doc/ref/dependency__graph_8py_source.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 depenency 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)

IMP::atom::show_molecular_hierarchy
void show_molecular_hierarchy(Hierarchy h)
Print out the molecular hierarchy.

IMP::get_dependency_graph
DependencyGraph get_dependency_graph(Model *m)

IMP::setup_from_argv
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)

IMP::container
Various classes to hold sets of particles.

IMP::core::RestraintsScoringFunction
Definition: RestraintsScoringFunction.h:22

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:72

IMP::atom::create_protein
Hierarchy create_protein(Model *m, std::string name, double target_radius, const Ints domain_boundaries)

IMP::atom::ATOMPDBSelector
Select all non-alternative ATOM records.
Definition: pdb.h:64

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:255

IMP::atom::create_protein
Hierarchy create_protein(Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
Create a coarse grained molecule.

IMP::SetLogState
A class to change and restore log state.
Definition: SetLogState.h:31

IMP::get_pruned_dependency_graph
DependencyGraph get_pruned_dependency_graph(Model *m)

IMP::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::atom::create_simplified_along_backbone
Hierarchy create_simplified_along_backbone(Chain input, const IntRanges &residue_segments, bool keep_detailed=false)

IMP::rmf::create_restraints
Restraints create_restraints(RMF::FileConstHandle fh, Model *m)

IMP::atom::create_rigid_body
IMP::core::RigidBody create_rigid_body(Hierarchy h)

IMP::Particle
Class to handle individual model particles.
Definition: Particle.h:37

IMP::show_graphviz
std::string show_graphviz(Graph g)

IMP::atom::create_distance_restraint
Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")

IMP::atom::Chain
Store info for a chain of a protein.
Definition: Chain.h:21

IMP::atom::create_connectivity_restraint
Restraint * create_connectivity_restraint(const Selections &s, double x0, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selections.

IMP::atom
Functionality for loading, creating, manipulating and scoring atomic structures.

IMP::atom::get_leaves
Hierarchies get_leaves(const Selection &h)

IMP::atom::create_excluded_volume_restraint
Restraint * create_excluded_volume_restraint(const Selections &s)
Create an excluded volume restraint for a list of selections.

IMP::atom::Selection
Select hierarchy particles identified by the biological name.
Definition: Selection.h:66