doc/ref/atom_2multiresolution_8py_source.html

 ## \example atom/multiresolution.py

 # This example shows how to use the multiresolution support available in

 # IMP.atom via the IMP.atom.Resolution decorator and IMP.atom.Selection


 from __future__ import print_function

 import IMP.atom

 import sys


 IMP.setup_from_argv(sys.argv, "multiresolution")


 # Create an IMP model and add a heavy atom-only protein from a PDB file

 m = IMP.Model()


 root = IMP.atom.Hierarchy.setup_particle(m, m.add_particle("root"))

 rigid_body = IMP.core.RigidBody.setup_particle(

     m, m.add_particle("rigid body"),

     IMP.algebra.ReferenceFrame3D())


 prot = IMP.atom.read_pdb(IMP.atom.get_example_path("example_protein.pdb"), m,

                          IMP.atom.NonWaterNonHydrogenPDBSelector())

 root.add_child(prot)

 print("adding rigid body for atoms")

 rigid_body.add_member(IMP.atom.create_rigid_body(prot))


 resolutions = IMP.atom.Representation.setup_particle(root)


 print("creating residue level rep")

 residues = IMP.atom.create_simplified_along_backbone(prot, 1)

 print("adding rigid body for residues")

 rigid_body.add_member(IMP.atom.create_rigid_body(residues))

 resolutions.add_representation(residues)


 print("creating triplet residue level rep")

 triplets = IMP.atom.create_simplified_along_backbone(prot, 3)

 resolutions.add_representation(triplets)

 print("adding rigid body for triplets")

 rigid_body.add_member(IMP.atom.create_rigid_body(triplets))


 whole = IMP.atom.create_simplified_along_backbone(prot, 10000)

 resolutions.add_representation(whole)


 print("resolutions are", resolutions)


 # note these resolutions need to be fixed

 print("atoms")

 print(IMP.atom.Selection(root, residue_index=15, resolution=1).get_selected_particles())

 print("residues")

 print(IMP.atom.Selection(root, residue_index=15, resolution=.3).get_selected_particles())

 print("several residues")

 print(IMP.atom.Selection(root, residue_index=15, resolution=.2).get_selected_particles())

 print("very coarse")

 print(IMP.atom.Selection(root, residue_index=15, resolution=.01).get_selected_particles())

 print("all")

 print(IMP.atom.Selection(root, residue_index=15, resolution=IMP.atom.ALL_RESOLUTIONS).get_selected_particles())

IMP::atom::NonWaterNonHydrogenPDBSelector
Select non water and non hydrogen atoms.
Definition: pdb.h:245

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

IMP::atom::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::Representation::setup_particle
static Representation setup_particle(Model *m, ParticleIndex pi)
Definition: Representation.h:55

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

IMP::algebra::ReferenceFrame3D
A reference frame in 3D.
Definition: ReferenceFrame3D.h:21

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

IMP::atom::Hierarchy::setup_particle
static Hierarchy setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor children=ParticleIndexesAdaptor())
Create a Hierarchy of level t by adding the needed attributes.
Definition: atom/Hierarchy.h:240

IMP::atom::create_simplified_along_backbone
Hierarchy create_simplified_along_backbone(Chain input, const IntRanges &residue_segments, bool keep_detailed=false)

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

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

IMP::atom::Selection
Select hierarchy particles identified by the biological name.
Definition: Selection.h:66

IMP::core::RigidBody::setup_particle
static RigidBody setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor ps)
Definition: rigid_bodies.h:174