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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
displaying_ensembles.py
1 ## \example display/displaying_ensembles.py
2 # The script shows a couple experiments with trying to visualize an
3 # ensemble of structures. The ensemble is fairly tight on the assembly
4 # scale, but there is significant variation between the location and
5 # orientation of the individual proteins (which were modeled as rigid
6 # bodies). To save space, the models have had their sidechain atoms
7 # removed.
8 
9 from __future__ import print_function
10 import IMP.display
11 import IMP.atom
12 import sys
13 
14 IMP.setup_from_argv(
15  sys.argv, "Experiments with trying to visualize an ensemble of structures")
16 
17 Segment = IMP.algebra.Segment3D
18 Cylinder = IMP.algebra.Cylinder3D
19 
20 # turn off internal checks to speed things up
21 IMP.set_check_level(IMP.USAGE)
22 
23 
24 def read(m, beyond_file):
25  print("reading")
26  hs = []
27  for i in range(0, beyond_file):
28  # create a simplified version for each chain to speed up computations
29  name = IMP.display.get_example_path(
30  "ensemble/aligned-" + str(i) + ".pdb")
31  h = IMP.atom.read_pdb(name, m, IMP.atom.CAlphaPDBSelector())
32  hr = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
33  hs.append(hr)
34  for c in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
35  simp = IMP.atom.create_simplified_along_backbone(
36  IMP.atom.Chain(c), 4)
37  hr.add_child(simp)
38  IMP.atom.destroy(h)
39  print(" ", i)
40  return hs
41 
42 
43 def add_markers(h, c, w):
44  """Add markers to a the passed conformation. The marker locations are chosen
45  pretty thoughtlessly and don't really illustrate the technique well."""
46  def add_marker(s, name):
47  g = IMP.core.XYZRGeometry(s.get_selected_particles()[0])
48  g.set_name(name)
49  g.set_color(c)
50  w.add_geometry(g)
51  s = IMP.atom.Selection(h, chain='B', residue_index=317)
52  add_marker(s, "m0")
53  s = IMP.atom.Selection(h, chain='G', residue_index=212)
54  add_marker(s, "m1")
55  s = IMP.atom.Selection(h, chain='I', residue_index=237)
56  add_marker(s, "m2")
57  s = IMP.atom.Selection(h, chain='F', residue_index=101)
58  add_marker(s, "m3")
59 
60 
61 def get_nice_name(h):
62  nm = h.get_name()
63  return nm[nm.find('-') + 1:nm.rfind('.')]
64 
65 
66 def add_axis(h, c, w, chain_colors):
67  """Add a coordinate axis to show the relative orientation of the protein"""
68  for hc in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
69  rb = IMP.core.RigidMember(hc).get_rigid_body()
70  g = IMP.display.ReferenceFrameGeometry(rb.get_reference_frame())
71  g.set_name(get_nice_name(h) + "_orient")
72  if c:
73  g.set_color(c)
74  else:
75  g.set_color(chain_colors[IMP.atom.Chain(hc).get_id()])
76  w.add_geometry(g)
77 
78 
79 def add_skeleton(h, c, r, w, chain_colors):
80  """Show the connectivity skeleton of the conformation to give an idea of
81  how things are laid out"""
82  for hc0 in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
83  for hc1 in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
84  if hc1 <= hc0:
85  continue
86  d = ps.evaluate_index(h.get_model(),
87  (hc0.get_particle_index(),
88  hc1.get_particle_index()), None)
89  if d < 1:
90  d0 = IMP.core.XYZ(hc0)
91  d1 = IMP.core.XYZ(hc1)
92  mp = .5 * (d0.get_coordinates() + d1.get_coordinates())
93  g = IMP.display.CylinderGeometry(
94  Cylinder(Segment(d0.get_coordinates(), mp), r))
95  if c:
96  g.set_color(c)
97  else:
98  g.set_color(chain_colors[IMP.atom.Chain(d0).get_id()])
99  g.set_name(get_nice_name(h) + "_skel")
100  w.add_geometry(g)
101  g = IMP.display.CylinderGeometry(
102  Cylinder(Segment(d1.get_coordinates(), mp), r))
103  if c:
104  g.set_color(c)
105  else:
106  g.set_color(chain_colors[IMP.atom.Chain(d1).get_id()])
107  g.set_name(get_nice_name(h) + "_skel")
108  w.add_geometry(g)
109 
110 
111 IMP.set_log_level(IMP.TERSE)
112 m = IMP.Model()
113 
114 # change to 46 to display all of them
115 hs = read(m, 3)
116 
117 # used to test of two molecules are touching one another
118 ps = IMP.core.KClosePairsPairScore(
119  IMP.core.SphereDistancePairScore(IMP.core.HarmonicUpperBound(10, 1)),
120  IMP.core.LeavesRefiner(IMP.atom.Hierarchy.get_traits()))
121 ps.set_log_level(IMP.SILENT)
122 
123 
124 print("creating rigid bodies")
125 base_chains = {}
126 for hc in IMP.atom.get_by_type(hs[0], IMP.atom.CHAIN_TYPE):
127  c = IMP.atom.Chain(hc)
128  base_chains[c.get_id()] = c
129 
130 for i, h in enumerate(hs):
131  for hc in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
132  c = IMP.atom.Chain(hc)
133  if h == hs[0]:
134  crb = IMP.atom.create_rigid_body(hc)
135  else:
136  # Make sure the rigid bodies have equivalent defining reference
137  # frames. If we just used IMP.atom.create_rigid_body, globular
138  # proteins are likely to have different axes computed when
139  # starting in different orientations
140  crb = IMP.atom.create_compatible_rigid_body(
141  hc, base_chains[c.get_id()])
142  print(" ", i)
143 
144 chains = IMP.atom.get_by_type(hs[0], IMP.atom.CHAIN_TYPE)
145 chains.sort(key=lambda x: IMP.core.XYZ(x).get_x() + IMP.core.XYZ(x).get_y())
146 chain_colors = {}
147 for i, c in enumerate(chains):
148  id = IMP.atom.Chain(c).get_id()
149  color = IMP.display.get_display_color(i)
150  # IMP.display.get_jet_color(f)
151  chain_colors[id] = color
152 
153 w = IMP.display.PymolWriter("markers.pym")
154 add_markers(hs[0], IMP.display.Color(1, 1, 1), w)
155 hso = hs[1:]
156 
157 
158 # sort them spatially so the colors are nicely arranged and allow one to
159 # visually connect the position of one end with that of the other
160 hso.sort(key=lambda h: IMP.core.XYZ(IMP.atom.Selection(
161  h, chain='I', residue_index=237).get_selected_particles()[0]).get_z())
162 print("adding markers", end=' ')
163 for i, h in enumerate(hso):
164  c = IMP.display.get_interpolated_rgb(
165  IMP.display.Color(1, 0, 0), IMP.display.Color(0, 0, 1), i / 50.)
166  add_markers(h, c, w)
167  print(" ", i)
168 w = IMP.display.PymolWriter("axis.pym")
169 print("adding axis", end=' ')
170 add_axis(hs[0], IMP.display.Color(1, 1, 1), w, chain_colors)
171 for i, h in enumerate(hs[1:]):
172  add_axis(h, None, w, chain_colors)
173  print(i, end=' ')
174 
175 w = IMP.display.PymolWriter("skeletons.pym")
176 add_skeleton(hs[0], IMP.display.Color(1, 1, 1), 5, w, chain_colors)
177 print("adding skeleton", end=' ')
178 for i, h in enumerate(hs[1:]):
179  add_skeleton(h, None, 1, w, chain_colors)
180  print(" ", i)
IMP::display::Color
Represent an RGB color.
Definition: Color.h:25
IMP::core::KClosePairsPairScore
Apply a score to a fixed number of close pairs from the two sets.
Definition: ClosePairsPairScore.h:30
IMP::core::LeavesRefiner
Return the hierarchy leaves under a particle.
Definition: LeavesRefiner.h:25
IMP::setup_from_argv
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
IMP::core::HarmonicUpperBound
Upper bound harmonic function (non-zero when feature > mean)
Definition: core/HarmonicUpperBound.h:22
IMP::atom::create_compatible_rigid_body
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
IMP::algebra::Cylinder3D
Represent a cylinder in 3D.
Definition: Cylinder3D.h:27
IMP::core::SphereDistancePairScore
A score on the distance between the surfaces of two spheres.
Definition: SphereDistancePairScore.h:42
IMP::display::get_interpolated_rgb
Color get_interpolated_rgb(const Color &a, const Color &b, double f)
Return a color interpolated between a and b in RGB space.
Definition: Color.h:151
IMP::atom::read_pdb
void read_pdb(TextInput input, int model, Hierarchy h)
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::display::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::display::get_display_color
Color get_display_color(unsigned int i)
IMP::core::XYZ
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
IMP::atom::Hierarchy::get_traits
static const IMP::core::HierarchyTraits & get_traits()
Get the molecular hierarchy HierarchyTraits.
IMP::set_log_level
void set_log_level(LogLevel l)
Set the current global log level.
IMP::algebra::Segment3D
Simple implementation of segments in 3D.
Definition: Segment3D.h:25
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::Particle
Class to handle individual particles of a Model object.
Definition: Particle.h:43
IMP::display::PymolWriter
Write a CGO file with the geometry.
Definition: PymolWriter.h:34
IMP::atom::Chain
Store info for a chain of a protein.
Definition: Chain.h:61
IMP::atom::CAlphaPDBSelector
Select all CA ATOM records.
Definition: pdb.h:80
IMP::display
Output IMP model data in various file formats.
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::set_check_level
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:72
IMP::core::XYZRGeometry
Display an IMP::core::XYZR particle as a ball.
Definition: XYZR.h:151