mcell/libmcell/api/elementary_molecule.cpp

/******************************************************************************
 *
 * Copyright (C) 2020 by
 * The Salk Institute for Biological Studies
 *
 * Use of this source code is governed by an MIT-style
 * license that can be found in the LICENSE file or at
 * https://opensource.org/licenses/MIT.
 *
******************************************************************************/

#include "api/elementary_molecule.h"
#include "api/elementary_molecule_type.h"
#include "api/component_type.h"
#include "api/component.h"
#include "api/complex.h"

using namespace std;

namespace MCell {
namespace API {


bool ElementaryMolecule::__eq__(const ElementaryMolecule& other) const {

  // do we have the same mol type?
  if (!eq_nonarray_attributes(other)) {
    return false;
  }

  string c1 = is_set(compartment_name) ? compartment_name : "";
  string c2 = is_set(other.compartment_name) ? other.compartment_name : "";
  if (c1 != c2) {
    return false;
  }

  // are components the same (order does not matter)
  std::set<Component> s1;
  for (auto& c: components) {
    s1.insert(*c);
  }
  std::set<Component> s2;
  for (auto& c: other.components) {
    s2.insert(*c);
  }
  return s1 == s2;
}


std::string ElementaryMolecule::to_bngl_str(const bool with_compartment) const {
  std::string res;

  res = elementary_molecule_type->name;

  if (!components.empty()) {
    res += "(";
    for (size_t i = 0; i < components.size(); i++) {
      res += components[i]->to_bngl_str();
      if (i + 1 != components.size()) {
        res += ",";
      }
    }
    res += ")";
  }

  if (with_compartment && is_set(compartment_name)) {
    res += "@" + compartment_name;
  }

  return res;
}


bool ElementaryMolecule::is_surf() const {
  assert(is_set(elementary_molecule_type));
  return is_set(elementary_molecule_type->diffusion_constant_2d);
}

} // namespace API
} // namespace MCell