/**
 *  \file atom/CHARMMAtom.h
 *  \brief A decorator for an atom that has a defined CHARMM type.
 *
 *  Copyright 2007-2013 IMP Inventors. All rights reserved.
 *
 */

#include <IMP/atom/CHARMMAtom.h>
#include <IMP/atom/Hierarchy.h>

IMPATOM_BEGIN_NAMESPACE

StringKey CHARMMAtom::get_charmm_type_key() {
  static StringKey k("CHARMM atom type");
  return k;
}

void CHARMMAtom::show(std::ostream &out) const
{
  Atom::show(out);
  out << " CHARMM type= " << get_charmm_type();
}

namespace {
  struct FindUntypedVisitor {
    Atoms *atoms_;
    FindUntypedVisitor(Atoms *atoms) : atoms_(atoms) {}
    bool operator()(Hierarchy h) {
      if (h.get_as_atom() && !CHARMMAtom::particle_is_instance(h)) {
        atoms_->push_back(Atom(h));
      }
      return true;
    }
  };
}

Atoms get_charmm_untyped_atoms(Hierarchy hierarchy)
{
  Atoms atoms;
  FindUntypedVisitor visitor(&atoms);
  IMP::core::visit_depth_first(hierarchy, visitor);
  return atoms;
}

void remove_charmm_untyped_atoms(Hierarchy hierarchy)
{
  Atoms untyped = get_charmm_untyped_atoms(hierarchy);
  for (Atoms::iterator it = untyped.begin(); it != untyped.end(); ++it) {
    destroy(Hierarchy(it->get_particle()));
  }
}

IMPATOM_END_NAMESPACE