3 This script shows how to simulate residue-protein
4 binding contacts inferred from mutagenesis studies.
5 This example shows protein A binding to protein B
6 through a set of residues predicted to be required
7 for binding in mutagensis studies.
10 from __future__
import print_function
27 print(
"This example is too slow to test in debug mode - run without")
28 print(
"internal tests enabled, or without the --run-quick-test flag")
32 |molecule_name|color|fasta_fn|fasta_id|pdb_fn|chain|residue_range|pdb_offset|bead_size|em_residues_per_gaussian|rigid_body|super_rigid_body|chain_of_super_rigid_bodies|
33 |Rpb4 |red |1WCM.fasta |1WCM:D |1WCM_fitted.pdb |D|1,END |0 |5|0 |1 | | ||
34 |Rpb7 |gold |1WCM.fasta |1WCM:G |1WCM_fitted.pdb |G|1,END |0 |5|0 |2 | | ||
39 tf = tempfile.NamedTemporaryFile(delete=
False, mode=
'w')
55 hier, dof = bs.execute_macro()
64 moldict = bs.get_molecules()[0]
66 for molname
in moldict:
67 for mol
in moldict[molname]:
70 output_objects.append(cr)
76 included_objects=mols)
78 output_objects.append(evr)
87 hier, selection=(
'Rpb7', 38, 44,
'Rpb4'), label=
'B38_44')
91 output_objects.append(br)
99 molecule=
"Rpb4").get_selected_particles()
101 xyzs, rbs = dof.disable_movers(part_p1,
109 dof.optimize_flexible_beads(100)
114 monte_carlo_sample_objects=dof.get_movers(),
115 global_output_directory=
'output/',
116 output_objects=output_objects,
117 monte_carlo_steps=10,
118 number_of_best_scoring_models=0,
119 number_of_frames=500)
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.
Modify the transformation of a rigid body.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
A macro to build a IMP::pmi::topology::System based on a TopologyReader object.
Protocols for sampling structures and analyzing them.
Class for storing model, its restraints, constraints, and particles.
Restrain residue/residues to bind to unknown location in a target.
Classes to handle different kinds of restraints.
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.
Automatically setup System and Degrees of Freedom with a formatted text file.
Python classes to represent, score, sample and analyze models.
Functionality for loading, creating, manipulating and scoring atomic structures.
Select hierarchy particles identified by the biological name.
Support for the RMF file format for storing hierarchical molecular data and markup.