32 nmc = ni * nj * np * 100
49 for i
in range(0, ni):
50 for j
in range(0, nj):
53 for k
in range(0, np):
55 p.set_name(
"P" + str(i) +
" " + str(j) +
" " + str(k))
59 d.set_coordinates_are_optimized(
True)
61 movers[-1].set_was_used(
True)
65 d.set_coordinates(base)
67 d.set_coordinates_are_optimized(
True)
80 restraints.append(bbr)
91 nbl.set_pair_filters(filters)
94 mc.set_scoring_function(sf)
98 mc.set_score_moved(
True)
105 cg.set_scoring_function(sf)
108 print(r.get_name(), r.evaluate(
False))
111 for i
in range(1, nouter):
121 for j
in range(0, ninner):
123 mc.set_kt(100.0 / (3 * j + 1))
124 print(
"mc", mc.optimize((j + 1) * nmc), cg.optimize(nmc))
127 print(r.get_name(), r.evaluate(
False))
Applies a SingletonScore to each Singleton in a list.
static FloatKey get_radius_key()
Get the key for the radius.
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
Various classes to hold sets of particles.
Upper bound harmonic function (non-zero when feature > mean)
static XYZR setup_particle(Model *m, ParticleIndex pi)
Simple conjugate gradients optimizer.
Create a scoring function on a list of restraints.
Move continuous particle variables by perturbing them within a ball.
Score distance between two particle centers using a harmonic function.
Vector3D get_random_vector_in(const Cylinder3D &c)
Generate a random vector in a cylinder with uniform density.
Class for storing model, its restraints, constraints, and particles.
Color get_display_color(unsigned int i)
static Colored setup_particle(Model *m, ParticleIndex pi, Color color)
Basic functionality that is expected to be used by a wide variety of IMP users.
Prevent a set of particles and rigid bodies from inter-penetrating.
Class to handle individual particles of a Model object.
Write a CGO file with the geometry.
Output IMP model data in various file formats.
Applies a list of movers one at a time.
Applies a PairScore to each Pair in a list.
Display an IMP::core::XYZR particle as a ball.
A decorator for a particle with x,y,z coordinates and a radius.