16 prb.set_coordinates_are_optimized(
True)
17 prb.set_name(name +
" rb")
31 d.set_name(name + str(i) + str(j) + str(k))
33 d.set_rotational_diffusion_coefficient(
34 d.get_rotational_diffusion_coefficient() * 100)
38 def display(i, w, hs):
55 m, rb0.get_rigid_members() + rb1.get_rigid_members()), 1, 3)
63 bd.set_scoring_function(sf)
64 bd.set_time_step(10000)
69 for i
in range(0, 100):
70 display(i, w, [h0, h1])
static RigidBodyDiffusion setup_particle(Model *m, ParticleIndex pi)
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
static Fragment setup_particle(Model *m, ParticleIndex pi)
static XYZR setup_particle(Model *m, ParticleIndex pi)
Create a scoring function on a list of restraints.
static Molecule setup_particle(Model *m, ParticleIndex pi)
Class for storing model, its restraints, constraints, and particles.
Simple Brownian dynamics simulator.
Store a list of ParticleIndexes.
static Mass setup_particle(Model *m, ParticleIndex pi, Float mass)
void set_log_level(LogLevel l)
Set the current global log level.
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
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.
Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
Select hierarchy particles identified by the biological name.
static RigidBody setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor ps)
Display an IMP::atom::Hierarchy particle as balls.
std::string create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file.