doc/ref/kernel_2dependency_graph_8py-example.html

## \example kernel/dependency_graph.py

# When trying to understand what is going on in \imp, it can often be useful

# to view the dependency graph, that is, the graph showing how various

# entities relate to one another. In it, an arrow leads from an IMP::Container

# or IMP::Particle to an IMP::Restraint if the IMP::Restraint reads from that

# container or particle. Similarly, an arrow leads from an IMP::Container or

# IMP::Particle to an IMP::ScoreState if the score state reads from it, and

# an arrow leads from an IMP::ScoreState to an IMP::Container or IMP::Particle

# if the score state updates the particle.

#

# The resulting pruned dependency graph is:

# \dotgraph{ \dot

# digraph pruned_dependencies {

# 0[label="Nup85-12"];

# 1[label="Fragment [213-218)"];

# 2[label="Nup145C-4"];

# 3[label="Atom k distance restraint 2"];

# 4[label="Nup1202-8"];

# 5[label="Model 0"];

# 6[label="Fragment [239-244)"];

# 7[label="Nup1332-10"];

# 8[label="Nup1201-12"];

# 9[label="Connectivity particles"];

# 10[label="Nup84-14"];

# 11[label="Atom k distance restraint 3"];

# 12[label="MovedSingletonContainer2"];

# 13[label="Nup1333-16"];

# 14[label="Atom k distance restraint 5"];

# 15[label="Atom k distance restraint 4"];

# 16[label="normalize rigid bodies"];

# 17[label="Atom k distance restraint 0"];

# 18[label="ListSingletonContainer2"];

# 19[label="Chain A rigid body"];

# 20[label="ConnectivityRestraint 0"];

# 21[label="MovedSingletonContainer1"];

# 22[label="ListSingletonContainer1"];

# 23[label="HarmonicUpperBoundSphereDistancePairScore2 and ConnectingPairContainer"];

# 24[label="HarmonicUpperBoundSphereDistancePairScore1 and ConnectingPairContainer"];

# 25[label="Sec13"];

# 26[label="Hierarchy EV"];

# 27[label="Chain A rigid body rigid body positions"];

# 28[label="rigid bodies list"];

# 29[label="Atom k distance restraint 1"];

# 30[label="HarmonicUpperBoundSphereDistancePairScore0 and ConnectingPairContainer"];

# 31[label="ConnectingPairContainer"];

# 32[label="ConnectingPairContainer"];

# 33[label="Chain A rigid body"];

# 34[label="ListSingletonContainer0"];

# 35[label="ConnectivityRestraint 1"];

# 36[label="MovedSingletonContainer0"];

# 37[label="Chain A rigid body rigid body positions"];

# 38[label="ConnectingPairContainer"];

# 39[label="Seh1"];

# 40[label="Hierarchy EV particles"];

# 16->19 ;

# 16->33 ;

# 27->6 ;

# 27->39 ;

# 37->25 ;

# 37->1 ;

# 4->3 ;

# 2->3 ;

# 11->5 ;

# 17->5 ;

# 23->5 ;

# 14->5 ;

# 35->5 ;

# 15->5 ;

# 30->5 ;

# 24->5 ;

# 29->5 ;

# 26->5 ;

# 3->5 ;

# 20->5 ;

# 13->11 ;

# 10->11 ;

# 2->12 ;

# 18->12 ;

# 25->14 ;

# 2->14 ;

# 1->14 ;

# 33->14 ;

# 0->15 ;

# 6->15 ;

# 19->15 ;

# 39->15 ;

# 28->16 ;

# 8->17 ;

# 4->17 ;

# 13->20 ;

# 7->20 ;

# 22->21 ;

# 10->21 ;

# 2->23 ;

# 38->23 ;

# 31->24 ;

# 10->24 ;

# 0->26 ;

# 13->26 ;

# 8->26 ;

# 7->26 ;

# 4->26 ;

# 2->26 ;

# 6->26 ;

# 19->26 ;

# 10->26 ;

# 40->26 ;

# 1->26 ;

# 33->26 ;

# 19->27 ;

# 0->29 ;

# 2->29 ;

# 0->30 ;

# 32->30 ;

# 21->31 ;

# 22->31 ;

# 10->31 ;

# 0->32 ;

# 36->32 ;

# 34->32 ;

# 25->35 ;

# 2->35 ;

# 10->35 ;

# 1->35 ;

# 33->35 ;

# 0->36 ;

# 34->36 ;

# 33->37 ;

# 12->38 ;

# 2->38 ;

# 18->38 ;

# }

# \enddot

# }


import IMP.atom

import IMP.container

import sys


IMP.setup_from_argv(sys.argv, "Example of dependency graphs")


def create_representation():

    m = IMP.Model()

    all = IMP.atom.Hierarchy.setup_particle(IMP.Particle(m))

    all.set_name("the universe")

    rs = []


    def create_protein(name, ds):

        h = IMP.atom.create_protein(m, name, 10, ds)

        # leaves = IMP.atom.get_leaves(h)

        all.add_child(h)

        r = IMP.atom.create_connectivity_restraint(

            [IMP.atom.Selection(c) for c in h.get_children()], 1)

        if r:

            rs.append(r)


    def create_protein_from_pdbs(name, files):

        def create_from_pdb(file):

            with IMP.SetLogState(IMP.NONE):

                t = IMP.atom.read_pdb(

                    IMP.get_example_path("data/" + file), m,

                    IMP.atom.ATOMPDBSelector())

            # IMP.atom.show_molecular_hierarchy(t)

            c = IMP.atom.Chain(IMP.atom.get_by_type(t, IMP.atom.CHAIN_TYPE)[0])

            if c.get_number_of_children() == 0:

                IMP.atom.show_molecular_hierarchy(t)

            # there is no reason to use all atoms, just approximate the pdb

            # shape instead

            s = IMP.atom.create_simplified_along_backbone(c,

                                                          10.0 / 2.0)

            IMP.atom.destroy(t)

            # make the simplified structure rigid

            rb = IMP.atom.create_rigid_body(s)

            rb.set_coordinates_are_optimized(True)

            return s

        if len(files) > 1:

            p = IMP.Particle(m)

            h = IMP.atom.Hierarchy.setup_particle(p)

            h.set_name(name)

            for i, f in enumerate(files):

                c = create_from_pdb(f)

                h.add_child(c)

                c.set_name(name + " chain " + str(i))

            r = IMP.atom.create_connectivity_restraint(

                [IMP.atom.Selection(c) for c in h.get_children()], 1)

            if r:

                rs.append(r)

        else:

            h = create_from_pdb(files[0])

            h.set_name(name)

        all.add_child(h)

    create_protein("Nup85", 570)

    create_protein("Nup84", 460)

    create_protein("Nup145C", 442)

    create_protein("Nup120", [0, 500, 761])

    create_protein("Nup133", [0, 450, 778, 1160])

    create_protein_from_pdbs("Seh1", ["seh1.pdb"])

    create_protein_from_pdbs("Sec13", ["sec13.pdb"])

    return (m, rs, all)


def create_restraints(m, rs, all):

    def add_connectivity_restraint(s):

        r = IMP.atom.create_connectivity_restraint(s, 1)

        rs.append(r)


    def add_distance_restraint(s0, s1):

        r = IMP.atom.create_distance_restraint(s0, s1, 0, 1)

        rs.append(r)

    evr = IMP.atom.create_excluded_volume_restraint([all])

    rs.append(evr)

    s0 = IMP.atom.Selection(hierarchy=all, molecule="Nup145C",

                            residue_indexes=range(0, 423))

    s1 = IMP.atom.Selection(hierarchy=all, molecule="Nup84")

    s2 = IMP.atom.Selection(hierarchy=all, molecule="Sec13")

    add_connectivity_restraint([s0, s1, s2])

    add_distance_restraint(

        IMP.atom.Selection(hierarchy=all, molecule="Nup145C",

                           residue_indexes=range(0, 423)),

        IMP.atom.Selection(hierarchy=all, molecule="Nup85"))

    add_distance_restraint(

        IMP.atom.Selection(hierarchy=all, molecule="Nup145C",

                           residue_indexes=range(0, 423)),

        IMP.atom.Selection(hierarchy=all, molecule="Nup120",

                           residue_indexes=range(500, 762)))

    add_distance_restraint(IMP.atom.Selection(hierarchy=all, molecule="Nup84"),

                           IMP.atom.Selection(

                               hierarchy=all, molecule="Nup133",

                               residue_indexes=range(778, 1160)))

    add_distance_restraint(IMP.atom.Selection(hierarchy=all, molecule="Nup85"),

                           IMP.atom.Selection(hierarchy=all, molecule="Seh1"))

    add_distance_restraint(

        IMP.atom.Selection(hierarchy=all, molecule="Nup145C",

                           residue_indexes=range(0, 423)),

        IMP.atom.Selection(hierarchy=all, molecule="Sec13"))


# now do the actual work

(m, rs, all) = create_representation()

create_restraints(m, rs, all)


sf = IMP.core.RestraintsScoringFunction(rs)


# we can get the full dependency graph for the whole model with all

# the restraints but it is pretty complex

dg = IMP.get_dependency_graph(m)

IMP.show_graphviz(dg)


# better thing to do is to get the "pruned" graph

pdg = IMP.get_pruned_dependency_graph(m)


IMP.show_graphviz(pdg)