def find_third_neighbors(self, dihedral_proxies):
""" Loop through dihedral angle proxies to find third neighbor
Fill in neighbors.b1 with iseq and angle proxy"""
for dp in dihedral_proxies:
for i_test in dp.i_seqs:
if (self.h_connectivity[i_test] is None
and not self.hd_sel[i_test]):
continue
ih = i_test
i1, i2, i3, i4 = dp.i_seqs
if (ih == i1):
i_third = i4
if (ih == i4):
i_third = i1
dihedral = dihedral_angle(sites=[
self.sites_cart[i1], self.sites_cart[i2],
self.sites_cart[i3], self.sites_cart[i4]
])
if dihedral is None:
return
dihedral_id = dp.angle_ideal
delta = geometry_restraints.angle_delta_deg(
angle_1=math.degrees(dihedral),
angle_2=dihedral_id,
periodicity=dp.periodicity)
dihedral_ideal = math.degrees(dihedral) + delta
b1 = {'iseq': i_third, 'dihedral_ideal': dihedral_ideal}
self.h_connectivity[ih].b1 = b1
self.assign_b1_for_H_atom_groups(ih=ih, i_third=i_third)
def run(args):
assert args in [[], ["--verbose"]]
if (len(args) == 0):
out = null_out()
else:
out = sys.stdout
#
mt = flex.mersenne_twister(seed=0)
#
for i_trial in xrange(10):
l0 = mt.random_double() + 0.5
l1 = mt.random_double() + 0.5
l2 = mt.random_double() + 0.5
angle_model = mt.random_double() * 178 + 1 \
+ 180 * (mt.random_size_t() % 3 - 1)
v = matrix.col(mt.random_double_point_on_sphere())
axis = v.ortho()
site1 = v * l1
site0 = site1 + v * l0
r = axis.axis_and_angle_as_r3_rotation_matrix(angle=angle_model, deg=True)
site2 = site1 + (r * v) * l2
a = angle(
sites=[site0, site1, site2],
angle_ideal=mt.random_double() * 720 - 360,
weight=mt.random_double() * 10 + 0.1)
assert approx_equal(min(
abs(angle_delta_deg(angle_1=a.angle_model, angle_2= angle_model)),
abs(angle_delta_deg(angle_1=a.angle_model, angle_2=-angle_model))), 0)
check_derivs(out=out, a=a)
#
for site2 in [(0,2.3,0), (0,0,2.5)]:
perm = flex.size_t([0,1,2])
while True:
a = angle(
sites=tuple(flex.vec3_double(
[(1.2,0,0), (0,0,0), site2]).select(perm)),
angle_ideal=mt.random_double() * 720 - 360,
weight=mt.random_double() * 10 + 0.1)
check_derivs(out=out, a=a)
if (not perm.next_permutation()):
break
#
for site0 in [(1,0,0),(0,1,0),(0,0,1),(1,1,1)]:
perm = flex.size_t([0,1,2])
while True:
a = angle(
sites=tuple(flex.vec3_double(
[site0, (0,0,0), -matrix.col(site0)]).select(perm)),
angle_ideal=180,
weight=1.3)
check_derivs(out=out, a=a, expect_failure=True)
if (not perm.next_permutation()):
break
#
plot_file_names = []
for method in ["ana", "fin"]:
plot_file_names.extend(write_plots(method=method))
f = open("angle_xy_as_pdf_commands", "w")
for file_name in plot_file_names:
print >> f, "ppdf %s > %s" % (file_name, file_name.replace(".xy", ".pdf"))
f.close()
#
print "OK"
