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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
cover_particles.py
1 ## \example core/cover_particles.py
2 # Show how to maintain a sphere per residue which includes all atoms
3 # of the residue. The derivatives are propagated from the sphere
4 # cover to the atoms so that restraints can be used at multiple
5 # levels.
6 
7 import IMP
8 import IMP.core
9 import IMP.atom
10 import sys
11 
12 IMP.setup_from_argv(sys.argv, "cover particles")
13 
14 m = IMP.Model()
15 prot = IMP.atom.read_pdb(IMP.core.get_example_path('example_protein.pdb'), m)
16 res = IMP.atom.get_by_type(prot, IMP.atom.RESIDUE_TYPE)
18 for r in res:
19  # add coordinates and a radius to the residue particle
21  # make sure that the coordinates and the radius define a sphere
22  # which contains all of the leaves (atoms) of the residue
23  IMP.core.Cover.setup_particle(r.get_particle(), pr)
24 # update the coordinates of the residue particles so that they cover the atoms
25 m.update()
Return the hierarchy children of a particle.
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
static XYZR setup_particle(Model *m, ParticleIndex pi)
Definition: XYZR.h:48
static Cover setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor members)
Definition: CoverRefined.h:72
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
void read_pdb(TextInput input, int model, Hierarchy h)
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:86
static const IMP::core::HierarchyTraits & get_traits()
Get the molecular hierarchy HierarchyTraits.
Basic functionality that is expected to be used by a wide variety of IMP users.
Functionality for loading, creating, manipulating and scoring atomic structures.