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IMP Reference Guide  2.16.0
The Integrative Modeling Platform
automatic.py
1 ## \example pmi/automatic.py
2 """This script shows how to use the BuildSystem macro to construct large
3  systems with minimal code
4 """
5 
6 from __future__ import print_function
7 import IMP
8 import IMP.atom
9 import IMP.rmf
10 import IMP.pmi
11 import IMP.pmi.topology
12 import IMP.pmi.dof
13 import IMP.pmi.macros
14 import IMP.pmi.restraints
16 import tempfile
17 import os
18 import sys
19 
20 IMP.setup_from_argv(sys.argv, "Automatic setup of a large system")
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")
24  sys.exit(0)
25 
26 # This is the topology table format.
27 # It allows you to create many components in a simple way
28 # By default it sets up each molecule as a rigid body, filling in missing
29 # pieces with beads
30 # You can create multiple domains by specifying different segments, as
31 # in Rpb1 below
32 # You can also create copies of molecules by appending '.X' to the name,
33 # as in Rpb4 below
34 topology = '''
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 | |
45 '''
46 
47 # Normally the topology table is kept in a text file but here we just write
48 # it to a temporary one
49 tf = tempfile.NamedTemporaryFile(delete=False, mode='w')
50 tf.write(topology)
51 tf.close()
52 
53 # The TopologyReader reads the text file, and the BuildSystem macro
54 # constructs it
55 mdl = IMP.Model()
57  tf.name, pdb_dir=IMP.pmi.get_example_path('data/'),
58  fasta_dir=IMP.pmi.get_example_path('data/'),
59  gmm_dir=IMP.pmi.get_example_path('data/'))
61 # note you can call this multiple times to create a multi-state system
62 bs.add_state(reader)
63 hier, dof = bs.execute_macro()
64 
65 # ##################### RESTRAINTS #####################
66 output_objects = [] # keep a list of functions that need to be reported
67 
68 # Connectivity keeps things connected along the backbone (ignores if inside
69 # same rigid body)
70 crs = []
71 moldict = bs.get_molecules()[0]
72 mols = []
73 for molname in moldict:
74  for mol in moldict[molname]:
76  cr.add_to_model()
77  output_objects.append(cr)
78  crs.append(cr)
79  mols.append(mol)
80 
81 # Excluded volume - automatically more efficient due to rigid bodies
83  included_objects=mols)
84 evr.add_to_model()
85 output_objects.append(evr)
86 
87 
88 # ##################### SAMPLING #####################
89 
90 
91 # mix it up so it looks cool
93 
94 # Quickly move all flexible beads into place
95 dof.optimize_flexible_beads(100)
96 
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)
101 rex.execute_macro()
102 
103 os.remove(tf.name)
Restraints for keeping correct stereochemistry.
bool get_is_quick_test()
Definition: flags.h:183
def shuffle_configuration
Shuffle particles.
Definition: tools.py:1318
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.
Definition: macros.py:566
Protocols for sampling structures and analyzing them.
Definition: macros.py:1
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:73
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.
A macro to help setup and run replica exchange.
Definition: macros.py:58
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.