if len(argv) != 3:
print 'Usage: %s MT_length MT_extra\nAll lengths should be specified in monomers. MT_length should be even: second half of tubule will bw for extra monomers during assembly\n'%argv[0]
exit(0)
MT_len = int(argv[1])
MT_extra = int(argv[2])
if MT_len % 2:
MT_len += 1
pdbxyzfilename = 'structs/xyz_{}_{}.pdb'.format(MT_len, MT_extra)
pdbangfilename = 'structs/ang_{}_{}.pdb'.format(MT_len, MT_extra)
pdbxyz = open(pdbxyzfilename, "w")
pdbang = open(pdbangfilename, "w")
pdbstr1 = 'ATOM 14 CB ALA A 7 8.120 -0.000 52.923 0.00 8.12 A'
pdbat1 = PDBAtom(pdbstr1)
pdbstr2 = 'ATOM 14 CB GLY A 7 8.120 -0.000 52.923 0.00 8.12 A'
pdbat2 = PDBAtom(pdbstr2)
chains = [chr(i) for i in range(ord('A'), ord('M')+1)]
for chain in chains:
for mon in range(MT_len):
R = R_MT
pdbat2.z = 0.0
pdbat1.z = 2*r_mon*mon + z_step*(ord(chain) - ord('A'))
alpha = alpha_step*(ord(chain) - ord('A'))
pdbat2.y = -alpha
pdbat2.x = 0.0
x = R*cos(-alpha)
y = R*sin(-alpha)
pdbat1.chainid = chain
if len(argv) == 4 and argv[3] == '-d':
delete = True
else:
delete = False
if MT_len < tail_len:
print 'Tail can not be longer, than MT'
exit(0)
pdbxyzfilename = 'structs/xyz_{}.pdb'.format(MT_len)
pdbangfilename = 'structs/ang_{}.pdb'.format(MT_len)
pdbxyz = open(pdbxyzfilename, "w")
pdbang = open(pdbangfilename, "w")
pdbstr1 = 'ATOM 14 CB ALA A 7 8.120 -0.000 52.923 0.00 8.12 A'
pdbat1 = PDBAtom(pdbstr1)
pdbstr2 = 'ATOM 14 CB GLY A 7 8.120 -0.000 52.923 0.00 8.12 A'
pdbat2 = PDBAtom(pdbstr2)
chains = [chr(i) for i in range(ord('A'), ord('M') + 1)]
for chain in chains:
for mon in range(MT_len):
if (MT_len - mon) < tail_len:
if delete == True and chain == chains[len(chains) - 1]:
break
R = R_MT + (tail_len - (MT_len - mon)) * 2 * r_mon * sin(
theta_tail) #tail_step*(tail_len - (MT_len - mon))
pdbat2.z = theta_tail #atan(tail_step/z_step)
pdbat1.z = 2 * r_mon * mon + z_step * (ord(chain) - ord('A'))
else:
R = R_MT
pdbat2.z = 0.0
atoms.remove(atom2)
while True:
generate(n)
sparse()
if len(atoms) == n:
break
pdbxyzfilename = 'volxyz_{}.pdb'.format(int(conc))
pdbangfilename = 'volang_{}.pdb'.format(int(conc))
pdbxyz = open(pdbxyzfilename, "w")
pdbang = open(pdbangfilename, "w")
pdbstr1 = 'ATOM 14 CB ALA A 7 8.120 -0.000 52.923 0.00 8.12 A'
pdbat1 = PDBAtom(pdbstr1)
pdbstr2 = 'ATOM 14 CB GLY A 7 8.120 -0.000 52.923 0.00 8.12 A'
pdbat2 = PDBAtom(pdbstr2)
for atom in atoms:
pdbat1.x = atom[0]
pdbat1.y = atom[1]
pdbat1.z = atom[2]
pdbat1.chainid = 'A'
pdbat1.residueseq = atoms.index(atom) + 1
pdbat1.number = 2 * atoms.index(atom) + 1
pdbat1.name = 'CA'
pdbxyz.write("%s\n" % str(pdbat1))
pdbat1.x = atom[0]
pdbat1.y = atom[1]
print 'Usage: %s MT_length MT_extra\nAll lengths should be specified in monomers. MT_length should be even: second half of tubule will bw for extra monomers during assembly\n' % argv[
0]
exit(0)
MT_len = int(argv[1])
MT_extra = int(argv[2])
if MT_len % 2:
MT_len += 1
pdbxyzfilename = 'structs/xyz_{}_{}.pdb'.format(MT_len, MT_extra)
pdbangfilename = 'structs/ang_{}_{}.pdb'.format(MT_len, MT_extra)
pdbxyz = open(pdbxyzfilename, "w")
pdbang = open(pdbangfilename, "w")
pdbstr1 = 'ATOM 14 CB ALA A 7 8.120 -0.000 52.923 0.00 8.12 A'
pdbat1 = PDBAtom(pdbstr1)
pdbstr2 = 'ATOM 14 CB GLY A 7 8.120 -0.000 52.923 0.00 8.12 A'
pdbat2 = PDBAtom(pdbstr2)
chains = [chr(i) for i in range(ord('A'), ord('M') + 1)]
for chain in chains:
for mon in range(MT_len):
R = R_MT
pdbat2.z = 0.0
pdbat1.z = 2 * r_mon * mon + z_step * (ord(chain) - ord('A'))
alpha = alpha_step * (ord(chain) - ord('A'))
pdbat2.y = -alpha
pdbat2.x = 0.0
x = R * cos(-alpha)
y = R * sin(-alpha)
pdbat1.chainid = chain
if len(argv) == 4 and argv[3] == '-d':
delete = True
else:
delete = False
if MT_len<tail_len:
print 'Tail can not be longer, than MT'
exit(0)
pdbxyzfilename = 'structs/xyz_{}.pdb'.format(MT_len)
pdbangfilename = 'structs/ang_{}.pdb'.format(MT_len)
pdbxyz = open(pdbxyzfilename, "w")
pdbang = open(pdbangfilename, "w")
pdbstr1 = 'ATOM 14 CB ALA A 7 8.120 -0.000 52.923 0.00 8.12 A'
pdbat1 = PDBAtom(pdbstr1)
pdbstr2 = 'ATOM 14 CB GLY A 7 8.120 -0.000 52.923 0.00 8.12 A'
pdbat2 = PDBAtom(pdbstr2)
chains = [chr(i) for i in range(ord('A'), ord('M')+1)]
for chain in chains:
for mon in range(MT_len):
if (MT_len - mon) < tail_len:
if delete == True and chain == chains[len(chains) - 1]:
break
R = R_MT + (tail_len - (MT_len - mon))*2*r_mon*sin(theta_tail) #tail_step*(tail_len - (MT_len - mon))
pdbat2.z = theta_tail #atan(tail_step/z_step)
pdbat1.z = 2*r_mon*mon + z_step*(ord(chain) - ord('A'))
else:
R = R_MT
pdbat2.z = 0.0
pdbat1.z = 2*r_mon*mon + z_step*(ord(chain) - ord('A'))
while True:
generate(n)
sparse()
if len(atoms) == n:
break
pdbxyzfilename = 'volxyz_{}.pdb'.format(int(conc))
pdbangfilename = 'volang_{}.pdb'.format(int(conc))
pdbxyz = open(pdbxyzfilename, "w")
pdbang = open(pdbangfilename, "w")
pdbstr1 = 'ATOM 14 CB ALA A 7 8.120 -0.000 52.923 0.00 8.12 A'
pdbat1 = PDBAtom(pdbstr1)
pdbstr2 = 'ATOM 14 CB GLY A 7 8.120 -0.000 52.923 0.00 8.12 A'
pdbat2 = PDBAtom(pdbstr2)
for atom in atoms:
pdbat1.x = atom[0]
pdbat1.y = atom[1]
pdbat1.z = atom[2]
pdbat1.chainid = 'A'
pdbat1.residueseq = atoms.index(atom) + 1
pdbat1.number = 2 * atoms.index(atom) + 1
pdbat1.name = 'CA'
pdbxyz.write("%s\n" % str(pdbat1))
pdbat1.x = atom[0]
pdbat1.y = atom[1]
