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 boundingSphere(self, conf=None):
"""Returns a sphere that contains all atoms in the object.
This is *not* the minimal bounding sphere, just *some*
bounding sphere."""
atoms = self.atomList()
r = Vector(0., 0., 0.)
for a in atoms:
r = r + a.position(conf)
center = r / len(atoms)
r = 0.
for a in self.atomList():
r = max(r, (a.position(conf) - center).length())
return Objects3D.Sphere(center, r)
def boundingSphere(self, conf=None):
"""
:param conf: a configuration object, or None for the
current configuration
:type conf: :class:~MMTK.ParticleProperties.Configuration or NoneType
:returns: a sphere that contains all atoms in the object.
This is B{not} the minimal bounding sphere, just B{some}
bounding sphere.
:rtype: Scientific.Geometry.Objects3D.Sphere
"""
atoms = self.atomList()
center = sum(
(a.position(conf) for a in atoms), Vector(0., 0., 0.)) / len(atoms)
r = 0.
for a in atoms:
r = max(r, (a.position(conf) - center).length())
return Objects3D.Sphere(center, r)
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)