,
axis=(p2.pos - self.points[-1].pos) / 2,
color=color.cyan,
radius=7)
new_pos = self.points[-1].pos + (p2.pos -
self.points[-1].pos) / 2
line2 = cylinder(pos=new_pos,
axis=(new_pos - self.points[-1].pos),
color=color.cyan,
radius=7)
self.lines.append(line)
self.lines.append(line2)
line3 = cylinder(pos=pos,
axis=-dir * 20,
color=color.cyan,
radius=7)
self.points.append(p2)
self.points.append(p1)
self.lines.append(line3)
#self._update_path()
return
if len(self.highlighted_ends) > 2:
return
pos = v_end.d
if len(self.points) > 0:
dist = util.distance(pos, self.points[-1].pos)
if dist < 1:
return
p = sphere(pos=pos, radius=0.1, color=color.cyan)
self.points.append(p)
dir = v_end.r[2]
line = cylinder(pos=pos,
axis=-dir * 20,
color=color.cyan,
radius=7)
self.lines.append(line)
new_pos = pos - dir * 20
p = sphere(pos=new_pos, radius=7.5, color=color.cyan)
self.points.append(p)
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 _add_points_on_rna(self, m1, state):
for ni, v_end in state.vmg.open_bp_ends:
if not v_end.clicked(m1.pick):
continue
included = 0
for i, high_end in self.highlighted_ends:
if v_end == high_end:
included = 1
if included:
continue
self.highlighted_ends.append([ni, v_end])
if len(self.points) > 1:
"""pos = v_end.d
p = sphere(pos=pos, radius=0.1, color=color.cyan)
self.points.append(p)
line = cylinder(pos=self.points[-2].pos,
axis=(p.pos - self.points[-2].pos)/2,
color=color.cyan,
radius = 7)
self.lines.append(line)
new_pos = self.points[-2].pos + (p.pos - self.points[-2].pos)/2
line = cylinder(pos=new_pos,
axis=(new_pos - self.points[-2].pos),
color=color.cyan,
radius = 7)
self.lines.append(line)"""
pos = v_end.d
p1 = sphere(pos=pos, radius=0.1, color=color.cyan)
dir = v_end.r[2]
new_pos = pos - dir*20
p2 = sphere(pos=new_pos, radius=7.5, color=color.cyan)
line = cylinder(pos=self.points[-1].pos,
axis=(p2.pos - self.points[-1].pos)/2,
color=color.cyan,
radius = 7)
new_pos = self.points[-1].pos + (p2.pos - self.points[-1].pos)/2
line2 = cylinder(pos=new_pos,
axis=(new_pos - self.points[-1].pos),
color=color.cyan,
radius = 7)
self.lines.append(line)
self.lines.append(line2)
line3 = cylinder(pos=pos, axis=-dir*20,
color=color.cyan, radius=7)
self.points.append(p2)
self.points.append(p1)
self.lines.append(line3)
#self._update_path()
return
if len(self.highlighted_ends) > 2:
return
pos = v_end.d
if len(self.points) > 0:
dist = util.distance(pos, self.points[-1].pos)
if dist < 1:
return
p = sphere(pos=pos, radius=0.1, color=color.cyan)
self.points.append(p)
dir = v_end.r[2]
line = cylinder(pos=pos, axis=-dir*20,
color=color.cyan, radius=7)
self.lines.append(line)
new_pos = pos - dir*20
p = sphere(pos=new_pos, radius=7.5, color=color.cyan)
self.points.append(p)