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IMP Reference Guide  develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
display_slab.py
1 import IMP.npctransport
2 import IMP
3 import RMF
4 import IMP.rmf
5 import IMP.atom
6 import IMP.display
7 
8 height = 20
9 radius = 30
10 particle_radius = 10
11 sz = 60
12 use_rmf = True
13 
14 m = IMP.Model()
15 m.set_log_level(IMP.WARNING)
16 p_slab = IMP.Particle(m, "slab")
17 pi_slab = p_slab.get_index()
18 slab = IMP.npctransport.SlabWithCylindricalPore.setup_particle(
19  p_slab, height, radius)
20 p = IMP.Particle(m)
21 pi = p.get_index()
22 d = IMP.core.XYZR.setup_particle(p)
23 d.set_radius(10)
24 d.set_coordinates_are_optimized(True)
25 IMP.atom.Mass.setup_particle(p, 1)
26 IMP.atom.Hierarchy.setup_particle(p)
27 
28 slabps = IMP.npctransport.SlabWithCylindricalPorePairScore(1)
29 r = IMP.core.PairRestraint(m, slabps, [pi_slab, pi], "slab")
30 r.set_log_level(IMP.WARNING)
31 nm = IMP.create_temporary_file_name("display_slab", ".pym")
32 w = IMP.display.create_writer(nm)
33 if use_rmf:
34  rnm = IMP.create_temporary_file_name("display_slab", ".rmf")
35  rmf = RMF.create_rmf_file(rnm)
36 sg = IMP.npctransport.SlabWithCylindricalPoreWireGeometry(height, radius, 100)
37 sg.set_was_used(True)
38 if use_rmf:
39  sg.set_color(IMP.display.Color(0, 1, 0))
40  sgs = sg.get_components()
41  nh = rmf.get_root_node().add_child("slab", RMF.GEOMETRY)
42  IMP.rmf.add_geometries(nh, sgs)
43 w.add_geometry(sg)
44 
45 bb = IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0, 0, 0),
46  IMP.algebra.Vector3D(sz, sz, sz))
47 
48 gs = []
49 if use_rmf:
50  nh = rmf.get_root_node().add_child("deriv", RMF.GEOMETRY)
51 for c in IMP.algebra.get_grid_interior_cover_by_spacing(bb, 5):
52  d.set_coordinates(c)
53  v = r.evaluate(True)
54  if v == 0:
55  continue
56  color = IMP.display.get_hot_color(v/20.0)
57  seg = IMP.algebra.Segment3D(c, c+d.get_derivatives())
58  g = IMP.display.SegmentGeometry(seg)
59  g.set_color(color)
60  g.set_name("deriv")
61  gs.append(g)
62 if use_rmf:
63  IMP.rmf.add_geometries(nh, gs)
64 w.add_geometry(gs)
65 if use_rmf:
66  nh = rmf.get_root_node().add_child("displacements", RMF.GEOMETRY)
67 
68 gs = []
69 for c in IMP.algebra.get_grid_interior_cover_by_spacing(bb, 5):
70  dv = slabps.get_displacement_direction(slab, c)
71  dm = slabps.get_displacement_magnitude(slab, c)
72  if dm > particle_radius:
73  continue
74  color = IMP.display.get_hot_color(
75  -(dm-particle_radius)/(height+particle_radius))
76  m.update()
77  seg = IMP.algebra.Segment3D(c, c+dv)
78  g = IMP.display.SegmentGeometry(seg)
79  g.set_color(color)
80  g.set_name("displace")
81  gs.append(g)
82 if use_rmf:
83  IMP.rmf.add_geometries(nh, gs)
84 w.add_geometry(gs)
85 
86 if use_rmf:
87  IMP.rmf.save_frame(rmf)
88  print("chimera", rnm)
89 print("pymol", nm)
IMP::display::Color
Represent an RGB color.
Definition: Color.h:25
IMP::npctransport
Simulation of transport through the Nuclear Pore Complex.
IMP::rmf::save_frame
RMF::FrameID save_frame(RMF::FileHandle file, std::string name="")
Save the current state of the linked objects as a new RMF frame.
IMP::core::XYZR::setup_particle
static XYZR setup_particle(Model *m, ParticleIndex pi)
Definition: XYZR.h:48
IMP::display::get_hot_color
Color get_hot_color(double f)
Return the color for f from the hot color map.
IMP::npctransport::SlabWithCylindricalPore::setup_particle
static SlabWithCylindricalPore setup_particle(Model *m, ParticleIndex pi, double thickness, double radius)
Definition: SlabWithCylindricalPore.h:67
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::Mass::setup_particle
static Mass setup_particle(Model *m, ParticleIndex pi, Float mass)
Definition: Mass.h:48
IMP::rmf::add_geometries
void add_geometries(RMF::NodeHandle parent, const display::GeometriesTemp &r)
Add geometries to a given parent node.
IMP::display::create_writer
Writer * create_writer(std::string filename)
IMP::algebra::Segment3D
Simple implementation of segments in 3D.
Definition: Segment3D.h:25
IMP::algebra::Vector3D
VectorD< 3 > Vector3D
Definition: VectorD.h:408
IMP::Particle
Class to handle individual particles of a Model object.
Definition: Particle.h:43
IMP::algebra::get_grid_interior_cover_by_spacing
Vector< VectorD< D > > get_grid_interior_cover_by_spacing(const BoundingBoxD< D > &bb, double s)
Definition: vector_generators.h:179
IMP::core::PairRestraint
Applies a PairScore to a Pair.
Definition: PairRestraint.h:31
IMP::display
Output IMP model data in various file formats.
IMP::atom
Functionality for loading, creating, manipulating and scoring atomic structures.
IMP::rmf
Support for the RMF file format for storing hierarchical molecular data and markup.
IMP::create_temporary_file_name
std::string create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file.