6 from __future__
import print_function
13 use_rigid_bodies =
True
26 prb.set_name(
"rigid body")
31 print(
"initial frame", drb.get_reference_frame())
33 drb.set_coordinates_are_optimized(
True)
39 d.set_coordinates_are_optimized(
True)
47 dheader.set_resolution(1)
49 dmap.set_particles([p])
67 m.set_log_level(IMP.SILENT)
70 opt.set_scoring_function(sf)
73 def try_point(i, j, k):
74 print(
"trying", i, j, k)
76 to_move.set_coordinates(vc)
83 print(
"score and derivatives", v, to_move.get_derivatives())
87 print(
"after", d.get_coordinates())
88 mag = to_move.get_coordinates().get_magnitude()
93 sg.set_color(converge_color)
94 sg.set_name(
"converge")
98 try_point(-bd, -bd, -bd)
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)
Simple conjugate gradients optimizer.
Create a scoring function on a list of restraints.
Color get_hot_color(double f)
Return the color for f from the hot color map.
Object used to hold a set of restraints.
Class for storing model, its restraints, constraints, and particles.
Class for sampling a density map from particles.
static Mass setup_particle(Model *m, ParticleIndex pi, Float mass)
DensityHeader create_density_header(const algebra::BoundingBoxD< 3 > &bb, float spacing)
Create a header from a bounding box in 3D.
Basic utilities for handling cryo-electron microscopy 3D density maps.
Calculate score based on fit to EM map.
Color get_gray_color(double f)
Return the a grayscale value for f.
Class to handle individual particles of a Model object.
Write a CGO file with the geometry.
Output IMP model data in various file formats.
static RigidBody setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor ps)