def _findPosition(self, unknown, a1, a2, a3, bond, angle, dihedral):
sphere = Objects3D.Sphere(a1, bond)
cone = Objects3D.Cone(a1, a2 - a1, angle)
plane = Objects3D.Plane(a3, a2, a1)
plane = plane.rotate(Objects3D.Line(a1, a2 - a1), dihedral)
points = sphere.intersectWith(cone).intersectWith(plane)
for p in points:
if (a1 - a2).cross(p - a1) * (plane.normal) > 0:
unknown.setPosition(p)
break
def _N4twoH(self, atom, known, unknown):
r = atom.position()
r1 = known[0].position()
r2 = known[1].position()
plane = Objects3D.Plane(r, r1, r2)
axis = -((r1 - r) + (r2 - r)).normal()
plane = plane.rotate(Objects3D.Line(r, axis), 90. * Units.deg)
cone = Objects3D.Cone(r, axis, 0.5 * self._hnh_angle)
sphere = Objects3D.Sphere(r, self._nh_bond)
circle = sphere.intersectWith(cone)
points = circle.intersectWith(plane)
unknown[0].setPosition(points[0])
unknown[1].setPosition(points[1])
def _N3twoH(self, atom, known, unknown):
r = atom.position()
r1 = known[0].position()
others = filter(lambda a: a.symbol != 'H', known[0].bondedTo())
r2 = others[0].position()
plane = Objects3D.Plane(r, r1, r2)
axis = (r - r1).normal()
cone = Objects3D.Cone(r, axis, 0.5 * self._hnh_angle)
sphere = Objects3D.Sphere(r, self._nh_bond)
circle = sphere.intersectWith(cone)
points = circle.intersectWith(plane)
unknown[0].setPosition(points[0])
unknown[1].setPosition(points[1])
def _N2oneH(self, atom, known, unknown):
r = atom.position()
r1 = known[0].position()
others = filter(lambda a: a.symbol != 'H', known[0].bondedTo())
r2 = others[0].position()
try:
plane = Objects3D.Plane(r, r1, r2)
except ZeroDivisionError:
# We get here when all three points are colinear.
# Add a small random displacement as a fix.
from MMTK.Random import randomPointInSphere
plane = Objects3D.Plane(r, r1, r2 + randomPointInSphere(0.001))
axis = (r - r1).normal()
cone = Objects3D.Cone(r, axis, 0.5 * self._hch_angle)
sphere = Objects3D.Sphere(r, self._nh_bond)
circle = sphere.intersectWith(cone)
points = circle.intersectWith(plane)
unknown[0].setPosition(points[0])
def _tetrahedralH(self, atom, known, unknown, bond):
r = atom.position()
n = (known[0].position() - r).normal()
cone = Objects3D.Cone(r, n, Numeric.arccos(-1. / 3.))
sphere = Objects3D.Sphere(r, bond)
circle = sphere.intersectWith(cone)
others = filter(lambda a: a.symbol != 'H', known[0].bondedTo())
others.remove(atom)
other = others[0]
ref = (Objects3D.Plane(circle.center, circle.normal) \
.projectionOf(other.position())-circle.center).normal()
p0 = circle.center + ref * circle.radius
p0 = Objects3D.rotatePoint(
p0, Objects3D.Line(circle.center, circle.normal), 60. * Units.deg)
p1 = Objects3D.rotatePoint(
p0, Objects3D.Line(circle.center, circle.normal), 120. * Units.deg)
p2 = Objects3D.rotatePoint(
p1, Objects3D.Line(circle.center, circle.normal), 120. * Units.deg)
unknown[0].setPosition(p0)
unknown[1].setPosition(p1)
unknown[2].setPosition(p2)