def R6(coords, atmidx, dismat, shakedata):
'''Wrapped R6 algorithm, include R6 and shakeH'''
shakes = [shakedata[idx] for idx in atmidx[1:-1]]
for baseresult in R6a(coords, atmidx, dismat):
newcoords = coords.copy()
for idx, newcoord in baseresult.items():
newcoords[idx] = newcoord
for refidxs, sidechain_ in shakes:
baseresult.update(sidechain.movesidechain(coords, newcoords,
refidxs, sidechain_))
yield baseresult
def R6(self, coords, atmidx, dismat, shakedata):
'''Wrapped R6 algorithm, include R6 and shakeH'''
shakes = [shakedata[idx] for idx in atmidx[1:-1]]
for baseresult in self.__R6(coords, atmidx, dismat):
newcoords = coords.copy()
abs_dist = 0.0
for idx, newcoord in baseresult.items():
newcoords[idx] = newcoord
abs_dist += sum(abs(newcoord - coords[idx]))
if abs_dist < self.min_abs_dist:
continue
for refidxs, sidechain_ in shakes:
baseresult.update(sidechain.movesidechain(coords, newcoords, refidxs, sidechain_))
yield baseresult
def test_1(self):
fromcoords = numpy.array(((-1.0, 0.0, 0.0),
(0.0, 0.0, 0.0),
(0.0, -1.0, 0.0),
(1.0, 1.0, 0.0)))
tocoords = numpy.array(((-1.0, 0.0, 0.0),
(-1.0, -1.0, 0.0),
(0.0, -1.0, 0.0),
(1.0, 1.0, 0.0)))
refidxs = (0, 1, 2)
s = (3,)
res = sidechain.movesidechain(fromcoords, tocoords, refidxs, s)
self.assertAlmostEqual(distance(res[3], numpy.array((-2.0, -2.0, 0))),
0.0)
def R6(coords, atmidx, dismat, shakedata):
'''Wrapped R6 algorithm, include R6 and shakeH'''
shakes = [shakedata[idx] for idx in atmidx[1:-1]]
mezeipro2 = Mezeipro2(coords, dismat, atmidx)
for result in mezeipro2():
baseresult = {}
for i in range(2,8):
baseresult[atmidx[i]] = result[i-2]
newcoords = coords.copy()
for idx, newcoord in baseresult.items():
newcoords[idx] = newcoord
for refidxs, sidechain_ in shakes:
baseresult.update(sidechain.movesidechain(coords, newcoords,
refidxs, sidechain_))
yield baseresult
def testsidechain(self):
import StringIO
mol = read.readxyz(StringIO.StringIO(test_in))
coords1 = mol.coords
coords2 = coords1.copy()
coords2[1] = coords1[3]
coords2[2] = coords1[4]
coords2[3] = coords1[1]
coords2[4] = coords1[2]
newcoords = sidechain.movesidechain(coords1, coords2,
(0, 1, 2),
(3, 4))
for key in newcoords:
coord = newcoords[key]
assert isinstance(coord, numpy.ndarray) and coord.shape == (3,) and coord.dtype == float, (coord, coord.shape, coord.dtype)
self.assertAlmostEqual(tools.length(newcoords[3] - coords2[3]), 0, 4)
self.assertAlmostEqual(tools.length(newcoords[4] - coords2[4]), 0, 4)