2 """This script shows how to use the BuildSystem macro to construct large systems with minimal code
5 from __future__
import print_function
20 print(
"This example is too slow to test in debug mode - run without")
21 print(
"internal tests enabled, or without the --run-quick-test flag")
30 |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|
31 |Rpb1 |blue |1WCM.fasta|1WCM:A|1WCM_fitted.pdb|A|1,100 |0 |5|0 |1|1,2| |
32 |Rpb1 |cyan |1WCM.fasta|1WCM:A|BEADS |A|101,150|0 |5|0 |2|1,2| |
33 |Rpb2 |red |1WCM.fasta|1WCM:B|1WCM_fitted.pdb|B|1,END |0 |5|0 |3|1 | |
34 |Rpb3 |green |1WCM.fasta|1WCM:C|1WCM_fitted.pdb|C|1,END |0 |5|0 |4|1 | |
35 |Rpb4 |orange |1WCM.fasta|1WCM:D|1WCM_fitted.pdb|D|1,END |0 |5|0 |5|1,3| |
36 |Rpb4.1|yellow |1WCM.fasta|1WCM:D|1WCM_fitted.pdb|D|1,END |0 |5|0 |6|1,3| |
37 |Rpb4.2|salmon |1WCM.fasta|1WCM:D|1WCM_fitted.pdb|D|1,END |0 |5|0 |7|1,3| |
38 |Rpb5 |gold |1WCM.fasta|1WCM:E|BEADS | |1,50 | |5|0 |8|1 | |
39 |Rpb5 |pink |1WCM.fasta|1WCM:E|IDEAL_HELIX | |51,100 | |5|0 |8|1 | |
43 tf = tempfile.NamedTemporaryFile(delete=
False, mode=
'w')
55 hier, dof = bs.execute_macro()
62 moldict = bs.get_molecules()[0]
64 for molname
in moldict:
65 for mol
in moldict[molname]:
68 output_objects.append(cr)
75 output_objects.append(evr)
85 dof.optimize_flexible_beads(100)
89 monte_carlo_sample_objects=dof.get_movers(),
90 global_output_directory=
'auto_output/',
91 output_objects=output_objects,
93 number_of_best_scoring_models=0,
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.
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.
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.
Automatically setup Sytem and Degrees of Freedom with a formatted text file.
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.