Re: [IMP-dev] [IMP-commits] r3986 - in trunk/modules/helper: . include pyext src test

29 Oct 2009


      >
> On another note, we definitely need to reconcile the excluded volume/ 
> collision detection names one way or the other. It think excluded  
> volume better fits the sense of the restraint since it is enforcing  
> excluded volume not collisions (similar to connectivity restraint  
> enforcing connectivity or fit enforcing that a fit to a map).
>
Excluded volume seems more descriptive.
>
> On Oct 29, 2009, at 10:30 PM, Elina Tjioe wrote:
>
>> Thx, Daniel. We'll keep that in mind. Also, I've added the wrapper  
>> for the FitRestraint.
>>
>> Elina
>>
>> On Wed, Oct 28, 2009 at 1:54 PM, Daniel Russel drussel@gmail.com  
>> wrote:
>> If (as I hope), there will be more such functionality, I suggest it  
>> go into a separate module so it provides a single logical group and  
>> is separate from other helper functions which don't provide similar  
>> interfaces. Perhaps a "simple" module or something similar.
>>
>>
>>
>> On Oct 28, 2009, at 1:25 PM, Notification of IMP commits wrote:
>>
>> Author: etjioe@SALILAB.ORG
>> Date: 2009-10-28 13:25:46 -0700 (Wed, 28 Oct 2009)
>> New Revision: 3986
>>
>> Added:
>>  trunk/modules/helper/include/simplify_restraint.h
>>  trunk/modules/helper/src/simplify_restraint.cpp
>>  trunk/modules/helper/test/test_simple_connectivity_on_molecules.py
>> Modified:
>>  trunk/modules/helper/SConscript
>>  trunk/modules/helper/pyext/swig.i-in
>> Log:
>> Add helper functions for restraints
>>
>> Modified: trunk/modules/helper/SConscript
>> ===================================================================
>> --- trunk/modules/helper/SConscript     2009-10-28 18:25:03 UTC  
>> (rev 3985)
>> +++ trunk/modules/helper/SConscript     2009-10-28 20:25:46 UTC  
>> (rev 3986)
>> @@ -2,5 +2,5 @@
>>
>>
>> env.IMPModuleBuild(version="SVN",
>> -                   required_modules=['em', 'display','atom',  
>> 'core', 'algebra'],
>> +                   required_modules=['em', 'display','atom',  
>> 'core', 'algebra', 'misc'],
>>                   optional_dependencies=['CGAL'])
>>
>> Added: trunk/modules/helper/include/simplify_restraint.h
>> ===================================================================
>> --- trunk/modules/helper/include/ 
>> simplify_restraint.h                            (rev 0)
>> +++ trunk/modules/helper/include/simplify_restraint.h   2009-10-28  
>> 20:25:46 UTC (rev 3986)
>> @@ -0,0 +1,450 @@
>> +/**
>> + *  \file helper/simplify_restraint.h
>> + *  \brief Helper functions for restraints
>> + *
>> + *  Copyright 2007-9 Sali Lab. All rights reserved.
>> + */
>> +
>> +#ifndef IMPHELPER_SIMPLIFY_RESTRAINT_H
>> +#define IMPHELPER_SIMPLIFY_RESTRAINT_H
>> +
>> +#include "config.h"
>> +#include <IMP/SingletonContainer.h>
>> +#include <IMP/atom.h>
>> +#include <IMP/core.h>
>> +#include <IMP/misc.h>
>> +#include <IMP/em/FitRestraint.h>
>> +#include <IMP/em/DensityMap.h>
>> +#include <IMP/core/rigid_bodies.h>
>> +
>> +IMPHELPER_BEGIN_NAMESPACE
>> +
>> +
>> +//! Simple collision detection.
>> +/**
>> +  \note SimpleCollision stores pointers to PairsRestraint,  
>> HarmonicLowerBound,
>> +        and ClosePairsScoreState.
>> +  \note It provides convenient methods to change mean, k, standard  
>> deviation,
>> +        slack and distance.
>> +  \see PairsRestraint
>> + */
>> +class IMPHELPEREXPORT SimpleCollision
>> +{
>> +public:
>> +  /** Creates collision detection on rigid bodies using
>> +      SphereDistancePairScore and ClosePairsScoreState.
>> +      The nonbonded list defined for the score state is refined  
>> using
>> +      RigidClosePairsFinder.
>> +
>> +    \see SphereDistancePairScore
>> +    \see HarmonicLowerBound
>> +    \see ClosePairsScoreState
>> +    \see ListSingletonContainer
>> +    \see RigidClosePairsFinder
>> +  */
>> +  friend SimpleCollision create_simple_collision_on_rigid_bodies(
>> +         core::RigidBodies *rbs);
>> +
>> +  core::PairsRestraint *restraint()
>> +  {
>> +    return pairs_restraint_;
>> +  }
>> +
>> +  core::HarmonicLowerBound *harmonic_lower_bound()
>> +  {
>> +    return harmonic_lower_bound_;
>> +  }
>> +
>> +  core::ClosePairsScoreState *close_pairs_score_state()
>> +  {
>> +    return close_pairs_score_state_;
>> +  }
>> +
>> +  //! Set the mean for the HarmonicLowerBound.
>> +  /** The default mean is 0.
>> +   */
>> +  void set_mean(Float mean)
>> +  {
>> +     harmonic_lower_bound_->set_mean(mean);
>> +  }
>> +
>> +  //! Set the standard deviation for the HarmonicLowerBound.
>> +  void set_stddev(Float sd)
>> +  {
>> +     static Float k = harmonic_lower_bound_- 
>> >k_from_standard_deviation(sd);
>> +     harmonic_lower_bound_->set_k(k);
>> +  }
>> +
>> +  //! Set the spring constant for the HarmonicLowerBound.
>> +  /** The default k is 1.
>> +   */
>> +  void set_k(Float k)
>> +  {
>> +     harmonic_lower_bound_->set_k(k);
>> +  }
>> +
>> +  //! Set the amount of slack for the ClosePairsScoreState.
>> +  /** The default slack is 2.
>> +   */
>> +  void set_slack(Float slack)
>> +  {
>> +     close_pairs_score_state_->set_slack(slack);
>> +  }
>> +
>> +  //! Set the distance threshold for the ClosePairsScoreState.
>> +  /** Uses the default distance in the ClosePairsScoreState.
>> +   */
>> +  void set_distance(Float distance)
>> +  {
>> +     close_pairs_score_state_->set_distance(distance);
>> +  }
>> +
>> +  VersionInfo get_version_info() const
>> +  {
>> +    return IMP::get_module_version_info();
>> +  }
>> +
>> +  void show(std::ostream &out = std::cout) const
>> +  {
>> +    out << "SimpleCollision(";
>> +    if ( pairs_restraint_ )
>> +      pairs_restraint_->show(out);
>> +    out << ")";
>> +  }
>> +
>> +private:
>> +  // prevent unauthorized creation
>> +  SimpleCollision(core::PairsRestraint *pairs_restraint,
>> +      core::HarmonicLowerBound *harmonic_lower_bound,
>> +      core::ClosePairsScoreState *close_pairs_score_state)
>> +    : pairs_restraint_(pairs_restraint)
>> +    , harmonic_lower_bound_(harmonic_lower_bound)
>> +    , close_pairs_score_state_(close_pairs_score_state)
>> +  {}
>> +
>> +  IMP::Pointercore::PairsRestraint pairs_restraint_;
>> +  IMP::Pointercore::HarmonicLowerBound harmonic_lower_bound_;
>> +  IMP::Pointercore::ClosePairsScoreState close_pairs_score_state_;
>> +};
>> +
>> +//! Simple connectivity restraint.
>> +/**
>> +  \note SimpleConnectivity stores pointers to ConnectivityRestraint,
>> +        and HarmonicUpperBound.
>> +  \note It provides convenient methods to change mean, k,
>> +        and standard deviation.
>> +  \see ConnectivityRestraint
>> + */
>> +class IMPHELPEREXPORT SimpleConnectivity
>> +{
>> +public:
>> +
>> +  /** Creates ConnectivityRestraint on rigid bodies using
>> +      RigidBodyDistancePairScore and RigidMembersRefiner.
>> +
>> +    \see RigidBodyDistancePairScore
>> +    \see SphereDistancePairScore
>> +    \see HarmonicUpperBound
>> +    \see core::RigidMembersRefiner
>> +  */
>> +  friend SimpleConnectivity  
>> create_simple_connectivity_on_rigid_bodies(
>> +         core::RigidBodies *rbs);
>> +
>> +  /** Creates ConnectivityRestraint on molecules using  
>> LowestRefinedPairScore
>> +      and LeavesRefiner.
>> +
>> +    \see LowestRefinedPairScore
>> +    \see SphereDistancePairScore
>> +    \see HarmonicUpperBound
>> +    \see LeavesRefiner
>> +  */
>> +  friend SimpleConnectivity create_simple_connectivity_on_molecules(
>> +         Particles *ps);
>> +
>> +  core::ConnectivityRestraint *restraint()
>> +  {
>> +    return connectivity_restraint_;
>> +  }
>> +
>> +  core::HarmonicUpperBound *harmonic_upper_bound()
>> +  {
>> +    return harmonic_upper_bound_;
>> +  }
>> +
>> +  //! Set the mean for the HarmonicUpperBound.
>> +  /** The default mean is 0.
>> +   */
>> +  void set_mean(Float mean)
>> +  {
>> +     harmonic_upper_bound_->set_mean(mean);
>> +  }
>> +
>> +  //! Set the standard deviation for the HarmonicUpperBound.
>> +  void set_stddev(Float sd)
>> +  {
>> +     static Float k = harmonic_upper_bound_- 
>> >k_from_standard_deviation(sd);
>> +     harmonic_upper_bound_->set_k(k);
>> +  }
>> +
>> +  //! Set the spring constant for the HarmonicUpperBound.
>> +  /** The default k is 1.
>> +   */
>> +  void set_k(Float k)
>> +  {
>> +     harmonic_upper_bound_->set_k(k);
>> +  }
>> +
>> +  VersionInfo get_version_info() const
>> +  {
>> +    return IMP::get_module_version_info();
>> +  }
>> +
>> +  void show(std::ostream &out = std::cout) const
>> +  {
>> +    out << "SimpleConnectivity(";
>> +    if ( connectivity_restraint_ )
>> +      connectivity_restraint_->show(out);
>> +    out << ")";
>> +  }
>> +
>> +private:
>> +  // prevent unauthorized creation
>> +  SimpleConnectivity(
>> +      core::ConnectivityRestraint *connectivity_restraint,
>> +      core::HarmonicUpperBound *harmonic_upper_bound)
>> +    : connectivity_restraint_(connectivity_restraint)
>> +    , harmonic_upper_bound_(harmonic_upper_bound)
>> +  {}
>> +
>> +  IMP::Pointercore::ConnectivityRestraint connectivity_restraint_;
>> +  IMP::Pointercore::HarmonicUpperBound harmonic_upper_bound_;
>> +};
>> +
>> +//! Simple distance restraint between two particles.
>> +/**
>> +   \note SimpleDistance stores pointers to DistanceRestraint, and
>> +         HarmonicUpperBound.
>> +   \note It provides convenient methods to change mean, k, and
>> +         standard deviation.
>> +
>> +   \see DistanceRestraint
>> + */
>> +class IMPHELPEREXPORT SimpleDistance
>> +{
>> +public:
>> +
>> +  /** Creates DistanceRestraint using HarmonicUpperBound scoring  
>> function
>> +      as default.
>> +      \param[in] ps Pointer to two particles in distance restraint.
>> +  */
>> +  friend SimpleDistance create_simple_distance(Particles *ps);
>> +
>> +  core::DistanceRestraint *restraint()
>> +  {
>> +    return distance_restraint_;
>> +  }
>> +
>> +  core::HarmonicUpperBound *harmonic_upper_bound()
>> +  {
>> +    return harmonic_upper_bound_;
>> +  }
>> +
>> +  //! Set the mean for the HarmonicUpperBound.
>> +  /** The default mean is 0.
>> +   */
>> +  void set_mean(Float mean)
>> +  {
>> +     harmonic_upper_bound_->set_mean(mean);
>> +  }
>> +
>> +  //! Set the standard deviation for the HarmonicUpperBound.
>> +  void set_stddev(Float sd)
>> +  {
>> +     static Float k = harmonic_upper_bound_- 
>> >k_from_standard_deviation(sd);
>> +     harmonic_upper_bound_->set_k(k);
>> +  }
>> +
>> +  //! Set the spring constant for the HarmonicUpperBound.
>> +  /** The default k is 1.
>> +   */
>> +  void set_k(Float k)
>> +  {
>> +     harmonic_upper_bound_->set_k(k);
>> +  }
>> +
>> +  VersionInfo get_version_info() const
>> +  {
>> +    return IMP::get_module_version_info();
>> +  }
>> +
>> +  void show(std::ostream &out = std::cout) const
>> +  {
>> +    out << "SimpleDistance(";
>> +    if ( distance_restraint_ )
>> +      distance_restraint_->show(out);
>> +    out << ")";
>> +  }
>> +
>> +private:
>> +  // prevent unauthorized creation
>> +  SimpleDistance(
>> +      core::DistanceRestraint *distance_restraint,
>> +      core::HarmonicUpperBound *harmonic_upper_bound)
>> +    : distance_restraint_(distance_restraint)
>> +    , harmonic_upper_bound_(harmonic_upper_bound)
>> +  {}
>> +
>> +  IMP::Pointercore::DistanceRestraint distance_restraint_;
>> +  IMP::Pointercore::HarmonicUpperBound harmonic_upper_bound_;
>> +};
>> +
>> +//! Simple diameter restraint.
>> +/**
>> +   \note SimpleDiameter stores pointers to DiameterRestraint, and
>> +         HarmonicUpperBound.
>> +   \note It provides convenient methods to change mean, k, and
>> +         standard deviation.
>> +   \see DiameterRestraint
>> + */
>> +class IMPHELPEREXPORT SimpleDiameter
>> +{
>> +public:
>> +
>> +  /** Creates DiameterRestraint using HarmonicUpperBound scoring  
>> function
>> +      as default.
>> +      \param[in] ps Pointer to particles in diameter restraint.
>> +      \param[in] diameter Diameter.
>> +     \see ListSingletonContainer
>> +  */
>> +  friend SimpleDiameter create_simple_diameter(Particles *ps,  
>> Float diameter);
>> +
>> +  core::DiameterRestraint *restraint()
>> +  {
>> +    return diameter_restraint_;
>> +  }
>> +
>> +  core::HarmonicUpperBound *harmonic_upper_bound()
>> +  {
>> +    return harmonic_upper_bound_;
>> +  }
>> +
>> +  //! Set the mean for the HarmonicUpperBound.
>> +  /** The default mean is 0.
>> +   */
>> +  void set_mean(Float mean)
>> +  {
>> +     harmonic_upper_bound_->set_mean(mean);
>> +  }
>> +
>> +  //! Set the standard deviation for the HarmonicUpperBound.
>> +  void set_stddev(Float sd)
>> +  {
>> +     static Float k = harmonic_upper_bound_- 
>> >k_from_standard_deviation(sd);
>> +     harmonic_upper_bound_->set_k(k);
>> +  }
>> +
>> +  //! Set the spring constant for the HarmonicUpperBound.
>> +  /** The default k is 1.
>> +   */
>> +  void set_k(Float k)
>> +  {
>> +     harmonic_upper_bound_->set_k(k);
>> +  }
>> +
>> +  VersionInfo get_version_info() const
>> +  {
>> +    return IMP::get_module_version_info();
>> +  }
>> +
>> +  void show(std::ostream &out = std::cout) const
>> +  {
>> +    out << "SimpleDiameter(";
>> +    if ( diameter_restraint_ )
>> +      diameter_restraint_->show(out);
>> +    out << ")";
>> +  }
>> +
>> +private:
>> +  // prevent unauthorized creation
>> +  SimpleDiameter(
>> +      core::DiameterRestraint *diameter_restraint,
>> +      core::HarmonicUpperBound *harmonic_upper_bound)
>> +    : diameter_restraint_(diameter_restraint)
>> +    , harmonic_upper_bound_(harmonic_upper_bound)
>> +  {}
>> +
>> +  IMP::Pointercore::DiameterRestraint diameter_restraint_;
>> +  IMP::Pointercore::HarmonicUpperBound harmonic_upper_bound_;
>> +};
>> +
>> +//! Simple excluded volume restraint.
>> +/**
>> +   \see ExcludedVolumeRestraint
>> + */
>> +class IMPHELPEREXPORT SimpleExcludedVolume
>> +{
>> +public:
>> +
>> +  /** Creates ExcludedVolumeRestraint using LeavesRefiner.
>> +   \see ListSingletonContainer
>> +  */
>> +  friend SimpleExcludedVolume  
>> create_simple_excluded_volume_on_rigid_bodies(
>> +         core::RigidBodies *rbs);
>> +
>> +  core::ExcludedVolumeRestraint *restraint()
>> +  {
>> +    return excluded_volume_restraint_;
>> +  }
>> +
>> +  VersionInfo get_version_info() const
>> +  {
>> +    return IMP::get_module_version_info();
>> +  }
>> +
>> +  void show(std::ostream &out = std::cout) const
>> +  {
>> +    out << "SimpleExcludedVolume(";
>> +    if ( excluded_volume_restraint_ )
>> +      excluded_volume_restraint_->show(out);
>> +    out << ")";
>> +  }
>> +
>> +private:
>> +  // prevent unauthorized creation
>> +  SimpleExcludedVolume(
>> +      core::ExcludedVolumeRestraint *excluded_volume_restraint)
>> +    : excluded_volume_restraint_(excluded_volume_restraint)
>> +  {}
>> +
>> +  IMP::Pointercore::ExcludedVolumeRestraint  
>> excluded_volume_restraint_;
>> +};
>> +
>> +IMPHELPEREXPORT SimpleCollision  
>> create_simple_collision_on_rigid_bodies(
>> +                core::RigidBodies *rbs);
>> +
>> +IMPHELPEREXPORT SimpleConnectivity  
>> create_simple_connectivity_on_rigid_bodies(
>> +                core::RigidBodies *rbs);
>> +
>> +IMPHELPEREXPORT SimpleConnectivity  
>> create_simple_connectivity_on_molecules(
>> +                Particles *ps);
>> +
>> +IMPHELPEREXPORT SimpleDistance create_simple_distance(Particles  
>> *ps);
>> +
>> +IMPHELPEREXPORT SimpleDiameter create_simple_diameter(
>> +                Particles *ps, Float diameter);
>> +
>> +IMPHELPEREXPORT SimpleExcludedVolume
>> +                create_simple_excluded_volume_on_rigid_bodies(
>> +                core::RigidBodies *rbs);
>> +
>> +IMPHELPEREXPORT em::DensityMap *load_map(
>> +                char const *map_fn, double spacing, double  
>> resolution);
>> +
>> +IMPHELPEREXPORT em::FitRestraint *create_em_restraint(
>> +                atom::Hierarchies const &mhs, em::DensityMap *dmap);
>> +
>> +IMPHELPEREXPORT Particles set_rigid_bodies(atom::Hierarchies const  
>> &mhs);
>> +
>> +IMPHELPER_END_NAMESPACE
>> +
>> +#endif /* IMPHELPER_SIMPLIFY_RESTRAINT_H */
>>
>> Modified: trunk/modules/helper/pyext/swig.i-in
>> ===================================================================
>> --- trunk/modules/helper/pyext/swig.i-in        2009-10-28 18:25:03  
>> UTC (rev 3985)
>> +++ trunk/modules/helper/pyext/swig.i-in        2009-10-28 20:25:46  
>> UTC (rev 3986)
>> @@ -3,3 +3,4 @@
>> %include "IMP/helper/covers.h"
>> %include "IMP/helper/atom_hierarchy.h"
>> %include "IMP/helper/simplify_atom_hierarchy.h"
>> +%include "IMP/helper/simplify_restraint.h"
>>
>> Added: trunk/modules/helper/src/simplify_restraint.cpp
>> ===================================================================
>> --- trunk/modules/helper/src/ 
>> simplify_restraint.cpp                          (rev 0)
>> +++ trunk/modules/helper/src/simplify_restraint.cpp     2009-10-28  
>> 20:25:46 UTC (rev 3986)
>> @@ -0,0 +1,263 @@
>> +/**
>> +    *  \file simplify_restraint.cpp
>> +    *  \brief Support for restraints.
>> +    *
>> +    *  Copyright 2007-9 Sali Lab. All rights reserved.
>> +    *
>> +    */
>> +
>> +#include "IMP/helper/simplify_restraint.h"
>> +#include "IMP/helper/rigid_bodies.h"
>> +#include <IMP/em/DensityMap.h>
>> +#include <IMP/em/MRCReaderWriter.h>
>> +
>> +IMPHELPER_BEGIN_NAMESPACE
>> +
>> +SimpleCollision  
>> create_simple_collision_on_rigid_bodies(core::RigidBodies *rbs)
>> +{
>> +  IMP_USAGE_CHECK(rbs->size() > 0, "At least one particle should  
>> be given",
>> +     ValueException);
>> +
>> +  /****** Set up the nonbonded list ******/
>> +  // Tell nbl on which particles you work on
>> +  // Look for close pairs within the list
>> +
>> +  IMP_NEW(core::ListSingletonContainer, lsc, ());
>> +  lsc->add_particles(*rbs);
>> +  IMP_NEW(core::ClosePairsScoreState, nbl, (lsc));
>> +
>> +  /****** Refine the nonbonded list ******/
>> +  // Set up the list of close pairs of each pair in NBL
>> +  // because you want to restraint the actual rigid bodies and not  
>> its particles
>> +  // Look for close members of the rigid bodies, one from each  
>> rigid body
>> +
>> +  //if set_close_pairs_finder is not called, then use the non  
>> refined list
>> +  //if rcpf omitted, then the score is between 2 spheres
>> +  IMP_NEW(core::RigidClosePairsFinder, rcpf, ());
>> +  nbl->set_close_pairs_finder(rcpf);
>> +  // Set the amount particles need to move before the list is  
>> updated
>> +  nbl->set_slack(2);
>> +
>> +  /****** Define the score used on each pair in the refined list  
>> ******/
>> +  // Score the distance between the spheres of each particles
>> +  // Each particle is required to have x,y,z and a radius
>> +  // The distance is going to be penalized by a harmonic lower  
>> bound with
>> +  // mean = 0 and force constant (k) = 1 kcal/mol/A/A
>> +  // The mean and k can be changed later on by calling set_mean  
>> and set_k
>> +  // k can also be obtained given the Gaussian standard deviation  
>> (angstroms),
>> +  // which can be changed using set_stddev
>> +
>> +  IMP_NEW(core::HarmonicLowerBound, h, (0, 1)); // (mean, force  
>> constant k)
>> +  IMP_NEW(core::SphereDistancePairScore, sdps, (h));
>> +
>> +  /****** Set the restraint ******/
>> +  // Define the restraint, work on all pairs and score them with  
>> sdps
>> +  // Add the restraint to the model
>> +
>> +  IMP_NEW(core::PairsRestraint, evr, (sdps, nbl- 
>> >get_close_pairs_container()));
>> +
>> +  /****** Add score state and restraint to the model ******/
>> +
>> +  Model *mdl = (*rbs)[0].get_model();
>> +  mdl->add_score_state(nbl);
>> +  mdl->add_restraint(evr);
>> +
>> +  /****** Return a SimpleCollision object ******/
>> +
>> +  return SimpleCollision(evr, h, nbl);
>> +}
>> +
>> +SimpleConnectivity create_simple_connectivity_on_rigid_bodies(
>> +                   core::RigidBodies *rbs)
>> +{
>> +  IMP_USAGE_CHECK(rbs->size() > 0, "At least one particle should  
>> be given",
>> +     ValueException);
>> +
>> +  /****** Define Refiner ******/
>> +  // Use RigidMembersRefiner when you want the set of particles  
>> representing
>> +  // a rigid body to be the same as the set of members
>> +
>> +  IMP_NEW(core::RigidMembersRefiner, rmr, ());
>> +
>> +  /****** Define PairScore ******/
>> +  // Use RigidBodyDistancePairScore to accelerate computation of  
>> the distance
>> +  // between two rigid bodies. The distance is defined as the  
>> minimal distance
>> +  // over all bipartite pairs with one particle taken from each  
>> rigid body.
>> +
>> +  IMP_NEW(core::HarmonicUpperBound, h, (0, 1));
>> +  IMP_NEW(core::SphereDistancePairScore, sdps, (h));
>> +  IMP_NEW(core::RigidBodyDistancePairScore, rdps, (sdps, rmr));
>> +
>> +  /****** Set the restraint ******/
>> +
>> +  IMP_NEW(core::ConnectivityRestraint, cr, (rdps));
>> +  for ( size_t i=0; i<rbs->size(); ++i )
>> +    cr->set_particles((*rbs)[i].get_particle());
>> +
>> +  /****** Add restraint to the model ******/
>> +
>> +  Model *mdl = (*rbs)[0].get_model();
>> +  mdl->add_restraint(cr);
>> +
>> +  /****** Return a SimpleConnectivity object ******/
>> +
>> +  return SimpleConnectivity(cr, h);
>> +}
>> +
>> +SimpleConnectivity  
>> create_simple_connectivity_on_molecules(Particles *ps)
>> +{
>> +  IMP_USAGE_CHECK(ps->size() > 0, "At least one particle should be  
>> given",
>> +     ValueException);
>> +
>> +
>> +  /****** Define Refiner ******/
>> +  // Use LeavesRefiner for the hierarchy leaves under a particle
>> +
>> +  IMP_NEW(core::LeavesRefiner, lr, (atom::Hierarchy::get_traits()));
>> +
>> +  /****** Define PairScore ******/
>> +  // Score on the lowest of the pairs defined by refining the two  
>> particles.
>> +
>> +  IMP_NEW(core::HarmonicUpperBound, h, (0, 1));
>> +  IMP_NEW(core::SphereDistancePairScore, sdps, (h));
>> +  IMP_NEW(misc::LowestRefinedPairScore, lrps, (lr, sdps));
>> +
>> +  /****** Set the restraint ******/
>> +
>> +  IMP_NEW(core::ConnectivityRestraint, cr, (lrps));
>> +  cr->set_particles((*ps));
>> +
>> +  /****** Add restraint to the model ******/
>> +
>> +  Model *mdl = (*ps)[0]->get_model();
>> +  mdl->add_restraint(cr);
>> +
>> +  /****** Return a SimpleConnectivity object ******/
>> +
>> +  return SimpleConnectivity(cr, h);
>> +}
>> +
>> +SimpleDistance create_simple_distance(Particles *ps)
>> +{
>> +  IMP_USAGE_CHECK(ps->size() == 2, "Two particles should be given",
>> +     ValueException);
>> +
>> +  /****** Set the restraint ******/
>> +
>> +  IMP_NEW(core::HarmonicUpperBound, h, (0, 1));
>> +  IMP_NEW(core::DistanceRestraint, dr, (h, (*ps)[0], (*ps)[1]));
>> +
>> +  /****** Add restraint to the model ******/
>> +
>> +  Model *mdl = (*ps)[0]->get_model();
>> +  mdl->add_restraint(dr);
>> +
>> +  /****** Return a SimpleDistance object ******/
>> +
>> +  return SimpleDistance(dr, h);
>> +}
>> +
>> +SimpleDiameter create_simple_diameter(Particles *ps, Float diameter)
>> +{
>> +  IMP_USAGE_CHECK(ps->size() >= 2, "At least two particles should  
>> be given",
>> +     ValueException);
>> +
>> +  /****** Set the restraint ******/
>> +
>> +  IMP_NEW(core::HarmonicUpperBound, h, (0, 1));
>> +  IMP_NEW(core::ListSingletonContainer, lsc, ());
>> +  lsc->add_particles(*ps);
>> +  IMP_NEW(core::DiameterRestraint, dr, (h, lsc, diameter));
>> +
>> +  /****** Add restraint to the model ******/
>> +
>> +  Model *mdl = (*ps)[0]->get_model();
>> +  mdl->add_restraint(dr);
>> +
>> +  /****** Return a SimpleDiameter object ******/
>> +
>> +  return SimpleDiameter(dr, h);
>> +}
>> +
>> +SimpleExcludedVolume create_simple_excluded_volume_on_rigid_bodies(
>> +                     core::RigidBodies *rbs)
>> +{
>> +  IMP_USAGE_CHECK(rbs->size() > 0, "At least one particle should  
>> be given",
>> +     ValueException);
>> +
>> +  /****** Set the restraint ******/
>> +
>> +  IMP_NEW(core::ListSingletonContainer, lsc, ());
>> +  lsc->add_particles(*rbs);
>> +
>> +  IMP_NEW(core::LeavesRefiner, lr, (atom::Hierarchy::get_traits()));
>> +  IMP_NEW(core::ExcludedVolumeRestraint, evr, (lsc, lr));
>> +
>> +  /****** Add restraint to the model ******/
>> +
>> +  Model *mdl = (*rbs)[0].get_model();
>> +  mdl->add_restraint(evr);
>> +
>> +  /****** Return a SimpleExcludedVolume object ******/
>> +
>> +  return SimpleExcludedVolume(evr);
>> +}
>> +
>> +Particles set_rigid_bodies(atom::Hierarchies const &mhs)
>> +{
>> +  size_t mhs_size = mhs.size();
>> +
>> +  IMP_USAGE_CHECK(mhs_size > 0, "At least one hierarchy should be  
>> given",
>> +     ValueException);
>> +
>> +  Particles rbs;
>> +  Model *mdl = mhs[0].get_model();
>> +
>> +  for ( size_t i=0; i<mhs_size; ++i )
>> +  {
>> +    // The rigid body is set to be optimized
>> +    ScoreState *rb_state = create_rigid_body(mhs[i]);
>> +
>> +    // Add the score state to the model to make the body rigid
>> +    // Remove the score state from the model to stop keeping the  
>> body rigid
>> +    mdl->add_score_state(rb_state);
>> +
>> +    rbs.push_back(mhs[i].get_particle());
>> +  }
>> +  return rbs;
>> +}
>> +
>> +em::DensityMap *load_map(char const *map_fn, double spacing,  
>> double resolution)
>> +{
>> +  em::MRCReaderWriter mrw;
>> +  em::DensityMap *dmap = em::read_map(map_fn, mrw);
>> +  em::DensityHeader *dmap_header = dmap->get_header_writable();
>> +  dmap_header->set_spacing(spacing);
>> +  dmap_header->set_resolution(resolution);
>> +
>> +  return dmap;
>> +}
>> +
>> +em::FitRestraint *create_em_restraint(
>> +    atom::Hierarchies const &mhs, em::DensityMap *dmap)
>> +{
>> +  size_t mhs_size = mhs.size();
>> +
>> +  IMP_USAGE_CHECK(mhs_size > 0, "At least one hierarchy should be  
>> given",
>> +     runtime_error);
>> +
>> +  Particles ps;
>> +  for ( size_t i=0; i<mhs_size; ++i )
>> +  {
>> +    Particles pss = core::get_leaves(mhs[i]);
>> +    for ( size_t j=0; j<pss.size(); ++j )
>> +      ps.push_back(pss[j]);
>> +  }
>> +  IMP_NEW(em::FitRestraint, fit_rs, (ps, dmap,
>> +        core::XYZR::get_default_radius_key(),
>> +        atom::Mass::get_mass_key(), 1.0));
>> +  fit_rs->set_model(mhs[0].get_particle()->get_model());
>> +  return fit_rs;
>> +}
>> +
>> +IMPHELPER_END_NAMESPACE
>>
>> Added: trunk/modules/helper/test/ 
>> test_simple_connectivity_on_molecules.py
>> ===================================================================
>> --- trunk/modules/helper/test/ 
>> test_simple_connectivity_on_molecules 
>> .py                                (rev 0)
>> +++ trunk/modules/helper/test/ 
>> test_simple_connectivity_on_molecules.py        2009-10-28 20:25:46  
>> UTC (rev 3986)
>> @@ -0,0 +1,77 @@
>> +import unittest
>> +import os
>> +import IMP
>> +import IMP.test
>> +import IMP.atom
>> +import IMP.helper
>> +
>> +class SimpleConnectivityTests(IMP.test.TestCase):
>> +    """Tests for the SimpleConnectivity """
>> +
>> +    def test_connectivity(self):
>> +
>> +        def create_particles(m, coordinates):
>> +            ps = IMP.Particles()
>> +            radkey = IMP.FloatKey("radius")
>> +            for pt in coordinates:
>> +                p = self.create_point_particle(m, *pt)
>> +                p.add_attribute(radkey, 1.0, False)
>> +                ps.append(p)
>> +            return ps
>> +
>> +        def compute_and_print_distances(ps):
>> +            distances = list()
>> +            for i, p0 in enumerate(ps):
>> +                print "*****************Distance  
>> %d******************" % i
>> +                for p1 in ps:
>> +                    if p1 == p0:
>> +                        continue
>> +                    dist = self.particle_distance(p0, p1)
>> +                    print dist
>> +                    distances.append(dist)
>> +            print "*******************************************"
>> +            return distances
>> +
>> +        def check_closer_distances(old, new):
>> +            for od, nd in zip(old, new):
>> +                self.assert_(od > nd)
>> +
>> +        IMP.set_log_level(IMP.VERBOSE)
>> +
>> +        m = IMP.Model()
>> +        ps = create_particles(m, [(0.0, 0.0, 0.0), (100.0, 0.0,  
>> 0.0), (0.0, 100.0, 0.0),
>> +          (0.0, 0.0, 100.0)])
>> +
>> +        old_dist = compute_and_print_distances(ps)
>> +
>> +        sc = IMP.helper.create_simple_connectivity_on_molecules(ps)
>> +
>> +        h = sc.harmonic_upper_bound()
>> +        r = sc.restraint()
>> +
>> +        sc.set_mean(0)
>> +        self.assertEquals(h.get_mean(), 0)
>> +
>> +        sc.set_k(1.5)
>> +        self.assertInTolerance(h.get_k(), 1.5, 1e-4)
>> +
>> +        sc.set_stddev(3.5)
>> +        self.assertInTolerance(h.get_k(),  
>> h.k_from_standard_deviation(3.5), 1e-4)
>> +
>> +        o = IMP.core.ConjugateGradients()
>> +        o.set_threshold(1e-4)
>> +        o.set_model(m)
>> +        o.optimize(1000)
>> +
>> +        new_dist = compute_and_print_distances(ps)
>> +
>> +        check_closer_distances(old_dist, new_dist)
>> +
>> +        r.show()
>> +        m.evaluate(False)
>> +
>> +        pps = r.get_connected_pairs()
>> +
>> +
>> +if __name__ == '__main__':
>> +    unittest.main()
>>
>> _______________________________________________
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>>
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>
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Re: [IMP-dev] [IMP-commits] r3986 - in trunk/modules/helper: . include pyext src test

Keren Lasker