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
pdbat2.chainid = chain
pdbat1.x = x
pdbat1.y = y
pdbat1.residueseq = mon/2 + 1
pdbat2.residueseq = mon/2 + 1
pdbat1.number = mon + MT_len*(ord(chain)-ord(chains[0])) + 1
pdbat2.number = mon + MT_len*(ord(chain)-ord(chains[0])) + 1
if mon%2 == 0:
pdbat1.name = 'CA'
pdbat2.name = 'CA'
else:
pdbat1.name = 'CB'
pdbat2.name = 'CB'
pdbxyz.write("%s\n" % str(pdbat1))
pdbang.write("%s\n" % str(pdbat2))
for chain in chains:
for mon in range(MT_len, MT_len + MT_extra):
R = R_MT
pdbat2.z = 0.0
pdbat2.y = 0.0
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'))
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
pdbat2.chainid = chain
pdbat1.x = x
pdbat1.y = y
pdbat1.residueseq = mon / 2 + 1
pdbat2.residueseq = mon / 2 + 1
pdbat1.number = mon + MT_len * (ord(chain) - ord(chains[0])) + 1
pdbat2.number = mon + MT_len * (ord(chain) - ord(chains[0])) + 1
if mon % 2 == 0:
pdbat1.name = 'CA'
pdbat2.name = 'CA'
else:
pdbat1.name = 'CB'
pdbat2.name = 'CB'
pdbxyz.write("%s\n" % str(pdbat1))
pdbang.write("%s\n" % str(pdbat2))
pdbxyz.write('END')
pdbang.write('END')
pdbxyz.close()
pdbang.close()
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]
pdbat1.z = atom[2]+2*r_mon
pdbat1.chainid = 'A'
pdbat1.residueseq = atoms.index(atom) + 1
pdbat1.number = 2 * atoms.index(atom) + 2
pdbat1.name = 'CB'
pdbxyz.write("%s\n" % str(pdbat1))
pdbat2.x = 0.0
pdbat2.y = 0.0
pdbat2.z = 0.0
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
pdbat2.chainid = chain
pdbat1.x = x
pdbat1.y = y
pdbat1.residueseq = mon / 2 + 1
pdbat2.residueseq = mon / 2 + 1
pdbat1.number = mon + MT_len * (ord(chain) - ord(chains[0])) + 1
pdbat2.number = mon + MT_len * (ord(chain) - ord(chains[0])) + 1
if mon % 2 == 0:
pdbat1.name = 'CA'
pdbat2.name = 'CA'
else:
pdbat1.name = 'CB'
pdbat2.name = 'CB'
pdbxyz.write("%s\n" % str(pdbat1))
pdbang.write("%s\n" % str(pdbat2))
for chain in chains:
for mon in range(MT_len, MT_len + MT_extra):
R = R_MT
pdbat2.z = 0.0
pdbat2.y = 0.0
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'))
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
pdbat2.chainid = chain
pdbat1.x = x
pdbat1.y = y
pdbat1.residueseq = mon/2 + 1
pdbat2.residueseq = mon/2 + 1
pdbat1.number = mon + MT_len*(ord(chain)-ord(chains[0])) + 1
pdbat2.number = mon + MT_len*(ord(chain)-ord(chains[0])) + 1
if mon%2 == 0:
pdbat1.name = 'CA'
pdbat2.name = 'CA'
else:
pdbat1.name = 'CB'
pdbat2.name = 'CB'
pdbxyz.write("%s\n" % str(pdbat1))
pdbang.write("%s\n" % str(pdbat2))
pdbxyz.write('END')
pdbang.write('END')
pdbxyz.close()
pdbang.close()
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]
pdbat1.z = atom[2] + 2 * r_mon
pdbat1.chainid = 'A'
pdbat1.residueseq = atoms.index(atom) + 1
pdbat1.number = 2 * atoms.index(atom) + 2
pdbat1.name = 'CB'
pdbxyz.write("%s\n" % str(pdbat1))
pdbat2.x = 0.0
pdbat2.y = 0.0
pdbat2.z = 0.0
