2 """This script shows how to use the BuildSystem macro to construct large
3 systems with minimal code
6 from __future__
import print_function
22 print(
"This example is too slow to test in debug mode - run without")
23 print(
"internal tests enabled, or without the --run-quick-test flag")
35 |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|
36 |Rpb1 |blue |1WCM.fasta|1WCM:A|1WCM_fitted.pdb|A|1,100 |0 |5|0 |1|1,2| |
37 |Rpb1 |cyan |1WCM.fasta|1WCM:A|BEADS |A|101,150|0 |5|0 |2|1,2| |
38 |Rpb2 |red |1WCM.fasta|1WCM:B|1WCM_fitted.pdb|B|1,END |0 |5|0 |3|1 | |
39 |Rpb3 |green |1WCM.fasta|1WCM:C|1WCM_fitted.pdb|C|1,END |0 |5|0 |4|1 | |
40 |Rpb4 |orange |1WCM.fasta|1WCM:D|1WCM_fitted.pdb|D|1,END |0 |5|0 |5|1,3| |
41 |Rpb4.1|yellow |1WCM.fasta|1WCM:D|1WCM_fitted.pdb|D|1,END |0 |5|0 |6|1,3| |
42 |Rpb4.2|salmon |1WCM.fasta|1WCM:D|1WCM_fitted.pdb|D|1,END |0 |5|0 |7|1,3| |
43 |Rpb5 |gold |1WCM.fasta|1WCM:E|BEADS | |1,50 | |5|0 |8|1 | |
44 |Rpb5 |pink |1WCM.fasta|1WCM:E|IDEAL_HELIX | |51,100 | |5|0 |8|1 | |
49 tf = tempfile.NamedTemporaryFile(delete=
False, mode=
'w')
63 hier, dof = bs.execute_macro()
71 moldict = bs.get_molecules()[0]
73 for molname
in moldict:
74 for mol
in moldict[molname]:
77 output_objects.append(cr)
83 included_objects=mols)
85 output_objects.append(evr)
95 dof.optimize_flexible_beads(100)
98 mdl, root_hier=hier, monte_carlo_sample_objects=dof.get_movers(),
99 global_output_directory=
'auto_output/', output_objects=output_objects,
100 monte_carlo_steps=10, number_of_best_scoring_models=0, number_of_frames=5)
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)
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.
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 Sytem 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.
Support for the RMF file format for storing hierarchical molecular data and markup.