doc/html/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.kernel

 import IMP.atom

 import IMP.container

 import IMP.base

 import sys


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


 def create_representation():

     m = IMP.kernel.Model()

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

     all.set_name("the universe")


     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:

             m.add_restraint(r)


     def create_protein_from_pdbs(name, files):

         def create_from_pdb(file):

             sls = IMP.base.SetLogState(IMP.base.NONE)

             t = IMP.atom.read_pdb(

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

                 IMP.atom.ATOMPDBSelector())

             del sls

             # 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.kernel.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:

                 m.add_restraint(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, all)


 def create_restraints(m, all):

     def add_connectivity_restraint(s):

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

         m.add_restraint(r)


     def add_distance_restraint(s0, s1):

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

         m.add_restraint(r)

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

     m.add_restraint(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, all) = create_representation()

 create_restraints(m, all)


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

 # but it is pretty complex

 dg = IMP.kernel.get_dependency_graph(m)

 IMP.base.show_graphviz(dg)


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

 pdg = IMP.kernel.get_pruned_dependency_graph(m)


 IMP.base.show_graphviz(pdg)

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

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

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

IMP::base
Low level functionality (logging, error handling, profiling, command line flags etc) that is used by ...

IMP::kernel::get_pruned_dependency_graph
DependencyGraph get_pruned_dependency_graph(kernel::Model *m)

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

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

IMP::kernel::get_dependency_graph
DependencyGraph get_dependency_graph(kernel::Model *m)

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

IMP::atom::ATOMPDBSelector
Select all non-alternative ATOM records.
Definition: pdb.h:63

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

IMP::atom::Hierarchy::setup_particle
static Hierarchy setup_particle(kernel::Model *m, kernel::ParticleIndex pi, kernel::ParticleIndexesAdaptor children=kernel::ParticleIndexesAdaptor())
Definition: atom/Hierarchy.h:270

IMP::atom::get_by_type
Hierarchies get_by_type(Hierarchy mhd, GetByType t)

IMP::kernel
Base functionality and abstract base classes for representation, scoring and sampling.

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

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

IMP::atom::destroy
void destroy(Hierarchy d)
Delete the Hierarchy.

IMP::kernel::get_example_path
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.

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

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

IMP::atom::create_protein
Hierarchy create_protein(kernel::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::atom::Chain
Store info for a chain of a protein.
Definition: Chain.h:21

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

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

IMP::atom::read_pdb
void read_pdb(base::TextInput input, int model, Hierarchy h)

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

IMP::atom::Selection
Select hierarchy particles identified by the biological name.
Definition: Selection.h:62

IMP::kernel::Model
Class for storing model, its restraints, constraints, and particles.
Definition: kernel/Model.h:73