2 """This script shows how to simulate an atomic system with MD,
3 with a secondary structure elastic network to speed things up.
6 from __future__
import print_function
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")
26 st1 = s.create_state()
30 gcp2 = st1.create_molecule(
"GCP2", sequence=seqs[
"GCP2_YEAST"], chain_id=
'A')
38 gcp2.add_representation(a1, resolutions=[0])
39 print(
'building molecule')
43 print(
'adding restraints')
49 name_map={
'A':
'GCP2'})
51 for sse
in sses[
'helix']+sses[
'beta']:
63 md_ps = dof.setup_md(gcp2)
67 molecular_dynamics_sample_objects=md_ps,
68 molecular_dynamics_steps=5,
70 number_of_best_scoring_models=0,
73 global_output_directory=
'atomistic_output/')
Simplify creation of constraints and movers for an IMP Hierarchy.
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)
Enable CHARMM force field.
def parse_dssp
Read a DSSP file, and return secondary structure elements (SSEs).
Add harmonic restraints between all pairs.
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.
Represent the root node of the global IMP.atom.Hierarchy.
Class for storing model, its restraints, constraints, and particles.
Create movers and set up constraints for PMI objects.
Python classes to represent, score, sample and analyze models.
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.