def rotate(degree, point_x, point_y):
radians = math.radians(degree)
x = point_x.x - point_y.x
y = point_x.y - point_y.y
temp_x = x*math.cos(radians) - y*math.sin(radians)
temp_y = x*math.sin(radians) + y*math.cos(radians)
return Point(temp_x+point_y.x,temp_y+point_y.y,point_y.z)
def rotate240(point_x, point_y):
'''
point_x rotate about point_y 240 degree
'''
sin240 = -math.sqrt(3) / 2
cos240 = -0.5
pointz = Point(point_y.x, point_y.y, point_y.z)
newpoint, magnitude = unit(pointz)
x = (cos240+newpoint.x**2*(1-cos240)) * point_x.x +\
(newpoint.x*newpoint.y*(1-cos240) - newpoint.z*sin240) * point_x.y +\
(newpoint.x*newpoint.z*(1-cos240) + newpoint.y*sin240) * point_x.z
y = (newpoint.y*newpoint.x*(1-cos240) + newpoint.z*sin240) * point_x.x +\
(cos240 + newpoint.y**2*(1-cos240)) * point_x.y +\
(newpoint.y*newpoint.z*(1-cos240) - newpoint.x*sin240) * point_x.z
z = (newpoint.z*newpoint.x*(1-cos240) - newpoint.y*sin240) * point_x.x +\
(newpoint.z*newpoint.y*(1-cos240) + newpoint.x*sin240) * point_x.y +\
(cos240 + newpoint.z**2*(1-cos240))*point_x.z
result_point = Point(x, y, z)
return result_point
def plot():
f = open("points","r")
content = f.read().splitlines()
point_1_list = content[0].split()
Point_1 = Point(float(point_1_list[0]),float(point_1_list[1]),float(point_1_list[2]),int(point_1_list[3]))
Point_1.setFather(1)
Point_1.editIndex(1)
old_point_2_list = content[1].split()
old_Point_2 = Point(float(old_point_2_list[0]),float(old_point_2_list[1]),float(old_point_2_list[2]),int(old_point_2_list[3]))
global R_radius
R_radius = Point_1.z
d_radius = distance(old_Point_2,Point_1)
Point_2 = Point(d_radius,0,R_radius,2)
Point_3 = rotate120(Point_2,Point_1)
Point_4 = rotate240(Point_2,Point_1)
Point_2.setFather(1)
Point_3.setFather(1)
Point_4.setFather(1)
Point_2.editIndex(2)
Point_3.editIndex(3)
Point_4.editIndex(4)
index_list = []
for i in content:
index_list.append(int(i.split()[3]))
dict_points = {
1:Point_1,
2:Point_2,
3:Point_3,
4:Point_4,
}
for i in dict_points.keys():
index_list.remove(i)
index_list.reverse()
while index_list:
temp = index_list.pop() # 1,2,5,6
if temp%2:
temp_father = (temp-1)/2
temp_grandfather = dict_points[temp_father].getFather()
dict_points[temp] = rotate(120,dict_points[temp_grandfather],dict_points[temp_father])
else:
temp_father = (temp-2)/2
temp_grandfather = dict_points[temp_father].getFather()
dict_points[temp] = rotate(240,dict_points[temp_grandfather],dict_points[temp_father])
dict_points[temp].setFather(temp_father)
dict_points[temp].editIndex(temp)
# global R_radius
dict_points[temp].z = R_radius
T_x_points_array = []
T_y_points_array = []
w = open("points_2D","w")
for i in sorted(dict_points.keys()):
w.write(str(dict_points[i]))
w.write("\n")
temp_father = dict_points[i].getFather()
T_x_points_array.append(dict_points[temp_father])
T_y_points_array.append(dict_points[i])
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# linesPlot.drawLines(T_x_points_array,T_y_points_array)
for i in range(len(T_y_points_array)):
ax.plot([T_x_points_array[i].x,T_y_points_array[i].x],\
[T_x_points_array[i].y,T_y_points_array[i].y],\
zs = [T_x_points_array[i].z,T_y_points_array[i].z],\
c = "b")
plt.savefig('lines_plot_2D.png')
plt.show()
def main():
print 'The default filename is points.'
fileName = raw_input('Input file name:')
inputFile = open(fileName,'r')
inputFileList = inputFile.read().splitlines()
pointMap = {}
for i in inputFileList:
tempList = i.split()
pointMap[int(tempList[3])] = Point(float(tempList[0]),float(tempList[1]),float(tempList[2]),int(tempList[3]))
Radius = float(inputFileList[0].split()[2])
r = distance(pointMap[1],pointMap[2])
print 'Eg: R.pdb or R.pse'
outPutFile = raw_input('Input output file name:')
# cmd.pseudoatom('center')
# cmd.set('surface_mode', 1)
# cmd.translate([0,0,0], 'center', camera=1)
# cmd.ramp_new('test', 'center', [640, 646, 647], ['black', 'forest', 'green'])
# cmd.set('surface_color', 'test', 't*')
#Plot the first 4 trimer-center's coordinates.
cmd.load('t1.pdb')
#first trimerIndex
cmd.select('/t1/PSDO')
# cmd.color('blue','t1')
cmd.show('line', 't1')
cmd.rotate ('z', -30, 't1', camera=1)
cmd.translate([0,0,Radius],'t1',camera=1)
#second trimerIndex
cmd.create('t2', 't1')
# cmd.color('red', 't2')
cmd.select('/t2/PSDO')
# cmd.color('yellow', 't2')
cmd.show('line', 't2')
cmd.translate([r, 0, 0], 't2', camera=1)
cmd.orient('t2')
cmd.rotate('z', 60, 't2', camera=1)
cmd.rotate('z', -30 )
#this angle changes to bring involved pseudo atoms to horizontal positions
cmd.rotate('y', 4.726, 't2', camera=1)
cmd.rotate('x', 0.004, 't2', camera=1)
# because we are rotating only one trimer, the 2 central pseudo atoms will not align. correction commands are:
cmd.translate([0, -0.0440605685747639, -2.14176156973178], 't2', camera=1)
# cmd.alter('/t2//A', chain='D')
# cmd.alter('/t2//B', chain='E')
# cmd.alter('/t2//C', chain='F')
#third trimerIndex
cmd.create('t3','t2')
cmd.select('/t3/PSDO')
cmd.show('line','t3')
cmd.origin('t1')
cmd.rotate(pointMap[1].getCoordinate(),120,'t3',camera=1)
#forth trimerIndex
cmd.create('t4','t2')
cmd.select('/t4/PSDO')
cmd.show('line','t4')
cmd.origin('t1')
cmd.rotate(pointMap[1].getCoordinate(),240,'t4',camera=1)
#According to the first 4 trimer-center coordinates, to plot the following trimers.
keyList = pointMap.keys()
keyList.sort()
# testCount = 1
for i in keyList:
if (i>4):
# testCount += 1
tempTName = 't'+str(i)
if (i%2)==1:
tempTFatherName = 't'+str((i-1)/2)
tempDegree = 120
else:
tempTFatherName = 't'+str((i-2)/2)
tempDegree = 240
tempTGrandFatherIndex = ((i-1)//2-1)//2
if tempTGrandFatherIndex == 0:
tempTGrandFatherIndex = 1
tempTGrandFatherName = 't'+str(tempTGrandFatherIndex)
cmd.create(tempTName,tempTGrandFatherName)
cmd.select('/'+tempTName+'/PSDO')
cmd.show('line',tempTName)
cmd.origin(tempTFatherName)
cmd.rotate(pointMap[(i-1)//2].getCoordinate(),tempDegree,tempTName,camera=1)
cmd.save(outPutFile)
def algorithm(R, r, writeInFile=True):
# The IO for researcher to input the R
# r = 52.0769942809
cosphi = (2 * R**2 - r**2) / (2 * R**2)
sinphi = math.sqrt(1 - cosphi**2)
K_dict = {}
K_dict[1] = Point(0, 0, R, 1)
K_dict[2] = Point(sinphi * R, 0, cosphi * R)
K_dict[2].editIndex(2)
K_dict[3] = rotate120(K_dict[2], K_dict[1])
K_dict[3].editIndex(3)
K_dict[4] = rotate240(K_dict[2], K_dict[1])
K_dict[4].editIndex(4)
K_queue = [2, 3, 4]
K_keepers = [K_dict[1], K_dict[2], K_dict[3], K_dict[4]]
K_index = 5
K_count = 4
# open the file to write, w is write the points' coordinations
if writeInFile:
w = open("points", "w")
w_plot = open("lines", "w")
# To write the first 4 points' coordination the file "points",
for i in K_keepers:
w.write(str(i))
w.write("\n")
# To write the first 3 lines 2 ends' points coordinations in the file "lines"
w_plot.write(str(K_keepers[0]) + " " + str(K_keepers[1]) + "\n")
w_plot.write(str(K_keepers[0]) + " " + str(K_keepers[2]) + "\n")
w_plot.write(str(K_keepers[0]) + " " + str(K_keepers[3]) + "\n")
# Repeat the step which finds the coordinations
# according to the points in the K_queue
# and push the new points in the K_queue
# Until we use all the points in the K_queue
while len(K_queue) != 0:
father = K_queue.pop(0)
grandfather = get_root_index(father)
if K_dict.has_key(father):
new_point = rotate120(K_dict[grandfather], K_dict[father])
K_index = father * 2 + 1
new_point.editIndex(K_index)
if check_everydistance(r, new_point, K_keepers):
K_keepers.append(new_point)
K_dict[K_index] = new_point
K_queue.append(K_index)
K_count += 1
if writeInFile:
w.write(str(new_point) + "\n")
w_plot.write(
str(new_point) + " " + str(K_dict[father]) + "\n")
K_index = father * 2 + 2
new_point = rotate240(K_dict[grandfather], K_dict[father])
new_point.editIndex(K_index)
if check_everydistance(r, new_point, K_keepers):
K_keepers.append(new_point)
K_dict[K_index] = new_point
K_queue.append(K_index)
K_count += 1
if writeInFile:
w.write(str(new_point) + "\n")
w_plot.write(
str(new_point) + " " + str(K_dict[father]) + "\n")
if writeInFile:
print "There are " + str(K_count) + " points."
print "There are " + str(T_points_count) + " T_points."
w_plot.close
w.close
return K_count