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# Internal coordinate tests
#
# Written by Konrad Hinsen
#
import unittest
from MMTK.Proteins import Protein
from MMTK.InternalCoordinates import BondLength, BondAngle, DihedralAngle
from Scientific import N
class ICTest(unittest.TestCase):
def setUp(self):
# Pick a proline residue because of its cycle
self.protein = Protein("insulin.pdb")
self.chain = self.protein[1]
self.res = self.chain[27]
def test_phipsi(self):
phi, psi = self.res.phiPsi()
phi_o = self.res.phiAngle()
psi_o = self.res.psiAngle()
self.assertAlmostEqual(phi, phi_o.getValue(), 10)
self.assertAlmostEqual(psi, psi_o.getValue(), 10)
def test_changephi(self):
phi = self.res.phiAngle()
current_phi = phi.getValue()
for dphi in [-0.2, -0.1, 0.1, 0.2]:
phi.setValue(current_phi+dphi)
self.assertAlmostEqual(phi.getValue() % (2.*N.pi),
(current_phi+dphi) % (2.*N.pi), 10)
def test_changebond(self):
b = BondLength(self.res.peptide.C_alpha, self.res.peptide.C)
current_b = b.getValue()
for db in [-0.02, -0.01, 0.01, 0.02]:
b.setValue(current_b + db)
self.assertAlmostEqual(b.getValue(), current_b + db)
def test_changeangle(self):
a = BondAngle(self.res.peptide.N, self.res.peptide.C_alpha,
self.res.peptide.C)
current_a = a.getValue()
for da in [-0.2, -0.1, 0.1, 0.2]:
a.setValue(current_a+da)
self.assertAlmostEqual(a.getValue() % (2.*N.pi),
(current_a+da) % (2.*N.pi), 10)
def test_cyclic(self):
self.assertRaises(ValueError, BondLength,
self.res.peptide.N, self.res.peptide.C_alpha)
self.assertRaises(ValueError, BondAngle,
self.res.peptide.N, self.res.peptide.C_alpha,
self.res.sidechain.C_beta)
self.assertRaises(ValueError, DihedralAngle,
self.res.peptide.N, self.res.peptide.C_alpha,
self.res.sidechain.C_beta, self.res.sidechain.C_gamma)
def suite():
return unittest.TestLoader().loadTestsFromTestCase(ICTest)
if __name__ == '__main__':
unittest.main()
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