subset_scores.h

Go to the documentation of this file.

/**
 *  \file IMP/domino/subset_scores.h
 *  \brief A Bayesian inference-based sampler.
 *
 *  Copyright 2007-2019 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMPDOMINO_SUBSET_SCORES_H
#define IMPDOMINO_SUBSET_SCORES_H

#include "particle_states.h"
#include "Assignment.h"
#include "Subset.h"
#include "Slice.h"
#include "utility.h"
#include <IMP/log.h>
#include <IMP/Object.h>
#include <IMP/cache.h>
#include <IMP/Restraint.h>
#include <IMP/log.h>
#include <boost/unordered_map.hpp>

#if IMP_DOMINO_HAS_RMF
#include <RMF/HDF5/Group.h>
#endif

IMPDOMINO_BEGIN_NAMESPACE

/** Implement a cache for restraint scores as well as management of restraints
    for domino.

    The cache size passed to the constructor is the maximum number of scores
    that will be saved. A least-recently-used eviction policy is used when
    that number is exceeded.
*/
class IMPDOMINOEXPORT RestraintCache : public Object {
  IMP_NAMED_TUPLE_2(Key, Keys, WeakPointer<Restraint>, restraint,
                    Assignment, assignment, );
  IMP_NAMED_TUPLE_3(RestraintData, RestraintDatas,
                    PointerMember<ScoringFunction>, scoring_function,
                    Subset, subset, double, max, );
  IMP_NAMED_TUPLE_2(RestraintSetData, RestraintSetDatas, Slice, slice,
                    WeakPointer<Restraint>, restraint, );
  IMP_NAMED_TUPLE_2(SetData, SetDatas, RestraintSetDatas, members, double,
                    max, );

#ifndef IMP_DOXYGEN
  class Generator {
    typedef boost::unordered_map<Restraint *, RestraintData> RMap;
    RMap rmap_;
    typedef boost::unordered_map<Restraint *, SetData> SMap;
    SMap sets_;
    PointerMember<ParticleStatesTable> pst_;

   public:
    Generator(ParticleStatesTable *pst) : pst_(pst) {}
    typedef double result_type;
    typedef Key argument_type;
    template <class Cache>
    result_type operator()(const argument_type &k, const Cache &cache) const {
      RMap::const_iterator it = rmap_.find(k.get_restraint());
      if (it != rmap_.end()) {
        Subset s = rmap_.find(k.get_restraint())->second.get_subset();
        load_particle_states(s, k.get_assignment(), pst_);
        double e;
        {
          SetLogState sls(SILENT);
          e = it->second.get_scoring_function()->evaluate_if_below(
              false, it->second.get_max());
        }
        IMP_LOG_TERSE("Restraint " << Showable(k.get_restraint())
                                   << " evaluated to " << e << " on "
                                   << k.get_assignment() << " vs "
                                   << it->second.get_max() << std::endl);
        // prob can go away with ScoreFunction change
        if (e > it->second.get_max()) e = std::numeric_limits<double>::max();
        return e;
      } else {
        SMap::const_iterator it = sets_.find(k.get_restraint());
        IMP_USAGE_CHECK(it != sets_.end(), "Restraint set "
                                               << Showable(k.get_restraint())
                                               << " not found.");
        double total = 0;
        for (unsigned int i = 0; i < it->second.get_members().size(); ++i) {
          Assignment cur = it->second.get_members()[i].get_slice().get_sliced(
              k.get_assignment());
          double score = cache.get(
              argument_type(it->second.get_members()[i].get_restraint(), cur));
          total += score * k.get_restraint()->get_weight();
          if (total >= it->second.get_max()) {
            break;
          }
        }
        IMP_LOG_TERSE("Restraint " << Showable(k.get_restraint())
                                   << " evaluated to " << total << " on "
                                   << k.get_assignment() << " with max "
                                   << it->second.get_max() << std::endl);
        if (total >= it->second.get_max()) {
          return std::numeric_limits<double>::max();
        } else {
          return total;
        }
      }
    }
    void add_to_set(RestraintSet *rs, Restraint *r, Slice slice,
                    double max) {
      IMP_USAGE_CHECK(!dynamic_cast<RestraintSet *>(r),
                      "don't pass restraint sets here as second arg");
      sets_[rs].access_members().push_back(RestraintSetData(slice, r));
      sets_[rs].set_max(max);
    }
    void add_restraint(Restraint *e, Subset s, double max) {
      IMP_USAGE_CHECK(!dynamic_cast<RestraintSet *>(e),
                      "don't pass restraint sets here");
      if (rmap_.find(e) == rmap_.end()) {
        rmap_[e] = RestraintData(e->create_scoring_function(1.0, max), s, max);
      } else {
        IMP_USAGE_CHECK(rmap_.find(e)->second.get_subset() == s,
                        "Subsets don't match on restraint update");
        rmap_[e].set_max(std::min(rmap_[e].get_max(), max));
      }
    }
    ParticleStatesTable *get_particle_states_table() const { return pst_; }
    void show_restraint_information(std::ostream &out) const;
  };
#endif  // IMP_DOXYGEN

  struct ApproximatelyEqual {
    bool operator()(double a, double b) const {
      return std::abs(a - b) < .1 * (a + b) + .1;
    }
  };
  typedef boost::unordered_map<Particle *, ParticlesTemp>
      DepMap;
  void add_restraint_internal(Restraint *r, unsigned int index,
                              RestraintSet *parent, double max,
                              Subset parent_subset, const DepMap &dependencies);
  void add_restraint_set_child_internal(Restraint *r,
                                        const Subset &cur_subset,
                                        RestraintSet *parent,
                                        double parent_max,
                                        Subset parent_subset);
  void add_restraint_set_internal(RestraintSet *rs, unsigned int index,
                                  const Subset &cur_subset, double cur_max,
                                  const DepMap &dependencies);
  Subset get_subset(Restraint *r, const DepMap &dependencies) const;
// otherwise doxygen seems to index this for some reason
#ifndef IMP_DOXYGEN
  typedef LRUCache<Generator, ApproximatelyEqual> Cache;
  Cache cache_;
#endif
  typedef boost::unordered_map<Pointer<Restraint>, Subset>
      KnownRestraints;
  KnownRestraints known_restraints_;
  // assign a unique index to each restraint for use with I/O
  typedef boost::unordered_map<Pointer<Restraint>, int>
      RestraintIndex;
  RestraintIndex restraint_index_;
  unsigned int next_index_;

 public:
  RestraintCache(ParticleStatesTable *pst,
                 unsigned int size = std::numeric_limits<unsigned int>::max());
  /** Recursively process the passed restraints (and sets) so all contained
      restraints and sets that have maximum are known.*/
  void add_restraints(const RestraintsAdaptor &rs);
  //! Get the score of a set or restraint
  /** The returned score will be std::numeric_limits<double>::max()
      if any of the limits are violated.

      The assignment passed is the assignment for the particles used by the
      restraint, not that for some whole subset. See the other get_score()
      function for a perhaps more useful one.
  */
  double get_score(Restraint *r, const Assignment &a) const {
    set_was_used(true);
    double s = cache_.get(Key(r, a));
    return s;
  }
  /** Get the score for a restraint given a subset and assignment on
      that subset.
   */
  double get_score(Restraint *r, const Subset &s,
                   const Assignment &a) const;

  //! Make it so Restraint::get_last_score() returns the score
  /** This is useful when writing the restraints to disk, as that
      code often goes off the last score to avoid recomputing the
      restraints.*/
  void load_last_score(Restraint *r, const Subset &s,
                       const Assignment &a);
  /** Return the restraints that should be evaluated for the subset,
      given the exclusions.*/
  RestraintsTemp get_restraints(const Subset &s,
                                        const Subsets &exclusions) const;

  RestraintsTemp get_restraints() const;

#if IMP_DOMINO_HAS_RMF || defined(IMP_DOXYGEN)
  /** This assumes that restraints are always added to the cache
      in the same order.
      \param[in] particle_ordering An ordering for the particles.
      \param[in] restraints Which restraints to write out entries for.
      You probably want to use get_restraints() to generate this.
      \param[in] max_entries How many entries to write out at most.
      \param[in] group Where to put the entries.
  */
  void save_cache(const ParticlesTemp &particle_ordering,
                  const RestraintsTemp &restraints,
                  RMF::HDF5::Group group, unsigned int max_entries);
  void load_cache(const ParticlesTemp &ps, RMF::HDF5::ConstGroup group);
#endif

  //! Return the slice for that restraint given the subset.
  Slice get_slice(Restraint *r, const Subset &s) const;

  //! Return the number of entries currently in the cache.
  unsigned int get_number_of_entries() const { return cache_.size(); }

  //! Check the entries in the cache.
  void validate() const;

  //! Print out information about the known restraints and restraint sets.
  void show_restraint_information(std::ostream &out = std::cout) const;
  double get_hit_rate() const { return cache_.get_hit_rate(); }
  IMP_OBJECT_METHODS(RestraintCache);
};

IMPDOMINO_END_NAMESPACE

#endif /* IMPDOMINO_SUBSET_SCORES_H */