def add_dna(self):
for i,j in enumerate(self.bond_MN):
self.L=[]
self.N=[]
self.S=[]
pt = self.ssDNA[self.bond_MN[i]]
if pt[2] == 0:
self.vx, self.vy, self.vz = points.unit_vect(pt[0],pt[1],pt[2],self.x_length/2.0, self.x_length/2.0,
10)
elif pt[2]<self.x_length/self.pheight/1.5:
self.vx, self.vy, self.vz = points.unit_vect(pt[0],pt[1],pt[2],self.x_length/2.0, self.x_length/2.0, -1)
else:
self.vx, self.vy, self.vz = points.unit_vect(pt[0],pt[1],pt[2],self.x_length/2.0, self.x_length/2.0,
self.x_length/self.pheight/2)
self.vx=self.vx/self.scale
self.vy=self.vy/self.scale
self.vz=self.vz/self.scale
if self.make_rigid:
spacer_ds(self,self.ssDNA[self.bond_MN[i]][0],self.ssDNA[self.bond_MN[i]][1],self.ssDNA[self.bond_MN[i]][2],i)
else:
spacer(self,self.ssDNA[self.bond_MN[i]][0],self.ssDNA[self.bond_MN[i]][1],self.ssDNA[self.bond_MN[i]][2],i,start_scale=1.5)
if self.no_linker == False:
linker(self,j)
nucleotide(self,j)
else:
end_bead(self,j)
def add_dna(self):
for i, j in enumerate(self.bond_MN):
self.L = []
self.N = []
self.S = []
pt = self.ssDNA[self.bond_MN[i]]
if pt[2] == 0:
self.vx, self.vy, self.vz = points.unit_vect(
pt[0], pt[1], pt[2], self.x_length / 2.0,
self.x_length / 2.0, 10)
elif pt[2] < self.x_length / self.pheight / 1.5:
self.vx, self.vy, self.vz = points.unit_vect(
pt[0], pt[1], pt[2], self.x_length / 2.0,
self.x_length / 2.0, -1)
else:
self.vx, self.vy, self.vz = points.unit_vect(
pt[0], pt[1], pt[2], self.x_length / 2.0,
self.x_length / 2.0, self.x_length / self.pheight / 2)
self.vx = self.vx / self.scale
self.vy = self.vy / self.scale
self.vz = self.vz / self.scale
if self.make_rigid:
spacer_ds(self, self.ssDNA[self.bond_MN[i]][0],
self.ssDNA[self.bond_MN[i]][1],
self.ssDNA[self.bond_MN[i]][2], i)
else:
spacer(self,
self.ssDNA[self.bond_MN[i]][0],
self.ssDNA[self.bond_MN[i]][1],
self.ssDNA[self.bond_MN[i]][2],
i,
start_scale=1.5)
if self.no_linker == False:
linker(self, j)
nucleotide(self, j)
else:
end_bead(self, j)
def add_dna(self):
for i in range(self.data['num_dna']):
self.L=[]
self.N=[]
self.S=[]
self.vx,self.vy,self.vz = points.unit_vect(self.ssDNA[self.bond_MN[i]][0],self.ssDNA[self.bond_MN[i]][1],self.ssDNA[self.bond_MN[i]][2],0,0,0)
self.vx=self.vx/self.scale
self.vy=self.vy/self.scale
self.vz=self.vz/self.scale
if self.make_rigid:
spacer_ds_mk(self,self.ssDNA[self.bond_MN[i]][0],self.ssDNA[self.bond_MN[i]][1],self.ssDNA[self.bond_MN[i]][2],i)
else:
spacer(self,self.ssDNA[self.bond_MN[i]][0],self.ssDNA[self.bond_MN[i]][1],self.ssDNA[self.bond_MN[i]][2],i)
if self.no_linker == False:
linker(self, i)
nucleotide(self, i)
else:
end_bead(self,i)
def add_dna(self):
for i,j in enumerate(self.bond_MN):
self.L=[]
self.N=[]
self.S=[]
pt = self.ssDNA[self.bond_MN[i]]
self.vx, self.vy, self.vz = points.unit_vect(pt[0],pt[1],pt[2],pt[0],pt[1],pt[2]-0.5)
self.vx=self.vx/self.scale
self.vy=self.vy/self.scale
self.vz=self.vz/self.scale
if self.make_rigid:
spacer_ds(self,self.ssDNA[self.bond_MN[i]][0],self.ssDNA[self.bond_MN[i]][1],self.ssDNA[self.bond_MN[i]][2],i)
else:
spacer(self,self.ssDNA[self.bond_MN[i]][0],self.ssDNA[self.bond_MN[i]][1],self.ssDNA[self.bond_MN[i]][2],i)
if self.no_linker == False:
linker(self,j)
nucleotide(self,j)
else:
end_bead(self,j)
def add_dna(self):
for i, j in enumerate(self.bond_MN):
self.L = []
self.N = []
self.S = []
pt = self.ssDNA[self.bond_MN[i]]
self.vx, self.vy, self.vz = points.unit_vect(
pt[0], pt[1], pt[2], pt[0], pt[1], pt[2] - 0.5)
self.vx = self.vx / self.scale
self.vy = self.vy / self.scale
self.vz = self.vz / self.scale
if self.make_rigid:
spacer_ds(self, self.ssDNA[self.bond_MN[i]][0],
self.ssDNA[self.bond_MN[i]][1],
self.ssDNA[self.bond_MN[i]][2], i)
else:
spacer(self, self.ssDNA[self.bond_MN[i]][0],
self.ssDNA[self.bond_MN[i]][1],
self.ssDNA[self.bond_MN[i]][2], i)
if self.no_linker == False:
linker(self, j)
nucleotide(self, j)
else:
end_bead(self, j)
def add_dna(self):
for i in range(self.data['num_dna']):
self.L = []
self.N = []
self.S = []
self.vx, self.vy, self.vz = points.unit_vect(
self.ssDNA[self.bond_MN[i]][0], self.ssDNA[self.bond_MN[i]][1],
self.ssDNA[self.bond_MN[i]][2], 0, 0, 0)
self.vx = self.vx / self.scale
self.vy = self.vy / self.scale
self.vz = self.vz / self.scale
if self.make_rigid:
spacer_ds_mk(self, self.ssDNA[self.bond_MN[i]][0],
self.ssDNA[self.bond_MN[i]][1],
self.ssDNA[self.bond_MN[i]][2], i)
else:
spacer(self, self.ssDNA[self.bond_MN[i]][0],
self.ssDNA[self.bond_MN[i]][1],
self.ssDNA[self.bond_MN[i]][2], i)
if self.no_linker == False:
linker(self, i)
nucleotide(self, i)
else:
end_bead(self, i)