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IMP Reference Guide  2.16.0
The Integrative Modeling Platform
atomistic.py
1 ## \example pmi/atomistic.py
2 """This script shows how to simulate an atomic system with MD,
3 with a secondary structure elastic network to speed things up.
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
15 import sys
16 
17 IMP.setup_from_argv(sys.argv, "Simulation of an atomic system")
19  print("This example is too slow to test in debug mode - run without")
20  print("internal tests enabled, or without the --run-quick-test flag")
21  sys.exit(0)
22 
23 # Setup System and add a State
24 mdl = IMP.Model()
26 st1 = s.create_state()
27 
28 # Read sequences and create Molecules
30 gcp2 = st1.create_molecule("GCP2", sequence=seqs["GCP2_YEAST"], chain_id='A')
31 
32 # Add structure. This function returns a list of the residues that now
33 # have structure
34 a1 = gcp2.add_structure(IMP.pmi.get_example_path('data/gcp2.pdb'),
35  chain_id='A')
36 
37 # Add structured part representation and then build
38 gcp2.add_representation(a1, resolutions=[0])
39 print('building molecule')
40 hier = s.build()
41 
42 # add charmm restraints
43 print('adding restraints')
45 charmm.add_to_model()
46 
47 # add elastic network on secondary structure units
48 sses = IMP.pmi.io.parse_dssp(IMP.pmi.get_example_path('data/gcp2.dssp'), 'A',
49  name_map={'A': 'GCP2'})
50 all_rs = []
51 for sse in sses['helix']+sses['beta']:
53  selection_tuples=sse,
54  strength=10.0,
55  dist_cutoff=5.0,
56  ca_only=True,
57  hierarchy=hier)
58  all_rs.append(er)
59  er.add_to_model()
60 
61 # setup MD and run
63 md_ps = dof.setup_md(gcp2)
65  mdl,
66  root_hier=hier,
67  # for visualizing SSEs in RMF
68  crosslink_restraints=all_rs,
69  molecular_dynamics_sample_objects=md_ps,
70  molecular_dynamics_steps=5,
71  # set >0 to store best PDB files (but this is slow to do online)
72  number_of_best_scoring_models=0,
73  # increase number of frames to get better results!
74  number_of_frames=1,
75  global_output_directory='atomistic_output/')
76 rex.execute_macro()
Simplify creation of constraints and movers for an IMP Hierarchy.
Restraints for keeping correct stereochemistry.
bool get_is_quick_test()
Definition: flags.h:183
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)
def parse_dssp
Read a DSSP file, and return secondary structure elements (SSEs).
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Protocols for sampling structures and analyzing them.
Definition: macros.py:1
Represent the root node of the global IMP.atom.Hierarchy.
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:73
Create movers and set up constraints for PMI objects.
Python classes to represent, score, sample and analyze models.
A macro to help setup and run replica exchange.
Definition: macros.py:58
A dictionary-like wrapper for reading and storing sequence data.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.