IMP logo
IMP Reference Guide  2.12.0
The Integrative Modeling Platform
/ideal_helix.py
1 ## \example pmi/ideal_helix.py
2 """Short example demonstrating ideal helices in PMI
3 """
4 
5 import IMP
6 import IMP.atom
7 import IMP.rmf
8 import IMP.pmi
9 import IMP.pmi.topology
10 import IMP.pmi.dof
11 import IMP.pmi.macros
12 import IMP.pmi.restraints
13 import sys
14 
15 IMP.setup_from_argv(sys.argv, "Demonstration of ideal helices")
16 
17 # Create System and State
18 mdl = IMP.Model()
20 st = s.create_state()
21 
22 # Create a molecule and add helix representation
23 # this makes a c-alpha chain in approximately the shape of a helix
24 mol = st.create_molecule("example_helix",sequence='A'*20,chain_id='A')
25 mol.add_representation(mol,
26  resolutions=[1,10],
27  ideal_helix=True)
28 hier = s.build()
29 
30 # write a single-frame RMF to view the helix
32 out.init_rmf("example_helix.rmf3",hierarchies=[hier])
33 out.write_rmf("example_helix.rmf3")
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)
Protocols for sampling structures and analyzing them.
Definition: macros.py:1
This class initializes the root node of the global IMP.atom.Hierarchy.
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:72
Classes to handle different kinds of restraints.
Class for easy writing of PDBs, RMFs, and stat files.
Definition: output.py:60
Create movers and set up constraints for PMI objects.
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.