def makeFragment(phiPsiList):
c_pos = Vector(0, 0, 0)
o_pos = Vector(C_O_distance, 0, 0)
ca_pos = makeXYZFromAngle(o_pos, c_pos, CA_C_distance, CA_C_O_angle, -Y)
nCap = Residue(1, "GLY")
nCap.subFeatures = [Atom("CA", ca_pos), Atom("C", c_pos), Atom("O", o_pos)]
(phi, psi) = phiPsiList[0]
N_CA_C_O_torsion = invertTorsion(psi)
n_pos = makeXYZFromAngle(o_pos, c_pos, C_N_distance, O_C_N_angle, Y)
ca_pos = makeXYZ(n_pos, N_CA_distance, c_pos, C_N_CA_angle, o_pos, 0)
c_pos = makeXYZ(ca_pos, CA_C_distance, n_pos, N_CA_C_angle, c_pos, phi)
o_pos = makeXYZ(c_pos, C_O_distance, ca_pos, CA_C_O_angle, n_pos, N_CA_C_O_torsion)
firstResidue = Residue(2, "GLY")
firstResidue.subFeatures = [Atom("N", n_pos), Atom("CA", ca_pos), Atom("C", c_pos), Atom("O", o_pos)]
chain = Chain("A")
chain.add(nCap)
chain.add(firstResidue)
extendChain(phiPsiList[1:], psi, chain)
last = chain.subFeatures[-1]
lastPsi = phiPsiList[-1][1]
n_pos = last.getAtomPosition("N")
ca_pos = last.getAtomPosition("CA")
c_pos = last.getAtomPosition("C")
o_pos = last.getAtomPosition("O")
n_pos = makeXYZ(c_pos, C_N_distance, ca_pos, CA_C_N_angle, n_pos, lastPsi)
cCap = Residue(last.number + 1, "GLY")
cCap.subFeatures = [Atom("N", n_pos)]
chain.add(cCap)
return chain
def makeNTerminalResidue(psi):
N_CA_C_O_torsion = invertTorsion(psi)
nitrogen = Vector(0.0, 0.0, 0.0)
cAlpha = Vector(N_CA_distance, 0.0, 0.0)
carbonylCarbon = makeXYZFromAngle(nitrogen, cAlpha, CA_C_distance, N_CA_C_angle, Y)
oxygen = makeXYZ(carbonylCarbon, C_O_distance, cAlpha, CA_C_O_angle, nitrogen, N_CA_C_O_torsion)
r = Residue(1, "GLY")
r.subFeatures = [Atom("N", 1, nitrogen), Atom("CA", 2, cAlpha), Atom("C", 3, carbonylCarbon), Atom("O", 4, oxygen)]
return r
def makeResidue(previousResidue, phi, psi, lastPsi):
previousNitrogen = previousResidue.getAtomPosition("N")
previousCAlpha = previousResidue.getAtomPosition("CA")
previousC = previousResidue.getAtomPosition("C")
N_CA_C_O_torsion = invertTorsion(psi)
nitrogen = makeXYZ(previousC, C_N_distance, previousCAlpha, CA_C_N_angle, previousNitrogen, lastPsi)
cAlpha = makeXYZ(nitrogen, N_CA_distance, previousC, C_N_CA_angle, previousCAlpha, 180)
carbonylCarbon = makeXYZ(cAlpha, CA_C_distance, nitrogen, N_CA_C_angle, previousC, phi)
oxygen = makeXYZ(carbonylCarbon, C_O_distance, cAlpha, CA_C_O_angle, nitrogen, N_CA_C_O_torsion)
residueNumber = previousResidue.number + 1
r = Residue(residueNumber, "GLY")
r.subFeatures = [Atom("N", nitrogen), Atom("CA", cAlpha), Atom("C", carbonylCarbon), Atom("O", oxygen)]
return r