IMP-dev

imp-dev@salilab.org

869 discussions

problem linking helper module outside of IMP
by Keren Lasker 09 Nov '09

09 Nov '09

hi, Compiling an external exe, I am getting an error in the linkage stage, basically saying that helper can not see misc: /usr/bin/ld: warning: libimp_misc.so, needed by /viola1/home/kerenl/ bioinformatics/projects/imp/build/lib/libi\ mp_helper.so, not found (try using -rpath or -rpath-link) /viola1/home/kerenl/bioinformatics/projects/imp/build/lib/ libimp_helper.so: undefined reference to `IMP::misc:\ :get_module_version_info()' /viola1/home/kerenl/bioinformatics/projects/imp/build/lib/ libimp_helper.so: undefined reference to `IMP::misc:\ :LowestRefinedPairScore::LowestRefinedPairScore(IMP::Refiner*, IMP::PairScore*)' collect2: ld returned 1 exit status scons: *** [bin/clustering_coefficient] Error 1 I tried changing the dependency order in the SCons files, but did not succeed - can someone help ? thanks, Keren.

2 3

This week in IMP
by Daniel Russel 06 Nov '09

06 Nov '09

There is a new method IMP::display::create_writer() which creates the appropriate writer based on the file name passed. - You can now add members to rigid bodies via IMP::core::RigidBody::add_member(). These members can be other rigid bodies (although this functionality is only lightly tested). - The code to get bounding volumes for IMP::atom::Hierarchy has been moved to the atom module, as as the clone and destroy code. They can be found at IMP::atom::clone(), IMP::atom::destroy(), IMP::atom::get_bounding_box(). - Added IMP::core::VolumeRestraint. - Several functions have been added to helper in creating restraints. They are create_simple_connectivity_on_rigid_bodies(), create_simple_connectivitiy_on_molecules(), create_simple_distance(), create_simple_diameter(), create_simple_em_fit(), and create_simple_excluded_volume_on_rigid_bodies(). Functions load_em_density_map() and set_rigid_bodies() are added as well. See IMP::helper for more information. - IMP::ScoreStates are further hidden. Namely, IMP::core::RigidBody constructs the needed score states internally, doing away with the need for the create functions (which have been done away with). In addition there are new decorators IMP::core::Cover and IMP::core::Centroid which manage their respective score states, further doing away with more create methods. The hierarchy-based create method for rigid bodies has been moved to the atom module and is called IMP::atom::rigid_body_setup_hierarchy(). - IMP::em::read_map() will figure out the file type to use automatically from the extension. Other such methods should follow suite. - A class IMP::core::StructureSet has been added to provide a convenient way to manage solutions of optimization runs. - IMP::core::RigidBodyMover now takes its angle argument in radians and is documented as such. - IMP::core::ClosePairsScoreState and IMP::core::CloseBipartitePairsScoreState have been replaced by IMP::core::ClosePairContainer and IMP::core::CloseBipartitePairContainer. The score states have been marked as deprecated and are mostly still there, but are more limited than they were. - IMP::core::AllPairsPairContainer has been renamed to IMP::core::AllPairContainer and a bipartite version has been added.

1 0

scripts/utils directory
by Keren Lasker 04 Nov '09

04 Nov '09

hi, I would like to add various python scripts to the DOMINO module. These scripts would have functionalities such as junction tree construction etc. Currently we have a global helper module, but I think it makes sense to add helper directory also within a module for more specific setup scripts. so calling junction tree construction would be: IMP.domino.helper.create_junction_tree() does it make sense ? Keren.

3 2

helper cleanup
by Daniel Russel 02 Nov '09

02 Nov '09

The helper module contains various atom.Hierarchy-specific code (get_bounding_box, clone, destroy, and the functions for creating simplified versions). Externally, this doesn't make much sense, but code is there since some of it internally uses em for computations. In addition, Elina's new code for simplified restraint management forms a nice, coherent set of functionality which could take over the helper module by itself. As a result, I propose - helper.get_bound_box, helper.clone and helper.destroy be moved to atom. - the helper.create_simplified function be renamed em.create_simplified_from_density putting it in the em module and making it more clear why it is there (there current name is too vague anyway). It should also create the rigid bodies it needs internally. - helper.create_simplified_by_residue needs to be thought about since its current method of asigning radii doesn't make sense for anything other than density based restraints (so it may make sense to move it to em). I don't think any of the code is too widely used, so changing things now should be minimally disruptive. Thoughts?

2 8

Curious Error and PDBs with more than 1 model
by Javier Ángel Velázquez Muriel 02 Nov '09

02 Nov '09

Hi. I'm testing IMP with a PDB file that has 3 models inside, and is quite big: ~900 kDa, 60 chains. I was expecting problems with reading more than one model, but I'm also getting this: ERROR: Can only allocate 150000 particles. Yell at Daniel. 1) Can IMP read multi-model PDBs now ? The code seems that it can. 2) How are the models treated? One IMP model per PDB model ? I would like to have all the PDB models into the IMP model in this case. 3) How does IMP identify chains internally? How can I access chain 54, for example, given that it's name is repeated in the PDB file? (The PDB has 3 models, 20 chains each, repeated name). Btw ... the PDB file was valid enough to be part of RCSB. Cheers.

2 1

problem evaluating restraints
by Keren Lasker 01 Nov '09

01 Nov '09

hi, I think something is wrong now with calling to restraint evaluation. After adding the restraint to the model, I am keep getting the message: ERROR: ---------------------------------------------------------------------- Traceback (most recent call last): File "simple_test.py", line 49, in test_ev print r.evaluate(None) File "/viola1/home/kerenl/bioinformatics/projects/imp/build/lib/IMP/ __init__.py", line 1193, in evaluate def evaluate(self, *args): return _IMP.Restraint_evaluate(self, *args) ValueError: Restraint::evaluate() cannot be called during model evaluatio I think the attached test case should work and I am not sure why it does not ..... thanks, Keren.

2 3

This week (and last week) in IMP
by Daniel Russel 30 Oct '09

30 Oct '09

Lots of nice improvements recently. IMP::ScoreStates are further hidden. Namely, IMP::core::RigidBody constructures the needed score states internally, doing away with the need for the create functions (which have been done away with). In addition there are new decorators IMP::core::Cover and IMP::core::Centroid which manage their respective score states, further doing away with more create methods. The hierarchy-based create mehtod for rigid bodies has been moved to the atom module and is called IMP::atom::rigid_body_setup_hierarchy(). IMP::em::read_map() will figure out the file type to use automatically from the extension. Other such methods should follow suite. A class IMP::core::StructureSet has been added to provide a convenient way to manage solutions of optimization runs. IMP::core::RigidBodyMover now takes its angle argument in radians and is documented as such. IMP::core::ClosePairsScoreState and IMP::core::CloseBipartitePairsScoreState have been replaced by IMP::core::ClosePairContainer andIMP::core::CloseBipartitePairContainer. The score states have been marked as deprecated and are mostly still there, but are more limited than they were. IMP::core::AllPairsPairContainer has been renamed to IMP::core::AllPairContainer and a bipartite version has been added. All containers now keep track of what they looked like on the previous time step. The IMP::core::ListPairContainer and IMP::core::ListSingletonContainer have had their interface reduced a bit in order to make implementing change tracking easier. The set of exceptions has been simplified to go along with simplification of the checks. We now have IMP::InternalException and IMP::UsageException which are thrown by the respective checks (and the former is thrown by IMP_FAILURE()). When you want to to pass an exception back to python use one ofIMP::ValueException or IMP::IndexException or IMP::IOException. There is also a new macro, IMP_THROW() to be used when you want to throw an exception with a nice error message. Please look at code you have worked on and make sure that the exceptions make sense given the new clarifications. An IMP::ModelException is now thrown when IMP::Particle attributes attain invalid values. This exception can be caught to recover from failures ofIMP::core::ConjugateGradients or difficult restraints. The set of functions needed to get meta information about IMP::Restraint and IMP::ScoreState objects has hopefully stabilized. Sorry about the thrashing. If you have restraints or score states not in SVN, see the corresponding IMP_RESTRAINT() type macros, the IMP::Interaction class and base classes for what exactly you need to implement.

1 0

Re: [IMP-dev] [IMP-commits] r3986 - in trunk/modules/helper: . include pyext src test
by Daniel Russel 29 Oct '09

29 Oct '09

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(a)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::Pointer<core::PairsRestraint> pairs_restraint_; > + IMP::Pointer<core::HarmonicLowerBound> harmonic_lower_bound_; > + IMP::Pointer<core::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::Pointer<core::ConnectivityRestraint> connectivity_restraint_; > + IMP::Pointer<core::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::Pointer<core::DistanceRestraint> distance_restraint_; > + IMP::Pointer<core::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::Pointer<core::DiameterRestraint> diameter_restraint_; > + IMP::Pointer<core::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::Pointer<core::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(a)salilab.org > https://salilab.org/mailman/listinfo/imp-commits

3 3

Proposed change to rigid body helpers
by Daniel Russel 29 Oct '09

29 Oct '09

Currently the rigid body helpers and cover helpers return a score state which must be added to the model to have rigid bodies work properly. I think this is confusing and error prone and doesn't offer real benefit. I would propose that the decorators or create functions simply add the score state themselves. We can add a function to tear down the rigid body/cover if people want to be able to turn them off later. The change would result in a compilation error in C++ and an mismatched type error in python, both of which can be fixed by simply removing the "score_state_variable=" from the "score_state_variable= create...." and the "model->add_score_state(score_state_variable)", so easy enough. Thoughts? Objections? The high level object is to make score states something that users are unlikely to have to be aware of: that is, you just create a rigid body and it works.

3 4

Re: [IMP-dev] [IMP-commits] r3986 - in trunk/modules/helper: . include pyext src test
by Daniel Russel 28 Oct '09

28 Oct '09

I would also recommend making the return types more symmetric by providing a similar wrapper for the FitRestraint (it doesn't have to do anything extra, but that way it looks the same as the others and you store it by value too). On Oct 28, 2009, at 1:25 PM, Notification of IMP commits wrote: > Author: etjioe(a)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::Pointer<core::PairsRestraint> pairs_restraint_; > + IMP::Pointer<core::HarmonicLowerBound> harmonic_lower_bound_; > + IMP::Pointer<core::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::Pointer<core::ConnectivityRestraint> connectivity_restraint_; > + IMP::Pointer<core::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::Pointer<core::DistanceRestraint> distance_restraint_; > + IMP::Pointer<core::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::Pointer<core::DiameterRestraint> diameter_restraint_; > + IMP::Pointer<core::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::Pointer<core::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(a)salilab.org > https://salilab.org/mailman/listinfo/imp-commits

1 0

← Newer
1
...
34
35
36
37
38
39
40
...
87
Older →

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

IMP-dev