3 This script shows how to simulate an a protein using a
4 Membrane restraint. This example show 3 ideal helices
5 that have different segments inside the membrane
22 "Simulation of a protein using a membrane restraint")
32 for i, len_helix
in enumerate([20, 40, 80]):
33 mol = st.create_molecule(
34 "helix_%s" % (str(i)), sequence=
"A" * len_helix, chain_id=
"A"
36 mol.add_representation(mol, resolutions=[1], ideal_helix=
True)
42 dof.create_rigid_body(mol,
55 cr.set_label(mol.get_name())
57 output_objects.append(cr)
64 included_objects=mols, resolution=1
68 output_objects.append(evr1)
74 mr = IMP.pmi.restraints.basic.MembraneRestraint(
76 objects_inside=[
"helix_0", (1, 20,
"helix_1"), (20, 40,
"helix_2")],
77 objects_above=[(21, 40,
"helix_1"), (1, 19,
"helix_2")],
78 objects_below=[(41, 80,
"helix_2")],
83 output_objects.append(mr)
86 mr.create_membrane_density()
98 print(dof.get_movers())
107 crosslink_restraints=rmf_restraints,
108 monte_carlo_sample_objects=dof.get_movers(),
109 replica_exchange_maximum_temperature=3.0,
110 global_output_directory=
"output/",
111 output_objects=output_objects,
112 monte_carlo_steps=10,
113 number_of_frames=frames,
114 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)
Some miscellaneous simple restraints.
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.
Restraint to keep all structures inside sphere.
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.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.