IMP  2.2.1
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 # ensembe 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 import IMP.display
10 import IMP.atom
11 
12 Segment = IMP.algebra.Segment3D
13 Cylinder = IMP.algebra.Cylinder3D
14 
15 # turn off internal checks to speed things up
16 IMP.base.set_check_level(IMP.base.USAGE)
17 
18 
19 def read(m, beyond_file):
20  print "reading"
21  hs = []
22  for i in range(0, beyond_file):
23  # create a simplified version for each chain to speed up computations
25  "ensemble/aligned-" + str(i) + ".pdb")
28  hs.append(hr)
29  for c in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
31  IMP.atom.Chain(c), 4)
32  hr.add_child(simp)
34  if i == 0:
35  base = IMP.atom.get_leaves(hr)
36  print " ", i
37  return hs
38 
39 
40 def add_markers(h, c, w):
41  """Add markers to a the passed conformation. The marker locations are chosen
42  pretty thoughtlessly and don't really illustrate the technique well."""
43  def add_marker(s, name):
44  g = IMP.core.XYZRGeometry(s.get_selected_particles()[0])
45  g.set_name(name)
46  g.set_color(c)
47  w.add_geometry(g)
48  s = IMP.atom.Selection(h, chain='B', residue_index=317)
49  add_marker(s, "m0")
50  s = IMP.atom.Selection(h, chain='G', residue_index=212)
51  add_marker(s, "m1")
52  s = IMP.atom.Selection(h, chain='I', residue_index=237)
53  add_marker(s, "m2")
54  s = IMP.atom.Selection(h, chain='F', residue_index=101)
55  add_marker(s, "m3")
56 
57 
58 def get_nice_name(h):
59  nm = h.get_name()
60  return nm[nm.find('-') + 1:nm.rfind('.')]
61 
62 
63 def add_axis(h, c, w, chain_colors):
64  """Add a coordinate axis to show the relative orientation of the protein"""
65  for hc in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
66  rb = IMP.core.RigidMember(hc).get_rigid_body()
67  g = IMP.display.ReferenceFrameGeometry(rb.get_reference_frame())
68  g.set_name(get_nice_name(h) + "_orient")
69  if c:
70  g.set_color(c)
71  else:
72  g.set_color(chain_colors[IMP.atom.Chain(hc).get_id()])
73  w.add_geometry(g)
74 
75 
76 def add_skeleton(h, c, r, w, chain_colors):
77  """Show the connectivity skeleton of the conformation to give an idea of
78  how things are layed out"""
79  for hc0 in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
80  for hc1 in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
81  if hc1 <= hc0:
82  continue
83  d = ps.evaluate((hc0, hc1), None)
84  if d < 1:
85  d0 = IMP.core.XYZ(hc0)
86  d1 = IMP.core.XYZ(hc1)
87  mp = .5 * (d0.get_coordinates() + d1.get_coordinates())
89  Cylinder(Segment(d0.get_coordinates(), mp), r))
90  if c:
91  g.set_color(c)
92  else:
93  g.set_color(chain_colors[IMP.atom.Chain(d0).get_id()])
94  g.set_name(get_nice_name(h) + "_skel")
95  w.add_geometry(g)
97  Cylinder(Segment(d1.get_coordinates(), mp), r))
98  if c:
99  g.set_color(c)
100  else:
101  g.set_color(chain_colors[IMP.atom.Chain(d1).get_id()])
102  g.set_name(get_nice_name(h) + "_skel")
103  w.add_geometry(g)
104 
105 IMP.base.set_log_level(IMP.base.TERSE)
106 m = IMP.kernel.Model()
107 
108 # change to 46 to display all of them
109 hs = read(m, 3)
110 
111 # used to test of two molecules are touching one another
115 ps.set_log_level(IMP.base.SILENT)
116 
117 
118 print "creating rigid bodies"
119 base_chains = {}
120 for hc in IMP.atom.get_by_type(hs[0], IMP.atom.CHAIN_TYPE):
121  c = IMP.atom.Chain(hc)
122  base_chains[c.get_id()] = c
123 
124 for i, h in enumerate(hs):
125  for hc in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
126  c = IMP.atom.Chain(hc)
127  if h == hs[0]:
129  else:
130  # make sure the rigid bodies have equivalent defining reference frames
131  # if we just used IMP.atom.create_rigid_body, globular proteins are likely
132  # to have different axis computed when starting in different
133  # orientations
135  hc, base_chains[c.get_id()])
136  print " ", i
137 
138 chains = IMP.atom.get_by_type(hs[0], IMP.atom.CHAIN_TYPE)
139 chains.sort(lambda x, y: cmp(IMP.core.XYZ(x).get_x() + IMP.core.XYZ(x).get_y(),
140  IMP.core.XYZ(y).get_x() + IMP.core.XYZ(y).get_y()))
141 chain_colors = {}
142 for i, c in enumerate(chains):
143  id = IMP.atom.Chain(c).get_id()
144  #f= i/float(len(chains))
146  # IMP.display.get_jet_color(f)
147  chain_colors[id] = color
148 
149 w = IMP.display.PymolWriter("markers.pym")
150 add_markers(hs[0], IMP.display.Color(1, 1, 1), w)
151 hso = hs[1:]
152 
153 
154 # sort them spatially so the colors are nicely arranged and allow one to visually connect
155 # the position of one end with that of the other
156 hso.sort(lambda h0, h1: cmp(IMP.core.XYZ(IMP.atom.Selection(h0, chain='I',
157  residue_index=237).get_selected_particles(
158 )[0]).get_z(),
159  IMP.core.XYZ(IMP.atom.Selection(h1, chain='I',
160  residue_index=237).get_selected_particles()[0]).get_z()))
161 print "adding markers",
162 for i, h in enumerate(hso):
164  IMP.display.Color(1, 0, 0), IMP.display.Color(0, 0, 1), i / 50.)
165  add_markers(h, c, w)
166  print " ", i
167 w = IMP.display.PymolWriter("axis.pym")
168 print "adding axis",
169 add_axis(hs[0], IMP.display.Color(1, 1, 1), w, chain_colors)
170 for i, h in enumerate(hs[1:]):
171  add_axis(h, None, w, chain_colors)
172  print i,
173 
174 w = IMP.display.PymolWriter("skeletons.pym")
175 add_skeleton(hs[0], IMP.display.Color(1, 1, 1), 5, w, chain_colors)
176 print "adding skeleton",
177 for i, h in enumerate(hs[1:]):
178  add_skeleton(h, None, 1, w, chain_colors)
179  print " ", i
Represent an RGB color.
Definition: Color.h:24
Return the hierarchy leaves under a particle.
Definition: LeavesRefiner.h:25
Upper bound harmonic function (non-zero when feature > mean)
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
void set_log_level(LogLevel l)
Set the current global log level.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
A score on the distance between the surfaces of two spheres.
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:143
static Hierarchy setup_particle(kernel::Model *m, kernel::ParticleIndex pi, kernel::ParticleIndexesAdaptor children=kernel::ParticleIndexesAdaptor())
Hierarchies get_by_type(Hierarchy mhd, GetByType t)
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
Color get_display_color(unsigned int i)
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
Class to handle individual model particles.
static const IMP::core::HierarchyTraits & get_traits()
Get the molecular hierarchy HierararchyTraits.
void destroy(Hierarchy d)
Delete the Hierarchy.
Hierarchy create_simplified_along_backbone(Chain input, const IntRanges &residue_segments, bool keep_detailed=false)
IMP::core::RigidBody create_rigid_body(Hierarchy h)
Write a CGO file with the geometry.
Definition: PymolWriter.h:34
Store info for a chain of a protein.
Definition: Chain.h:21
Select all CA ATOM records.
Definition: pdb.h:76
See IMP.display for more information.
Definition: ChimeraWriter.h:17
See IMP.atom for more information.
void read_pdb(base::TextInput input, int model, Hierarchy h)
Hierarchies get_leaves(const Selection &h)
Class for storing model, its restraints, constraints, and particles.
Definition: kernel/Model.h:72
Display an IMP::core::XYZR particle as a ball.
Definition: XYZR.h:150