def ssDNA_gauss(M,VW, Z,L, frames, rcut=1.0, step=5e4):
try:
#V = util.pickle_load('V.pkl')
P = util.pickle_load('SSDNA.pkl')
except:
P = M.cord_auto(['K','T'])
util.pickle_dump(P,'SSDNA.pkl')
gauss_map = []
w = np.array([[1,0,0],[0,1,0],[0,0,1]])
ndna = P.shape[1]/VW.shape[1]
print P.shape
for k in frames:
location = []
print k
try:
for i in range(VW.shape[1]):
#we must rotate about a specific cube reference frame
if i in range(20):
V = VW[k][i]
x_r = points.unit(points.vector1d(V,Z[k][i*6+1],L[k]))
y_r = points.unit(points.vector1d(V,Z[k][i*6+2],L[k]))
z_r = points.unit(points.vector1d(V,Z[k][i*6+5],L[k]))
dd = points.dist(V,Z[k][i*6+5],L[k])[0]
v = np.array([x_r,y_r,z_r])
R = points.reference_rotation(v,w)
for j in range(ndna):
d = points.dist(V,P[k][j+i*ndna],L[k])[0]
c_r = points.unit(points.vector1d(V,P[k][j+i*ndna],L[k]))
location.append(points.unit(np.dot(R,np.transpose(c_r)))*d)
except:
print 'something went wrong here'
gauss_map.append(location)
#########
fid = open('gaussmap_dna.xyz','w')
max_gauss = 0
for k in gauss_map:
if len(k) > max_gauss:
max_gauss = len(k)
for k in range(len(gauss_map)):
fid.write('%i\n%i\n'%(max_gauss+4,frames[k]))
fid.write('E %.2f 0 0\n'%dd)
fid.write('E 0 %.2f 0\n'%dd)
fid.write('E 0 0 %.2f\n'%dd)
fid.write('V 0 0 0\n')
for i in gauss_map[k]:
fid.write('N %.3f %.3f %.3f\n'%(i[0],i[1],i[2]))
for i in range(max_gauss - len(gauss_map[k])):
fid.write('N 0 0 0\n')
fid.close()
###########
fid = open('gaussmap_dna_step.xyz','w')
max_gauss = 0
step = 10
for k in gauss_map:
if len(k) > max_gauss:
max_gauss = len(k)
max_gauss = max_gauss*step
for s in range(0,len(gauss_map)-step,step):
fid.write('%i\n\n'%(max_gauss+4))
fid.write('E 1 0 0\n')
fid.write('E 0 1 0\n')
fid.write('E 0 0 1\n')
fid.write('V 0 0 0\n')
count = 4
for k in range(s,s+step):
for i in gauss_map[k]:
fid.write('N %.3f %.3f %.3f\n'%(i[0],i[1],i[2]))
count+=1
for i in range(max_gauss+4 - count):
fid.write('N 0 0 0\n')
fid.close()
y = float(line.split()[2])
z = float(line.split()[3])
positions.append([x,y,z])
fid.close()
#Transform
L = np.array([50,50,50])
w = np.array([[1,0,0],[0,1,0],[0,0,1]])
V = np.array([0,0,0])
x_r = points.unit(np.array(orientations[1]))
y_r = points.unit(np.array(orientations[2]))
z_r = points.unit(np.array(orientations[3]))
v = np.array([x_r,y_r,z_r])
print points
R = points.reference_rotation(w,v)
location = []
for i in range(len(P)):
d = points.dist(V,P[i],L)[0]
c_r = points.unit(points.vector1d(V,P[i],L))
location.append(points.unit(np.dot(R,np.transpose(c_r)))*d)
#write out
positions.extend([0,0,0])
fid.open('cube_unit_cell.xyz','w')
fid.write('%i \n\n'%(len(positions)*len(location)))
for i in range(len(positions)):
for j in range(len(location)):
x = location[j][0] + positions[i][0]
y = location[j][1] + positions[i][1]
z = location[j][2] + positions[i][2]
def polymer_gauss(M,VW, Z,L, frames, rcut=1.0, step=5e4):
#\brief find the gauss map of polymers surrounding NC
try:
#V = util.pickle_load('V.pkl')
P = util.pickle_load('M.pkl')
except:
P = M.cord_auto(['M'])
util.pickle_dump(P,'M.pkl')
A = VW.shape[1]/2
gauss_map = []
w = np.array([[1,0,0],[0,1,0],[0,0,1]])
ndna = P.shape[1]/VW.shape[1]
print P.shape
for k in frames:
location = []
print k
try:
for i in range(VW.shape[1]):
#we must rotate about a specific cube reference frame
if i in range(1):
V = VW[k][i]
x_r = points.unit(points.vector1d(V,Z[k][i*6+1],L[k]))
y_r = points.unit(points.vector1d(V,Z[k][i*6+2],L[k]))
z_r = points.unit(points.vector1d(V,Z[k][i*6+5],L[k]))
v = np.array([x_r,y_r,z_r])
R = points.reference_rotation(v,w)
for j in range(1,ndna,2):
d = points.dist(V,P[k][j+i*ndna],L[k])[0]
c_r = points.unit(points.vector1d(V,P[k][j+i*ndna],L[k]))
location.append(points.unit(np.dot(R,np.transpose(c_r)))*d)
except:
print 'something went wrong here'
gauss_map.append(location)
#########
#fid = open('gaussmap_polymer.xyz','w')
#max_gauss = 0
#for k in gauss_map:
# if len(k) > max_gauss:
# max_gauss = len(k)
#for k in range(len(gauss_map)):
# fid.write('%i\n%i\n'%(max_gauss+4,frames[k]))
# fid.write('E 1 0 0\n')
# fid.write('E 0 1 0\n')
# fid.write('E 0 0 1\n')
# fid.write('V 0 0 0\n')
# for i in gauss_map[k]:
# fid.write('N %.3f %.3f %.3f\n'%(i[0],i[1],i[2]))
# for i in range(max_gauss - len(gauss_map[k])):
# fid.write('N 0 0 0\n')
#fid.close()
###########
fid = open('gaussmap_polymers_total.xyz','w')
max_gauss = 0
for k in gauss_map:
if len(k) > max_gauss:
max_gauss = len(k)
max_gauss = max_gauss*len(gauss_map)
fid.write('%i\n\n'%(max_gauss+4))
fid.write('E 1 0 0\n')
fid.write('E 0 1 0\n')
fid.write('E 0 0 1\n')
fid.write('V 0 0 0\n')
count = 4
for k in range(len(gauss_map)):
for i in gauss_map[k]:
fid.write('N %.3f %.3f %.3f\n'%(i[0],i[1],i[2]))
count+=1
fid.close()
