Example module. More...

Detailed Description

Example module.

This module contains simple classes that span many parts of IMP functionality, so it can be used to see how to write a new class, export it to Python, document it, and provide tests and examples.

The overview section of the module page can contain any MarkDown or doxygen markup as well as references to IMP classes such as IMP::Model.

Info

Author(s): Daniel Russel

Maintainer: benmwebb

License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

See main IMP papers list.

Classes
class	ExampleComplexRestraint
	Restrain the diameter of a set of points. More...

class	ExampleConstraint
	A trivial constraint that just increments a counter. More...

class	ExampleDecorator
	A simple decorator which adds a name to a particle. More...

class	ExampleObject
	An example simple object which is reference counted. More...

class	ExamplePairScore
	Apply a harmonic to the distance between two particles. More...

class	ExampleRestraint
	Restrain a particle to be in the x,y plane. More...

class	ExampleSingletonModifier
	An example singleton modifer. More...

class	ExampleSubsetFilterTable

class	ExampleTemplateClassD
	A line segment templated on the dimension. More...

class	ExampleUnaryFunction
	A simple unary function. More...

Typedefs
typedef IMP::base::Vector < ExampleDecorator >	ExampleDecorators

typedef base::Vector < base::Pointer< ExampleObject > >	ExampleObjects

typedef base::Vector < base::WeakPointer < ExampleObject > >	ExampleObjectsTemp

typedef IMP::base::Vector < IMP::base::Pointer < ExamplePairScore > >	ExamplePairScores

typedef IMP::base::Vector < IMP::base::WeakPointer < ExamplePairScore > >	ExamplePairScoresTemp

typedef ExampleTemplateClassD< 3 >	ExampleTemplateClass3D

typedef base::Vector < ExampleTemplateClassD< 3 > >	ExampleTemplateClass3Ds

Functions
kernel::Restraint *	create_chain_restraint (const kernel::ParticlesTemp &ps, double length_factor, double k, std::string name)

container::ClosePairContainer *	create_excluded_volume (const kernel::ParticlesTemp &ps, double k, std::string name)

core::MonteCarloMover *	create_serial_mover (const kernel::ParticlesTemp &ps)

unsigned int	get_number_of_incidences (const kernel::ParticlesTemp &psa, const kernel::ParticlesTemp &psb, double point_distance)

void	optimize_assembly (kernel::Model m, const kernel::ParticlesTemp &components, const kernel::RestraintsTemp &interactions, const kernel::RestraintsTemp &other_restraints, const algebra::BoundingBox3D &bb, PairScore ev, double cutoff, const PairPredicates &excluded=PairPredicates())

void	optimize_balls (const kernel::ParticlesTemp &ps, const kernel::RestraintsTemp &rs=kernel::RestraintsTemp(), const PairPredicates &excluded=PairPredicates(), const OptimizerStates &opt_states=OptimizerStates(), base::LogLevel ll=base::DEFAULT)

template<class ParticlesList , class BoundingVolume >
void	randomize_particles (const ParticlesList &ps, const BoundingVolume &bv)

template<class RigidBody , class BoundingVolume >
void	randomize_rigid_body (RigidBody rbi, const BoundingVolume &bv)

Standard module functions
All `IMP` modules have a set of standard functions to help get information about the module and about files associated with the module.
std::string	get_module_version ()

std::string	get_module_name ()

std::string	get_data_path (std::string file_name)
	Return the full path to installed data. More...

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

Typedef Documentation

typedef IMP::base::Vector<IMP::base::Pointer< ExamplePairScore > > IMP::example::ExamplePairScores

Store a set of objects.

Definition at line 40 of file ExamplePairScore.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< ExamplePairScore > > IMP::example::ExamplePairScoresTemp

Pass a set of objects.

See Also: ExamplePairScore

Definition at line 40 of file ExamplePairScore.h.

Function Documentation

kernel::Restraint* IMP::example::create_chain_restraint	(	const kernel::ParticlesTemp &	ps,
		double	length_factor,
		double	k,
		std::string	name
	)

Restrain the passed particles to be connected in a chain. The distance between consecutive particles is length_factor*the sum of the radii.

Note, this assumes that all such chains will be disjoint and so you can use the container::ExclusiveConsecutivePairFilter if you want to filter out all pairs of particles connected by such chain restraints.

The restraint is not added to the model.

Definition at line 31 of file creating_restraints.h.

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container::ClosePairContainer* IMP::example::create_excluded_volume	(	const kernel::ParticlesTemp &	ps,
		double	k,
		std::string	name
	)

Create an excluded-volume style ClosePairsContainer based score.

Definition at line 50 of file creating_restraints.h.

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core::MonteCarloMover* IMP::example::create_serial_mover ( const kernel::ParticlesTemp & ps )

Create a serial mover from a list of core::XYZR particles.

std::string IMP::example::get_data_path ( std::string file_name )

Return the full path to installed data.

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.

std::string IMP::example::get_example_path ( std::string file_name )

Return the path to installed example data for this module.

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb",

model));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.

unsigned int IMP::example::get_number_of_incidences	(	const kernel::ParticlesTemp &	psa,
		const kernel::ParticlesTemp &	psb,
		double	point_distance
	)

Return the number of times particles from one set are close to those from another set.

Note: This method uses the distance between the centers of the particles and does not use their radii.

Definition at line 23 of file counting.h.

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void IMP::example::optimize_assembly	(	kernel::Model *	m,
		const kernel::ParticlesTemp &	components,
		const kernel::RestraintsTemp &	interactions,
		const kernel::RestraintsTemp &	other_restraints,
		const algebra::BoundingBox3D &	bb,
		PairScore *	ev,
		double	cutoff,
		const PairPredicates &	excluded = `PairPredicates()`
	)

Provide an example of a more involved protocol for assembly a complex. The protocol adds the particles one at a time based on how well connected they are to the already added particles (in the interaction graph). After each addition, the assembly is optimized. The protocol seems to work at assembling the residues of a protein from a truncated distance matrix.

void IMP::example::optimize_balls	(	const kernel::ParticlesTemp &	ps,
		const kernel::RestraintsTemp &	rs = `kernel::RestraintsTemp()`,
		const PairPredicates &	excluded = `PairPredicates()`,
		const OptimizerStates &	opt_states = `OptimizerStates()`,
		base::LogLevel	ll = `base::DEFAULT`
	)

Take a set of core::XYZR particles and relax them relative to a set of restraints. Excluded volume is handle separately, so don't include it in the passed list of restraints.

/**
 *  \file optimize_balls.cpp
 *  \brief A Score on the distance between a pair of particles.
 *
 *  Copyright 2007-2014 IMP Inventors. All rights reserved.
 */
#include <IMP/example/optimizing.h>
#include <IMP/container/generic.h>
#include <IMP/core/ConjugateGradients.h>
#include <IMP/core/MonteCarlo.h>
#include <IMP/core/SerialMover.h>
#include <IMP/core/BallMover.h>
#include <IMP/container/ClosePairContainer.h>
#include <IMP/core/rigid_bodies.h>
#include <IMP/core/SphereDistancePairScore.h>
#include <IMP/base/log_macros.h>
#include <IMP/container/ListSingletonContainer.h>
#include <boost/ptr_container/ptr_vector.hpp>
#include <IMP/scoped.h>
#include <IMP/PairPredicate.h>
/*
   \example optimize_balls.cpp
   This is a C++ equivalent to the optimize_balls.py python example.
*/
IMPEXAMPLE_BEGIN_NAMESPACE
core::MonteCarloMover *create_serial_mover(const kernel::ParticlesTemp &ps) {
  core::MonteCarloMovers movers;
  for (unsigned int i = 0; i < ps.size(); ++i) {
    double scale = core::XYZR(ps[i]).get_radius();
    movers.push_back(
        new core::BallMover(ps[i]->get_model(), ps[i]->get_index(), scale * 2));
  }
  IMP_NEW(core::SerialMover, sm, (get_as<core::MonteCarloMoversTemp>(movers)));
  return sm.release();
}
/** Take a set of core::XYZR particles and relax them relative to a set of
    restraints. Excluded volume is handle separately, so don't include it
in the passed list of restraints. */
void optimize_balls(const kernel::ParticlesTemp &ps,
                    const kernel::RestraintsTemp &rs,
                    const PairPredicates &excluded,
                    const OptimizerStates &opt_states, base::LogLevel ll) {
  // make sure that errors and log messages are marked as coming from this
  // function
  IMP_FUNCTION_LOG;
  base::SetLogState sls(ll);
  IMP_ALWAYS_CHECK(!ps.empty(), "No kernel::Particles passed.", ValueException);
  kernel::Model *m = ps[0]->get_model();
  // double scale = core::XYZR(ps[0]).get_radius();
  IMP_NEW(core::SoftSpherePairScore, ssps, (10));
  IMP_NEW(core::ConjugateGradients, cg, (m));
  cg->set_optimizer_states(opt_states);
  {
    // set up restraints for cg
    IMP_NEW(container::ListSingletonContainer, lsc, (ps));
    IMP_NEW(container::ClosePairContainer, cpc,
            (lsc, 0, core::XYZR(ps[0]).get_radius()));
    cpc->add_pair_filters(excluded);
    base::Pointer<kernel::Restraint> r =
        container::create_restraint(ssps.get(), cpc.get());
    cg->set_scoring_function(rs + kernel::RestraintsTemp(1, r.get()));
    cg->set_optimizer_states(opt_states);
  }
  IMP_NEW(core::MonteCarlo, mc, (m));
  mc->set_optimizer_states(opt_states);
  IMP_NEW(core::IncrementalScoringFunction, isf, (ps, rs));
  {
    // set up MC
    mc->add_mover(create_serial_mover(ps));
    // we are special casing the nbl term for montecarlo, but using all for CG
    mc->set_incremental_scoring_function(isf);
    // use special incremental support for the non-bonded part
    isf->add_close_pair_score(ssps, 0, ps, excluded);
    // make pointer vector
  }
  IMP_LOG_PROGRESS("Performing initial optimization" << std::endl);
  {
    boost::ptr_vector<ScopedSetFloatAttribute> attrs;
    for (unsigned int j = 0; j < attrs.size(); ++j) {
      attrs.push_back(
          new ScopedSetFloatAttribute(ps[j], core::XYZR::get_radius_key(), 0));
    }
    cg->optimize(1000);
  }
  // shrink each of the particles, relax the configuration, repeat
  for (int i = 0; i < 11; ++i) {
    boost::ptr_vector<ScopedSetFloatAttribute> attrs;
    double factor = .1 * i;
    IMP_LOG_PROGRESS("Optimizing with radii at " << factor << " of full"
                                                 << std::endl);
    for (unsigned int j = 0; j < ps.size(); ++j) {
      attrs.push_back(
          new ScopedSetFloatAttribute(ps[j], core::XYZR::get_radius_key(),
                                      core::XYZR(ps[j]).get_radius() * factor));
    }
    // changed all radii
    isf->set_moved_particles(isf->get_movable_indexes());
    for (int j = 0; j < 5; ++j) {
      mc->set_kt(100.0 / (3 * j + 1));
      mc->optimize(ps.size() * (j + 1) * 100);
      double e = cg->optimize(10);
      IMP_LOG_PROGRESS("Energy is " << e << std::endl);
      if (e < .000001) break;
    }
  }
}
IMPEXAMPLE_END_NAMESPACE

template<class ParticlesList , class BoundingVolume >

void IMP::example::randomize_particles	(	const ParticlesList &	ps,
		const BoundingVolume &	bv
	)

Randomize the positions of a set of particles within a bounding volume. Rigid bodies have their orientation randomized too.

Definition at line 32 of file randomizing.h.

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Detailed Description

Info

Classes

Typedefs

Functions

Standard module functions

Typedef Documentation

Function Documentation