23 p = m.add_particle(
"P%d" % i)
26 d.set_coordinates_are_optimized(
True)
36 for i
in [0.0, -1.0, +1.0]:
37 for j
in [0.0, -1.0, +1.0]:
38 for k
in [0.0, -1.0, +1.0]:
40 float(i) * S_, float(j) * S_, float(k) * S_))
51 [m.get_particle(ps[1])], 1.0, ctrs, trs))
59 mc.set_scoring_function([pr])
61 mc.set_return_best(
False)
65 log = open(
"traj.xyz",
"w")
68 for istep
in range(0, 5000):
78 log.write(
"Na %6.3f %6.3f %6.3f\n" % (xyz0[0], xyz0[1], xyz0[2]))
79 log.write(
"Cl %6.3f %6.3f %6.3f\n" % (xyz1[0], xyz1[1], xyz1[2]))
Support for basic symmetry, such as periodic boundary conditions (PBC).
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
static XYZR setup_particle(Model *m, ParticleIndex pi)
Move a particle and keep it in the primitive cell of a periodic lattice.
A score on the distance between the surfaces of two spheres.
Move continuous particle variables by perturbing them within a ball.
Class for storing model, its restraints, constraints, and particles.
Basic functionality that is expected to be used by a wide variety of IMP users.
Applies a PairScore to a Pair.
Applies a list of movers one at a time.
Harmonic function (symmetric about the mean)
A decorator for a particle with x,y,z coordinates and a radius.