doc/html/atom_2multiresolution_8py_source.html

 ## \example 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


 import IMP.atom


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

 m = IMP.kernel.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:197

IMP::core::RigidBody::setup_particle
static RigidBody setup_particle(kernel::Model *m, ParticleIndex pi, kernel::ParticleIndexesAdaptor ps)
Definition: rigid_bodies.h:168

IMP::atom::get_example_path
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.

IMP::algebra::ReferenceFrame3D
A reference frame in 3D.
Definition: ReferenceFrame3D.h:20

IMP::atom::Hierarchy::setup_particle
static Hierarchy setup_particle(kernel::Model *m, kernel::ParticleIndex pi, kernel::ParticleIndexesAdaptor children=kernel::ParticleIndexesAdaptor())
Definition: atom/Hierarchy.h:270

IMP::atom::Representation::setup_particle
static Representation setup_particle(kernel::Model *m, ParticleIndex pi)
Definition: Representation.h:50

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

IMP::atom::Selection
Select hierarchy particles identified by the biological name.
Definition: Selection.h:62

IMP::kernel::Model
Class for storing model, its restraints, constraints, and particles.
Definition: kernel/Model.h:73