1 from __future__
import print_function
15 p_slab, height, radius)
20 d.set_coordinates_are_optimized(
True)
33 rmf = RMF.create_rmf_file(nm)
38 sgs = sg.get_components()
46 bd.set_scoring_function([bbr, r])
47 bd.set_log_level(IMP.SILENT)
48 bd.add_optimizer_state(os)
49 bd.set_maximum_time_step(2000)
Upper bound harmonic function (non-zero when feature > mean)
static XYZR setup_particle(Model *m, ParticleIndex pi)
static SlabWithCylindricalPore setup_particle(Model *m, ParticleIndex pi, double thickness, double radius)
Class for storing model, its restraints, constraints, and particles.
static Hierarchy setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor children=ParticleIndexesAdaptor())
Create a Hierarchy of level t by adding the needed attributes.
Simple Brownian dynamics simulator.
static Mass setup_particle(Model *m, ParticleIndex pi, Float mass)
void add_hierarchies(RMF::NodeHandle fh, const atom::Hierarchies &hs)
void add_restraints(RMF::NodeHandle fh, const Restraints &hs)
Periodically dump the state of all associated objects into the RMF file.
static Diffusion setup_particle(Model *m, ParticleIndex pi, Float D)
Setup the particle with the specified diffusion coefficient.
Class to handle individual particles of a Model object.
Applies a PairScore to a Pair.
void add_static_geometries(RMF::FileHandle parent, const display::GeometriesTemp &r)
Add geometries, assuming they do not move between frames.
Functionality for loading, creating, manipulating and scoring atomic structures.
Applies a SingletonScore to a Singleton.
Support for the RMF file format for storing hierarchical molecular data and markup.
std::string create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file.