def test_normal(self, vec1, vec2, value):
assert_equal(mdamath.normal(vec1, vec2), value)
def testNormalNullVector(self):
assert_equal(mdamath.normal(self.e1, self.null), 0.0)
def testNormal(self):
assert_equal(mdamath.normal(self.e1, self.e2), self.e3)
fout = open(folder + 'cationpi.dat', 'w')
for ts in u.trajectory:
sys.stdout.write('\rTime = %d' % u.trajectory.time)
boxvec = mdamath.triclinic_vectors(u.dimensions)
for ipi in range(npigroup):
pigroup = pigroups[ipi]
picenter = pigroup.centroid(pbc=True)
for icat in range(ncat):
cation = cations[icat]
dist = distances.calc_bonds(coords1=cation.position,
coords2=picenter,
box=u.dimensions)
if dist < 7.0:
vec = vector(cation.position, picenter, boxvec)
v1 = vector(pigroup.positions[0], pigroup.positions[5], boxvec)
v2 = vector(pigroup.positions[1], pigroup.positions[4], boxvec)
v3 = vector(pigroup.positions[2], pigroup.positions[3], boxvec)
n1 = mdamath.normal(v1, v2)
n2 = mdamath.normal(v3, v1)
n3 = mdamath.normal(v3, v2)
n = (n1 + n2 + n3)
angle = np.degrees(mdamath.angle(n, vec))
if angle > 120 or angle < 60:
fout.write(
'%.1f %d %s %d %s %.6f %.6f\n' %
(u.trajectory.time, catresid[icat], catresname[icat],
piresid[ipi], piresname[ipi], angle, dist))
sys.stdout.write('\n')
fout.close()
def testNormalNullVector(self):
assert_equal(mdamath.normal(self.e1, self.null), 0.0)
def testNormal(self):
assert_equal(mdamath.normal(self.e1, self.e2), self.e3)