doc/ref/rigid__bodies_8py_source.html

 ## \example core/rigid_bodies.py

 # This example shows how to set up rigid bodies, one per residue in a protein. A score

 # state is then used to ensure that the bodies remain rigid during the optimization process.

 #


 import IMP

 import IMP.core

 import IMP.atom

 import IMP.container

 import sys


 IMP.setup_from_argv(sys.argv, "rigid bodies")


 m = IMP.Model()

 # create a new IMP.atom.Hierarchy for the pdb file

 mp1 = IMP.atom.read_pdb(IMP.core.get_example_path('example_protein.pdb'), m)

 chains = IMP.atom.get_by_type(mp1, IMP.atom.CHAIN_TYPE)

 rd = IMP.atom.Hierarchy(chains[0])

 # Create a rigid body from the first chain

 # note that rbs != chains[0] as the bounding volume for rbs needs to include all of the

 # chain, but chains[0] might have a smaller sphere associated with it.

 rbs = IMP.atom.create_rigid_body(chains[0])

 print("all done")

IMP::setup_from_argv
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)

IMP::container
Various classes to hold sets of particles.

IMP::core::get_example_path
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.

IMP::atom::read_pdb
void read_pdb(TextInput input, int model, Hierarchy h)

IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:72

IMP::atom::Hierarchy
The standard decorator for manipulating molecular structures.
Definition: atom/Hierarchy.h:203

IMP::atom::get_by_type
Hierarchies get_by_type(Hierarchy mhd, GetByType t)
Gather all the molecular particles of a certain level in the hierarchy.

IMP::core
Basic functionality that is expected to be used by a wide variety of IMP users.

IMP::atom::create_rigid_body
IMP::core::RigidBody create_rigid_body(Hierarchy h)

IMP::atom
Functionality for loading, creating, manipulating and scoring atomic structures.