Esempio n. 1
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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
Esempio n. 2
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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
Esempio n. 3
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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