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 _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])