2 """This script shows how to simulate an atomic system with MD,
3 with a secondary structure elastic network to speed things up.
19 st1 = s.create_state()
23 gcp2 = st1.create_molecule(
"GCP2",sequence=seqs[
"GCP2_YEAST"],chain_id=
'A')
30 gcp2.add_representation(a1,resolutions=[0])
31 print(
'building molecule')
35 print(
'adding restraints')
42 for sse
in sses[
'helix']+sses[
'beta']:
54 md_ps = dof.setup_md(gcp2)
57 crosslink_restraints = all_rs,
58 molecular_dynamics_sample_objects=md_ps,
59 molecular_dynamics_steps=5,
60 number_of_best_scoring_models=0,
62 global_output_directory=
'atomistic_output/')
A class to simplify create of constraints and movers for an IMP Hierarchy.
Restraints for keeping correct stereochemistry.
Set of python classes to create a multi-state, multi-resolution IMP hierarchy.
Enable CHARMM force field.
def parse_dssp
read dssp file, get 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.
This class initializes the root node of the global IMP.atom.Hierarchy.
Class for storing model, its restraints, constraints, and particles.
Create movers and setup constraints for PMI objects.
Python classes to represent, score, sample and analyze models.
A macro to help setup and run replica exchange.
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.