displaying_ensembles.py

## \example display/displaying_ensembles.py
# The script shows a couple experiments with trying to visualize an
# ensemble of structures. The ensemble is fairly tight on the assembly
# scale, but there is significant variation between the location and
# orientation of the individual proteins (which were modeled as rigid
# bodies). To save space, the models have had their sidechain atoms
# removed.

from __future__ import print_function
import IMP.display
import IMP.atom
import sys

IMP.setup_from_argv(sys.argv,
    "Experiments with trying to visualize an ensemble of structures")

Segment = IMP.algebra.Segment3D
Cylinder = IMP.algebra.Cylinder3D

# turn off internal checks to speed things up
IMP.set_check_level(IMP.USAGE)


def read(m, beyond_file):
    print("reading")
    hs = []
    for i in range(0, beyond_file):
        # create a simplified version for each chain to speed up computations
        name = IMP.display.get_example_path(
            "ensemble/aligned-" + str(i) + ".pdb")
        h = IMP.atom.read_pdb(name, m, IMP.atom.CAlphaPDBSelector())
        hr = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))
        hs.append(hr)
        for c in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
            simp = IMP.atom.create_simplified_along_backbone(
                IMP.atom.Chain(c), 4)
            hr.add_child(simp)
        IMP.atom.destroy(h)
        if i == 0:
            base = IMP.atom.get_leaves(hr)
        print(" ", i)
    return hs


def add_markers(h, c, w):
    """Add markers to a the passed conformation. The marker locations are chosen
    pretty thoughtlessly and don't really illustrate the technique well."""
    def add_marker(s, name):
        g = IMP.core.XYZRGeometry(s.get_selected_particles()[0])
        g.set_name(name)
        g.set_color(c)
        w.add_geometry(g)
    s = IMP.atom.Selection(h, chain='B', residue_index=317)
    add_marker(s, "m0")
    s = IMP.atom.Selection(h, chain='G', residue_index=212)
    add_marker(s, "m1")
    s = IMP.atom.Selection(h, chain='I', residue_index=237)
    add_marker(s, "m2")
    s = IMP.atom.Selection(h, chain='F', residue_index=101)
    add_marker(s, "m3")


def get_nice_name(h):
    nm = h.get_name()
    return nm[nm.find('-') + 1:nm.rfind('.')]


def add_axis(h, c, w, chain_colors):
    """Add a coordinate axis to show the relative orientation of the protein"""
    for hc in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
        rb = IMP.core.RigidMember(hc).get_rigid_body()
        g = IMP.display.ReferenceFrameGeometry(rb.get_reference_frame())
        g.set_name(get_nice_name(h) + "_orient")
        if c:
            g.set_color(c)
        else:
            g.set_color(chain_colors[IMP.atom.Chain(hc).get_id()])
        w.add_geometry(g)


def add_skeleton(h, c, r, w, chain_colors):
    """Show the connectivity skeleton of the conformation to give an idea of
    how things are layed out"""
    for hc0 in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
        for hc1 in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
            if hc1 <= hc0:
                continue
            d = ps.evaluate_index(h.get_model(),
                                  (hc0.get_particle_index(),
                                   hc1.get_particle_index()), None)
            if d < 1:
                d0 = IMP.core.XYZ(hc0)
                d1 = IMP.core.XYZ(hc1)
                mp = .5 * (d0.get_coordinates() + d1.get_coordinates())
                g = IMP.display.CylinderGeometry(
                    Cylinder(Segment(d0.get_coordinates(), mp), r))
                if c:
                    g.set_color(c)
                else:
                    g.set_color(chain_colors[IMP.atom.Chain(d0).get_id()])
                g.set_name(get_nice_name(h) + "_skel")
                w.add_geometry(g)
                g = IMP.display.CylinderGeometry(
                    Cylinder(Segment(d1.get_coordinates(), mp), r))
                if c:
                    g.set_color(c)
                else:
                    g.set_color(chain_colors[IMP.atom.Chain(d1).get_id()])
                g.set_name(get_nice_name(h) + "_skel")
                w.add_geometry(g)

IMP.set_log_level(IMP.TERSE)
m = IMP.Model()

# change to 46 to display all of them
hs = read(m, 3)

# used to test of two molecules are touching one another
ps = IMP.core.KClosePairsPairScore(
    IMP.core.SphereDistancePairScore(IMP.core.HarmonicUpperBound(10, 1)),
    IMP.core.LeavesRefiner(IMP.atom.Hierarchy.get_traits()))
ps.set_log_level(IMP.SILENT)


print("creating rigid bodies")
base_chains = {}
for hc in IMP.atom.get_by_type(hs[0], IMP.atom.CHAIN_TYPE):
    c = IMP.atom.Chain(hc)
    base_chains[c.get_id()] = c

for i, h in enumerate(hs):
    for hc in IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE):
        c = IMP.atom.Chain(hc)
        if h == hs[0]:
            crb = IMP.atom.create_rigid_body(hc)
        else:
            # make sure the rigid bodies have equivalent defining reference frames
            # if we just used IMP.atom.create_rigid_body, globular proteins are likely
            # to have different axis computed when starting in different
            # orientations
            crb = IMP.atom.create_compatible_rigid_body(
                hc, base_chains[c.get_id()])
    print(" ", i)

chains = IMP.atom.get_by_type(hs[0], IMP.atom.CHAIN_TYPE)
chains.sort(key = lambda x: IMP.core.XYZ(x).get_x() + IMP.core.XYZ(x).get_y())
chain_colors = {}
for i, c in enumerate(chains):
    id = IMP.atom.Chain(c).get_id()
    #f= i/float(len(chains))
    color = IMP.display.get_display_color(i)
    # IMP.display.get_jet_color(f)
    chain_colors[id] = color

w = IMP.display.PymolWriter("markers.pym")
add_markers(hs[0], IMP.display.Color(1, 1, 1), w)
hso = hs[1:]


# sort them spatially so the colors are nicely arranged and allow one to visually connect
# the position of one end with that of the other
hso.sort(key=lambda h: IMP.core.XYZ(IMP.atom.Selection(h, chain='I',
                       residue_index=237).get_selected_particles()[0]).get_z())
print("adding markers", end=' ')
for i, h in enumerate(hso):
    c = IMP.display.get_interpolated_rgb(
        IMP.display.Color(1, 0, 0), IMP.display.Color(0, 0, 1), i / 50.)
    add_markers(h, c, w)
    print(" ", i)
w = IMP.display.PymolWriter("axis.pym")
print("adding axis", end=' ')
add_axis(hs[0], IMP.display.Color(1, 1, 1), w, chain_colors)
for i, h in enumerate(hs[1:]):
    add_axis(h, None, w, chain_colors)
    print(i, end=' ')

w = IMP.display.PymolWriter("skeletons.pym")
add_skeleton(hs[0], IMP.display.Color(1, 1, 1), 5, w, chain_colors)
print("adding skeleton", end=' ')
for i, h in enumerate(hs[1:]):
    add_skeleton(h, None, 1, w, chain_colors)
    print(" ", i)