2 """This script shows how to represent a system at multiple scales and do basic sampling.
19 components = [
"Rpb1",
"Rpb2",
"Rpb3",
"Rpb4"]
20 colors = [0.1,0.9,0.5,0.8]
31 for n
in range(len(components)):
32 print(
'PMI: setting up',components[n],
'1WCM:'+chains[n])
33 mol = st.create_molecule(
35 sequence=seqs[
'1WCM:'+chains[n]],
40 mol.add_representation(atomic,
43 mol.add_representation(mol[:]-atomic,
44 resolutions=[beadsize],
62 dof.create_rigid_body(mol,
63 nonrigid_parts=mol.get_non_atomic_residues(),
66 nonrigid_max_trans=0.1)
77 output_objects.append(cr)
83 output_objects.append(evr)
92 dof.optimize_flexible_beads(100)
97 crosslink_restraints=crs,
98 monte_carlo_sample_objects=dof.get_movers(),
99 global_output_directory=
'multiscale_output/',
100 output_objects=output_objects,
101 monte_carlo_steps=10,
102 number_of_best_scoring_models=0,
A class to simplify create 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.
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 setup 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.