2 """This script shows how to represent a system at multiple scales and do basic sampling.
5 from __future__
import print_function
19 print(
"This example is too slow to test in debug mode - run without")
20 print(
"internal tests enabled, or without the --run-quick-test flag")
26 components = [
"Rpb1",
"Rpb2",
"Rpb3",
"Rpb4"]
27 colors = [
'medium purple',
'goldenrod',
'orchid',
'olive drab']
38 for n
in range(len(components)):
39 print(
'PMI: setting up',components[n],
'1WCM:'+chains[n])
40 mol = st.create_molecule(
42 sequence=seqs[
'1WCM:'+chains[n]],
47 mol.add_representation(atomic,
50 mol.add_representation(mol[:]-atomic,
51 resolutions=[beadsize],
69 dof.create_rigid_body(mol,
70 nonrigid_parts=mol.get_non_atomic_residues(),
73 nonrigid_max_trans=0.1)
87 output_objects.append(cr)
93 output_objects.append(evr)
102 dof.optimize_flexible_beads(100)
107 crosslink_restraints=crs,
108 monte_carlo_sample_objects=dof.get_movers(),
109 global_output_directory=
'multiscale_output/',
110 output_objects=output_objects,
111 monte_carlo_steps=10,
112 number_of_best_scoring_models=0,
Simplify creation of constraints and movers for an IMP Hierarchy.
Restraints for keeping correct stereochemistry.
Set of Python classes to create a multi-state, multi-resolution IMP hierarchy.
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Protocols for sampling structures and analyzing them.
This class initializes the root node of the global IMP.atom.Hierarchy.
Class for storing model, its restraints, constraints, and particles.
Classes to handle different kinds of restraints.
This class creates a restraint between consecutive TempResidue objects OR an entire PMI MOlecule obje...
Create movers and set up constraints for PMI objects.
A class to create an excluded volume restraint for a set of particles at a given resolution.
Python classes to represent, score, sample and analyze models.
A macro to help setup and run replica exchange.
A dictionary-like wrapper for reading and storing sequence data.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.