def minor_pair(universe, i, bp, seg1="SYSTEM", seg2="SYSTEM"):
"""Minor-Groove basepair distance for residue *i* with residue *bp*.
The distance of the nitrogen and oxygen atoms in a Minor-groove hydrogen bond is
computed.
:Arguments:
*universe*
:class:`~MDAnalysis.core.AtomGroup.Universe` containing the trajectory
*seg1*
segment id for first base
*i*
resid of the first base
*seg2*
segment id for second base
*bp*
resid of the second base
NOTE: if failure occurs be sure to check the segment identification
.. versionadded:: 0.7.6
"""
if universe.selectAtoms(" resid %s " % (i,)).resnames()[0] in ["DC", "DT", "U", "C", "T", "CYT", "THY", "URA"]:
a1, a2 = "O2", "C2"
if universe.selectAtoms(" resid %s " % (i,)).resnames()[0] in ["DG", "DA", "A", "G", "ADE", "GUA"]:
a1, a2 = "C2", "O2"
c2o2_dist = universe.selectAtoms(
" (segid %s and resid %s and name %s) or (segid %s and resid %s and name %s) " % (seg1, i, a1, seg2, bp, a2))
c2o2 = norm(c2o2_dist[0].pos - c2o2_dist[1].pos)
return c2o2
def calc_eucl_distance(self, a1, a2):
"""Calculate the Euclidean distance between two atoms. """
return norm(a2.pos - a1.pos)
def calc_eucl_distance(self, a1, a2):
"""Calculate the Euclidean distance between two atoms. """
return norm(a2.pos - a1.pos)
def testNormRandom(self):
for x in numpy.random.uniform(0, pi, 20):
r = numpy.random.uniform(0, 1000)
v = r * numpy.array([cos(x), sin(x), 0])
assert_almost_equal(util.norm(v), r, 6)
def testNormNullVector(self):
assert_equal(util.norm(self.null), 0.0)
def testNorm(self):
assert_equal(util.norm(self.e3), 1)
assert_equal(util.norm(self.a), numpy.linalg.norm(self.a))
def _calc_angle(self,xyz):
a = xyz[0, :] - xyz[1, :]
b = xyz[2, :] - xyz[1, :]
return np.rad2deg(np.arccos(np.dot(a, b) / (mdutil.norm(a) * mdutil.norm(b))))
def _calc_bond(self,xyz):
return mdutil.norm(xyz[0, :] - xyz[1, :])