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)
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())
106 model, root_hier=hier, monte_carlo_sample_objects=dof.get_movers(),
107 replica_exchange_maximum_temperature=3.0,
108 global_output_directory=
"output/", output_objects=output_objects,
109 monte_carlo_steps=10, number_of_frames=frames,
110 number_of_best_scoring_models=0)
Simplify creation of constraints and movers for an IMP Hierarchy.
Restraints for keeping correct stereochemistry.
A macro to help setup and run replica exchange.
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.
Represent 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.
Restrain particles to be above, below, or inside a planar membrane.
Keeps all structures inside a sphere.
Create a restraint between consecutive TempResidue objects or an entire PMI Molecule object...
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.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.