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IMP Reference Guide  develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
atom/multiresolution.py
1 ## \example atom/multiresolution.py
2 # This example shows how to use the multiresolution support available in
3 # IMP.atom via the IMP.atom.Resolution decorator and IMP.atom.Selection
4 
5 import IMP.atom
6 import sys
7 
8 IMP.setup_from_argv(sys.argv, "multiresolution")
9 
10 # Create an IMP model and add a heavy atom-only protein from a PDB file
11 m = IMP.Model()
12 
13 root = IMP.atom.Hierarchy.setup_particle(m, m.add_particle("root"))
14 rigid_body = IMP.core.RigidBody.setup_particle(
15  m, m.add_particle("rigid body"),
16  IMP.algebra.ReferenceFrame3D())
17 
18 prot = IMP.atom.read_pdb(IMP.atom.get_example_path("example_protein.pdb"), m,
19  IMP.atom.NonWaterNonHydrogenPDBSelector())
20 root.add_child(prot)
21 print("adding rigid body for atoms")
22 rigid_body.add_member(IMP.atom.create_rigid_body(prot))
23 
24 resolutions = IMP.atom.Representation.setup_particle(root)
25 
26 print("creating residue level rep")
27 residues = IMP.atom.create_simplified_along_backbone(prot, 1)
28 print("adding rigid body for residues")
29 rigid_body.add_member(IMP.atom.create_rigid_body(residues))
30 resolutions.add_representation(residues)
31 
32 print("creating triplet residue level rep")
33 triplets = IMP.atom.create_simplified_along_backbone(prot, 3)
34 resolutions.add_representation(triplets)
35 print("adding rigid body for triplets")
36 rigid_body.add_member(IMP.atom.create_rigid_body(triplets))
37 
38 whole = IMP.atom.create_simplified_along_backbone(prot, 10000)
39 resolutions.add_representation(whole)
40 
41 print("resolutions are", resolutions)
42 
43 # note these resolutions need to be fixed
44 print("atoms")
45 print(IMP.atom.Selection(
46  root, residue_index=15, resolution=1).get_selected_particles())
47 print("residues")
48 print(IMP.atom.Selection(
49  root, residue_index=15, resolution=.3).get_selected_particles())
50 print("several residues")
51 print(IMP.atom.Selection(
52  root, residue_index=15, resolution=.2).get_selected_particles())
53 print("very coarse")
54 print(IMP.atom.Selection(
55  root, residue_index=15, resolution=.01).get_selected_particles())
56 print("all")
57 print(IMP.atom.Selection(
58  root, residue_index=15,
59  resolution=IMP.atom.ALL_RESOLUTIONS).get_selected_particles())
IMP::atom::NonWaterNonHydrogenPDBSelector
Select non water and non hydrogen atoms.
Definition: pdb.h:314
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:22
IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:86
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:70
IMP::core::RigidBody::setup_particle
static RigidBody setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor ps)
Definition: rigid_bodies.h:180