HierarchyLoadLink.h

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/**
 *  \file IMP/rmf/HierarchyLoadLink.h
 *  \brief Manages loading links from an RMF file to an atom::Hierarchy.
 *
 *  Copyright 2007-2022 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMPRMF_HIERARCHY_LOAD_LINK_H
#define IMPRMF_HIERARCHY_LOAD_LINK_H

#include <IMP/rmf/rmf_config.h>
#include "simple_links.h"
#include "internal/atom_links_static.h"
#include "internal/atom_links_rigid_bodies.h"
#include "internal/atom_links_xyzs.h"
#include "internal/atom_links_gaussians.h"
#include <RMF/decorator/alternatives.h>
#include <RMF/decorator/provenance.h>
#include <IMP/object_macros.h>
#include <IMP/utility_macros.h>
#include <RMF/NodeHandle.h>
#include <RMF/FileHandle.h>
#include <IMP/atom/Hierarchy.h>
#include <IMP/core/provenance.h>
#include <IMP/rmf/links.h>
#include <IMP/rmf/link_macros.h>
#include <IMP/tuple_macros.h>
#include <RMF/decorators.h>
#include <memory>
#include <boost/unordered_map.hpp>

IMPRMF_BEGIN_NAMESPACE

/** Manage the loading link between an RMF file and an atom::Hierarchy.

    \unstable{HierarchyLoadLink}
 */
class IMPRMFEXPORT HierarchyLoadLink : public SimpleLoadLink<Particle> {
  typedef SimpleLoadLink<Particle> P;
  RMF::decorator::IntermediateParticleFactory intermediate_particle_factory_;
  RMF::decorator::ReferenceFrameFactory reference_frame_factory_;
  RMF::decorator::AlternativesFactory af_;
  RMF::decorator::StructureProvenanceFactory strucpf_;
  RMF::decorator::SampleProvenanceFactory samppf_;
  RMF::decorator::CombineProvenanceFactory combpf_;
  RMF::decorator::FilterProvenanceFactory filtpf_;
  RMF::decorator::ClusterProvenanceFactory clustpf_;
  RMF::decorator::ScriptProvenanceFactory scriptpf_;
  RMF::decorator::SoftwareProvenanceFactory softpf_;
  RMF::decorator::ExplicitResolutionFactory explicit_resolution_factory_;
  RMF::IntKey external_rigid_body_key_;
  struct Data {
    internal::HierarchyLoadStatic load_static;
    internal::HierarchyLoadBonds load_bonds;
    internal::HierarchyLoadXYZs load_xyzs;
    internal::HierarchyLoadGaussians load_gaussians;
    internal::HierarchyLoadRigidBodies load_rigid_bodies;
    Data(RMF::FileConstHandle h)
        : load_static(h),
          load_bonds(h),
          load_xyzs(h),
          load_gaussians(h),
          load_rigid_bodies(h) {}
  };
  typedef boost::unordered_map<ParticleIndex, std::shared_ptr<Data> >
      DM;
  DM data_;
  virtual bool get_is(RMF::NodeConstHandle nh) const override {
    return nh.get_type() == RMF::REPRESENTATION;
  }
  virtual void add_link_recursive(Model *m, ParticleIndex root,
                                  ParticleIndex o,
                                  RMF::NodeConstHandle node,
                                  ParticleIndexes rigid_bodies,
                                  Data &data);

  virtual void do_add_link(Particle *o,
                           RMF::NodeConstHandle node) final override;
  using P::do_create;
  virtual Particle *do_create(RMF::NodeConstHandle name,
                                      Model *m) final override;
  void create_recursive(Model *m, ParticleIndex root,
                        ParticleIndex cur, RMF::NodeConstHandle name,
                        ParticleIndexes rigid_bodies, Data &data);

  // Make tree of *Provenance IMP particles corresponding to those in the RMF
  void create_provenance(Model *m, RMF::NodeConstHandle node,
                         ParticleIndex cur);

  // Make *Provenance IMP particle corresponding to that in the RMF
  core::Provenance create_one_provenance(Model *m, RMF::NodeConstHandle node);

  virtual void do_load_one(RMF::NodeConstHandle nh,
                           Particle *o) final override;

 protected:
  /** This method is called for the hierarchy.*/
  virtual void do_load_hierarchy(RMF::NodeConstHandle root_node,
                                 Model *m, ParticleIndex root) {
    IMP_UNUSED(root_node);
    IMP_UNUSED(m);
    IMP_UNUSED(root);
  }
  /** Overload this to take specific action on creating
      a member of the hierarchy.
      \unstable{do_create_recursive} */
  virtual void do_setup_particle(Model *m, ParticleIndex root,
                                 ParticleIndex cur,
                                 RMF::NodeConstHandle node) {
    IMP_UNUSED(m);
    IMP_UNUSED(root);
    IMP_UNUSED(cur);
    IMP_UNUSED(node);
  }

  /** Overload this to take specific action on linking
     a member of the hierarchy.
     \unstable{do_add_link_recursive} */
  virtual void do_link_particle(Model *m, ParticleIndex root,
                                ParticleIndex cur,
                                RMF::NodeConstHandle node) {
    IMP_UNUSED(root);
    IMP_UNUSED(m);
    IMP_UNUSED(cur);
    IMP_UNUSED(node);
  }

 public:
  HierarchyLoadLink(RMF::FileConstHandle fh);

  static const char *get_name() { return "atom load"; }

  IMP_OBJECT_METHODS(HierarchyLoadLink);
};

IMPRMF_END_NAMESPACE

#endif /* IMPRMF_HIERARCHY_LOAD_LINK_H */