> > 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() >> >> _______________________________________________ >> IMP-commits mailing list >> IMP-commits@salilab.org >> https://salilab.org/mailman/listinfo/imp-commits >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev