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 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)

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
Create a scoring function on a list of restraints.
Definition: RestraintsScoringFunction.h:23

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::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:67

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::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:30

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 particles of a Model object.
Definition: Particle.h:43

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:61

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::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:70