diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 0cebc05..816fb79 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,6 +1,17 @@
 Changelog
 =========
 
+Release 1.4.0
+-------------
+
+Changes (DB schema changing)
+ - Remove `MODEL_TRANSFORMATION` elementary step type
+
+Additions (backwards compatible):
+ - Exact type of stored integers in the database is checked before retrieval in case fields have been manipulated with other MongoDB applications
+ - Projection options are added to almost all internal database queries to reduce the bandwidth requirements.
+ - Added support for list-of-lists of integers as elements in value collections (calculation settings etc.).
+
 Release 1.3.0
 -------------
 
@@ -13,8 +24,12 @@ Changes (DB schema changing):
 
 Additions (backwards compatible):
  - Python package now includes pure Python code for more complex query utilities. This code is added in the modules
- `queries`, `energy_query_functions`, `compound_and_flask_creation`, `concentration_query_functions`, and `insert_concentration`.
- All of them are top level modules (`import scine_database.energy_query_functions`)
+    - `queries`
+    - `energy_query_functions`
+    - `compound_and_flask_creation`
+    - `concentration_query_functions`
+    - `insert_concentration`.
+   All of them are top level modules (`import scine_database.energy_query_functions`)
  - Added the possibility to configure the connection based on a custom URI instead of credentials.
 
 Release 1.2.0
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 98acc25..7207e8a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.9)
 
 project(Database
-  VERSION 1.3.0
+  VERSION 1.4.0
   DESCRIPTION "The SCINE database interface."
 )
 
diff --git a/README.rst b/README.rst
index 92b8b3d..11b637f 100644
--- a/README.rst
+++ b/README.rst
@@ -66,6 +66,13 @@ J. P. Unsleber, S. A. Grimmel, M. Reiher,
 "Chemoton 2.0: Autonomous Exploration of Chemical Reaction Networks",
 *J. Chem. Theory Comput.*, **2022**, *18*, 5393.
 
+Furthermore, when publishing results obtained with any SCINE module, please cite the following paper:
+
+T. Weymuth, J. P. Unsleber, P. L. Türtscher, M. Steiner, J.-G. Sobez, C. H. Müller, M. Mörchen,
+V. Klasovita, S. A. Grimmel, M. Eckhoff, K.-S. Csizi, F. Bosia, M. Bensberg, M. Reiher,
+"SCINE—Software for chemical interaction networks", *J. Chem. Phys.*, **2024**, *160*, 222501
+(DOI `10.1063/5.0206974 <https://doi.org/10.1063/5.0206974>`_).
+
 Support and Contact
 -------------------
 
diff --git a/conanfile.py b/conanfile.py
index e96b2c7..b9a2255 100644
--- a/conanfile.py
+++ b/conanfile.py
@@ -10,7 +10,7 @@
 
 class ScineDatabaseConan(ScineConan):
     name = "scine_database"
-    version = "1.3.0"
+    version = "1.4.0"
     url = "https://github.com/qcscine/database"
     description = """
 The SCINE Database is a database wrapper for a MongoDB encoding reaction
@@ -48,7 +48,7 @@ class ScineDatabaseConan(ScineConan):
     requires = [
         "mongo-cxx-driver/3.6.0",
         "eigen/[~=3.3.7]",
-        "scine_utilities/9.0.0"
+        "scine_utilities/10.0.0"
     ]
     cmake_name = "Database"
     cmake_definitions = {
diff --git a/dev b/dev
index 518ab3c..2712fd3 160000
--- a/dev
+++ b/dev
@@ -1 +1 @@
-Subproject commit 518ab3c7f8a0a724081fcd7ed518c669724bcd37
+Subproject commit 2712fd3204d703c777244b077066ad75c6bc0db1
diff --git a/src/Database/Database/Exceptions.h b/src/Database/Database/Exceptions.h
index bd82e35..fa81a99 100644
--- a/src/Database/Database/Exceptions.h
+++ b/src/Database/Database/Exceptions.h
@@ -25,6 +25,17 @@ class DuplicateIDException : public std::exception {
   }
 };
 
+/**
+ * @class SelfDuplicateException
+ * @brief An exception to throw if a given structure is a duplicate of itself.
+ */
+class SelfDuplicateException : public std::exception {
+ public:
+  const char* what() const throw() {
+    return "The given structure is a duplicate of itself. This cannot be.";
+  }
+};
+
 /**
  * @class MissingCredentialsException
  * @brief An exception to throw if no credentials are present to establish a connection to a database.
diff --git a/src/Database/Database/Layout.cpp b/src/Database/Database/Layout.cpp
index 72e5a2c..61795ac 100644
--- a/src/Database/Database/Layout.cpp
+++ b/src/Database/Database/Layout.cpp
@@ -45,13 +45,11 @@ const std::map<CalculationStatus, std::string> EnumMaps::status2str = {
 // clang-format off
 const std::map<std::string, ElementaryStepType> EnumMaps::str2estype = {
   {"regular", ElementaryStepType::REGULAR},
-  {"barrierless", ElementaryStepType::BARRIERLESS},
-  {"model_transformation", ElementaryStepType::MODEL_TRANSFORMATION}
+  {"barrierless", ElementaryStepType::BARRIERLESS}
 };
 const std::map<ElementaryStepType, std::string> EnumMaps::estype2str = {
   {ElementaryStepType::REGULAR, "regular"},
-  {ElementaryStepType::BARRIERLESS, "barrierless"},
-  {ElementaryStepType::MODEL_TRANSFORMATION, "model_transformation"}
+  {ElementaryStepType::BARRIERLESS, "barrierless"}
 };
 // clang-format on
 
diff --git a/src/Database/Database/Layout.h b/src/Database/Database/Layout.h
index 718a60e..a64defc 100644
--- a/src/Database/Database/Layout.h
+++ b/src/Database/Database/Layout.h
@@ -57,7 +57,7 @@ enum class StructureLabel : unsigned {
   SCAN_OBSERVER = 107,
 };
 
-enum class ElementaryStepType : unsigned { REGULAR = 0, BARRIERLESS = 1, MODEL_TRANSFORMATION = 2 };
+enum class ElementaryStepType : unsigned { REGULAR = 0, BARRIERLESS = 1 };
 
 namespace Layout {
 
diff --git a/src/Database/Database/Manager.cpp b/src/Database/Database/Manager.cpp
index 555b92e..20c49bc 100644
--- a/src/Database/Database/Manager.cpp
+++ b/src/Database/Database/Manager.cpp
@@ -13,6 +13,7 @@
 #include "Database/Objects/Calculation.h"
 #include "Database/Objects/Compound.h"
 #include "Database/Objects/ElementaryStep.h"
+#include "Database/Objects/Impl/Fields.h"
 #include "Database/Objects/Property.h"
 #include "Database/Objects/Reaction.h"
 #include "Database/Objects/Structure.h"
@@ -20,7 +21,6 @@
 /* External Includes */
 #include <bsoncxx/builder/stream/document.hpp>
 #include <cassert>
-#include <iostream>
 #include <mongocxx/client.hpp>
 #include <mongocxx/collection.hpp>
 #include <mongocxx/database.hpp>
@@ -200,9 +200,10 @@ std::tuple<int, int, int> Manager::getDBVersion() {
   if (!optional)
     return {0, 0, 0};
   auto view = optional.value().view();
-  int major = view["version"]["major"].get_int32();
-  int minor = view["version"]["minor"].get_int32();
-  int patch = view["version"]["patch"].get_int32();
+  auto versionView = view["version"];
+  const int major = Fields::getIntegerFromElement<bsoncxx::document::element, int>(versionView["major"]);
+  const int minor = Fields::getIntegerFromElement<bsoncxx::document::element, int>(versionView["minor"]);
+  const int patch = Fields::getIntegerFromElement<bsoncxx::document::element, int>(versionView["patch"]);
   return {major, minor, patch};
 }
 void Manager::init(bool moreIndices) {
diff --git a/src/Database/Database/Objects/Calculation.cpp b/src/Database/Database/Objects/Calculation.cpp
index f1a6b26..2de1f8f 100644
--- a/src/Database/Database/Objects/Calculation.cpp
+++ b/src/Database/Database/Objects/Calculation.cpp
@@ -144,7 +144,7 @@ Calculation::Job Calculation::getJob() const {
   Calculation::Job job("dummy");
   job.order = jobDoc["order"].get_utf8().value.to_string();
   job.memory = jobDoc["memory"].get_double();
-  job.cores = jobDoc["cores"].get_int32();
+  job.cores = Fields::getInteger<int>(jobDoc, "cores");
   job.disk = jobDoc["disk"].get_double();
   return job;
 }
@@ -167,7 +167,9 @@ void Calculation::setJob(const Calculation::Job& job) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 /*=========*
@@ -201,7 +203,9 @@ void Calculation::addStructure(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::removeStructure(const ID& id) const {
@@ -219,7 +223,9 @@ void Calculation::removeStructure(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 bool Calculation::hasStructure(const ID& id) const {
@@ -275,7 +281,9 @@ void Calculation::setSetting(const std::string& key, const Utils::UniversalSetti
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 Utils::UniversalSettings::GenericValue Calculation::getSetting(const std::string& key) const {
@@ -319,7 +327,9 @@ void Calculation::removeSetting(const std::string& key) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::clearSettings() const {
@@ -337,7 +347,9 @@ void Calculation::clearSettings() const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 Utils::UniversalSettings::ValueCollection Calculation::getSettings() const {
@@ -372,7 +384,9 @@ void Calculation::setSettings(const Utils::UniversalSettings::ValueCollection& s
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 /*===========*
@@ -410,7 +424,9 @@ void Calculation::setResults(Calculation::Results& results) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::clearResults() const {
@@ -435,7 +451,9 @@ void Calculation::clearResults() const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 Calculation::Results Calculation::getResults() const {
@@ -487,7 +505,9 @@ void Calculation::setAuxiliary(std::string key, const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 ID Calculation::getAuxiliary(std::string key) const {
@@ -531,7 +551,9 @@ void Calculation::removeAuxiliary(std::string key) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::setAuxiliaries(std::map<std::string, ID> auxiliaries) const {
@@ -553,7 +575,9 @@ void Calculation::setAuxiliaries(std::map<std::string, ID> auxiliaries) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::clearAuxiliaries() const {
@@ -571,7 +595,9 @@ void Calculation::clearAuxiliaries() const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 std::map<std::string, ID> Calculation::getAuxiliaries() const {
@@ -615,7 +641,9 @@ void Calculation::setRestartInformation(const std::string& key, const ID& id) co
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 ID Calculation::getRestartInformation(const std::string& key) const {
@@ -659,7 +687,9 @@ void Calculation::removeRestartInformation(const std::string& key) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::setRestartInformation(const std::map<std::string, ID>& restart_information) const {
@@ -681,7 +711,9 @@ void Calculation::setRestartInformation(const std::map<std::string, ID>& restart
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Calculation::clearRestartInformation() const {
@@ -699,7 +731,9 @@ void Calculation::clearRestartInformation() const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 std::map<std::string, ID> Calculation::getRestartInformation() const {
diff --git a/src/Database/Database/Objects/Compound.cpp b/src/Database/Database/Objects/Compound.cpp
index 773d12b..0269e7c 100644
--- a/src/Database/Database/Objects/Compound.cpp
+++ b/src/Database/Database/Objects/Compound.cpp
@@ -29,7 +29,7 @@ namespace Scine {
 namespace Database {
 namespace {
 
-ID createImpl(const std::vector<ID>& structures, const Compound::CollectionPtr& collection) {
+ID createImpl(const std::vector<ID>& structures, const Compound::CollectionPtr& collection, bool explorationDisabled) {
   // Build structure array
   bsoncxx::builder::basic::array structureArray;
   for (const auto& id : structures) {
@@ -41,7 +41,7 @@ ID createImpl(const std::vector<ID>& structures, const Compound::CollectionPtr&
   auto doc = document{} << "_created" << now
                         << "_lastmodified" << now
                         << "analysis_disabled" << false
-                        << "exploration_disabled" << false
+                        << "exploration_disabled" << explorationDisabled
                         << "_objecttype" << Compound::objecttype
                         << "structures" << structureArray
                         << "reactions" << open_array << close_array
@@ -55,20 +55,20 @@ ID createImpl(const std::vector<ID>& structures, const Compound::CollectionPtr&
 
 constexpr const char* Compound::objecttype;
 
-Compound Compound::create(const std::vector<ID>& structures, const CollectionPtr& collection) {
+Compound Compound::create(const std::vector<ID>& structures, const CollectionPtr& collection, bool explorationDisabled) {
   if (!collection) {
     throw Exceptions::MissingCollectionException();
   }
 
-  return Compound{createImpl(structures, collection), collection};
+  return Compound{createImpl(structures, collection, explorationDisabled), collection};
 }
 
-ID Compound::create(const std::vector<ID>& structures) {
+ID Compound::create(const std::vector<ID>& structures, bool explorationDisabled) {
   if (!_collection) {
     throw Exceptions::MissingLinkedCollectionException();
   }
 
-  this->_id = std::make_unique<ID>(createImpl(structures, _collection));
+  this->_id = std::make_unique<ID>(createImpl(structures, _collection, explorationDisabled));
   return *this->_id;
 }
 
@@ -112,7 +112,9 @@ void Compound::addReaction(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Compound::removeReaction(const ID& id) const {
@@ -128,7 +130,9 @@ void Compound::removeReaction(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 int Compound::hasReactions() const {
@@ -178,7 +182,9 @@ void Compound::addStructure(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Compound::removeStructure(const ID& id) const {
@@ -194,7 +200,9 @@ void Compound::removeStructure(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 int Compound::hasStructures() const {
diff --git a/src/Database/Database/Objects/Compound.h b/src/Database/Database/Objects/Compound.h
index dabc9d0..3a877ca 100644
--- a/src/Database/Database/Objects/Compound.h
+++ b/src/Database/Database/Objects/Compound.h
@@ -51,18 +51,20 @@ class Compound : public Object {
    *
    * @param collection The collection to generate the compound in
    * @param structures The initial list of structures in the compound.
+   * @param explorationDisabled Disable this Compound for further explorations.
    *
    * @throws MissingLinkedCollectionException If @p collection does not hold a collection
    * @returns The new Compound instance.
    */
-  static Compound create(const std::vector<ID>& structures, const CollectionPtr& collection);
+  static Compound create(const std::vector<ID>& structures, const CollectionPtr& collection, bool explorationDisabled = false);
   /**
    * @brief Creates a new Compound in the remote database.
    * @throws MissingLinkedCollectionException Thrown if no collection is linked.
    * @param structures The initial list of structures in the compound.
+   * @param explorationDisabled Disable this Compound for further explorations.
    * @return ID        The ID of the newly inserted Compound.
    */
-  ID create(const std::vector<ID>& structures);
+  ID create(const std::vector<ID>& structures, bool explorationDisabled = false);
   /**
    * @brief Get the centroid structure.
    *
diff --git a/src/Database/Database/Objects/ElementaryStep.cpp b/src/Database/Database/Objects/ElementaryStep.cpp
index 0a1e68d..f6b5f78 100644
--- a/src/Database/Database/Objects/ElementaryStep.cpp
+++ b/src/Database/Database/Objects/ElementaryStep.cpp
@@ -174,7 +174,9 @@ void ElementaryStep::addReactant(const ID& id, const SIDE side) const {
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
   if (side == SIDE::BOTH || side == SIDE::RHS) {
     auto selection = document{} << "_id" << this->id().bsoncxx() << finalize;
@@ -187,7 +189,9 @@ void ElementaryStep::addReactant(const ID& id, const SIDE side) const {
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
 }
 
@@ -205,7 +209,9 @@ void ElementaryStep::removeReactant(const ID& id, const SIDE side) const {
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
   if (side == SIDE::BOTH || side == SIDE::RHS) {
     auto selection = document{} << "_id" << this->id().bsoncxx() << finalize;
@@ -218,7 +224,9 @@ void ElementaryStep::removeReactant(const ID& id, const SIDE side) const {
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
 }
 
@@ -240,7 +248,9 @@ void ElementaryStep::setReactants(const std::vector<ID>& ids, const SIDE side) c
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
   if (side == SIDE::BOTH || side == SIDE::RHS) {
     auto selection = document{} << "_id" << this->id().bsoncxx() << finalize;
@@ -253,7 +263,9 @@ void ElementaryStep::setReactants(const std::vector<ID>& ids, const SIDE side) c
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
 }
 
@@ -314,7 +326,9 @@ void ElementaryStep::clearReactants(const SIDE side) const {
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
   if (side == SIDE::BOTH || side == SIDE::RHS) {
     auto selection = document{} << "_id" << this->id().bsoncxx() << finalize;
@@ -327,7 +341,9 @@ void ElementaryStep::clearReactants(const SIDE side) const {
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
 }
 
@@ -395,7 +411,9 @@ void ElementaryStep::setSpline(const Utils::BSplines::TrajectorySpline& spline)
                            << finalize;
   // clang-format on
   auto selection = document{} << "_id" << this->id().bsoncxx() << finalize;
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void ElementaryStep::clearSpline() const {
@@ -444,7 +462,9 @@ void ElementaryStep::addIdxMaps(const std::vector<int>& lhsRhsMap, const boost::
                                 << close_document
                               << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
   else {
     // clang-format off
@@ -456,7 +476,9 @@ void ElementaryStep::addIdxMaps(const std::vector<int>& lhsRhsMap, const boost::
                                 << close_document
                               << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
 }
 
@@ -474,7 +496,9 @@ void ElementaryStep::removeIdxMaps() const {
                               << close_document
                             << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 bool ElementaryStep::hasIdxMap(const IdxMapType& mapType) const {
@@ -541,7 +565,9 @@ bool ElementaryStep::hasIdxMapByKey(const std::string& key) const {
                               << close_array
                               << finalize;
   // clang-format on
-  auto optional = _collection->mongocxx().find_one(selection.view());
+  mongocxx::options::find options{};
+  options.projection(document{} << "idx_maps" << 1 << finalize);
+  auto optional = _collection->mongocxx().find_one(selection.view(), options);
   return static_cast<bool>(optional);
 }
 
@@ -562,10 +588,10 @@ std::vector<int> ElementaryStep::getIdxMapByKey(const std::string& key) const {
   if (findIter == mapIt.end()) {
     throw Exceptions::MissingIdOrField();
   }
-  bsoncxx::array::view wantedMapArray = findIter->get_array();
+  const bsoncxx::array::view wantedMapArray = findIter->get_array();
   std::vector<int> wantedMap;
-  for (bsoncxx::array::element ele : wantedMapArray) {
-    wantedMap.emplace_back(ele.get_int32());
+  for (const bsoncxx::array::element ele : wantedMapArray) {
+    wantedMap.emplace_back(Fields::getIntegerFromElement<bsoncxx::array::element, int>(ele));
   }
   return wantedMap;
 }
diff --git a/src/Database/Database/Objects/Flask.cpp b/src/Database/Database/Objects/Flask.cpp
index 96d789e..9a86cee 100644
--- a/src/Database/Database/Objects/Flask.cpp
+++ b/src/Database/Database/Objects/Flask.cpp
@@ -29,7 +29,8 @@ namespace Scine {
 namespace Database {
 namespace {
 
-ID createImpl(const std::vector<ID>& structures, const std::vector<ID>& compounds, const Flask::CollectionPtr& collection) {
+ID createImpl(const std::vector<ID>& structures, const std::vector<ID>& compounds,
+              const Flask::CollectionPtr& collection, bool explorationDisabled) {
   // Build arrays
   bsoncxx::builder::basic::array structureArray;
   for (const auto& id : structures) {
@@ -45,7 +46,7 @@ ID createImpl(const std::vector<ID>& structures, const std::vector<ID>& compound
   auto doc = document{} << "_created" << now
                         << "_lastmodified" << now
                         << "analysis_disabled" << false
-                        << "exploration_disabled" << false
+                        << "exploration_disabled" << explorationDisabled
                         << "_objecttype" << Flask::objecttype
                         << "structures" << structureArray
                         << "compounds" << compoundArray
@@ -60,20 +61,21 @@ ID createImpl(const std::vector<ID>& structures, const std::vector<ID>& compound
 
 constexpr const char* Flask::objecttype;
 
-Flask Flask::create(const std::vector<ID>& structures, const std::vector<ID>& compounds, const CollectionPtr& collection) {
+Flask Flask::create(const std::vector<ID>& structures, const std::vector<ID>& compounds,
+                    const CollectionPtr& collection, bool explorationDisabled) {
   if (!collection) {
     throw Exceptions::MissingCollectionException();
   }
 
-  return Flask{createImpl(structures, compounds, collection), collection};
+  return Flask{createImpl(structures, compounds, collection, explorationDisabled), collection};
 }
 
-ID Flask::create(const std::vector<ID>& structures, const std::vector<ID>& compounds) {
+ID Flask::create(const std::vector<ID>& structures, const std::vector<ID>& compounds, bool explorationDisabled) {
   if (!_collection) {
     throw Exceptions::MissingLinkedCollectionException();
   }
 
-  this->_id = std::make_unique<ID>(createImpl(structures, compounds, _collection));
+  this->_id = std::make_unique<ID>(createImpl(structures, compounds, _collection, explorationDisabled));
   return *this->_id;
 }
 
@@ -115,7 +117,9 @@ bool Flask::hasReaction(const ID& id) const {
                               << close_array
                               << finalize;
   // clang-format on
-  auto optional = _collection->mongocxx().find_one(selection.view());
+  auto options = mongocxx::options::find();
+  options.projection(document{} << "_id" << 1 << finalize);
+  auto optional = _collection->mongocxx().find_one(selection.view(), options);
   return static_cast<bool>(optional);
 }
 
@@ -132,7 +136,9 @@ void Flask::addReaction(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Flask::removeReaction(const ID& id) const {
@@ -148,7 +154,9 @@ void Flask::removeReaction(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 int Flask::hasReactions() const {
@@ -196,7 +204,9 @@ bool Flask::hasStructure(const ID& id) const {
                               << close_array
                               << finalize;
   // clang-format on
-  auto optional = _collection->mongocxx().find_one(selection.view());
+  auto options = mongocxx::options::find();
+  options.projection(document{} << "_id" << 1 << finalize);
+  auto optional = _collection->mongocxx().find_one(selection.view(), options);
   return static_cast<bool>(optional);
 }
 
@@ -213,7 +223,9 @@ void Flask::addStructure(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Flask::removeStructure(const ID& id) const {
@@ -229,7 +241,9 @@ void Flask::removeStructure(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 int Flask::hasStructures() const {
@@ -277,7 +291,9 @@ bool Flask::hasCompound(const ID& id) const {
                               << close_array
                               << finalize;
   // clang-format on
-  auto optional = _collection->mongocxx().find_one(selection.view());
+  auto options = mongocxx::options::find();
+  options.projection(document{} << "_id" << 1 << finalize);
+  auto optional = _collection->mongocxx().find_one(selection.view(), options);
   return static_cast<bool>(optional);
 }
 
diff --git a/src/Database/Database/Objects/Flask.h b/src/Database/Database/Objects/Flask.h
index 79b58b0..7aaeac9 100644
--- a/src/Database/Database/Objects/Flask.h
+++ b/src/Database/Database/Objects/Flask.h
@@ -51,19 +51,22 @@ class Flask : public Object {
    * @param collection The collection to generate the Flask in
    * @param structures The initial list of Structures in the Flask.
    * @param compounds  The list of Compounds that are combined in the Flask.
+   * @param explorationDisabled Disable this Flask for further explorations.
    *
    * @throws MissingLinkedCollectionException If @p collection does not hold a collection
    * @returns The new Flask instance.
    */
-  static Flask create(const std::vector<ID>& structures, const std::vector<ID>& compounds, const CollectionPtr& collection);
+  static Flask create(const std::vector<ID>& structures, const std::vector<ID>& compounds,
+                      const CollectionPtr& collection, bool explorationDisabled = false);
   /**
    * @brief Creates a new Flask in the remote database.
    * @throws MissingLinkedCollectionException Thrown if no collection is linked.
    * @param structures The initial list of Structures in the Flask.
    * @param compounds  The list of Compounds that are combined in the Flask.
+   * @param explorationDisabled Disable this Flask for further explorations.
    * @return ID        The ID of the newly inserted Flask.
    */
-  ID create(const std::vector<ID>& structures, const std::vector<ID>& compounds);
+  ID create(const std::vector<ID>& structures, const std::vector<ID>& compounds, bool explorationDisabled = false);
   /**
    * @brief Get the centroid structure.
    *
diff --git a/src/Database/Database/Objects/Impl/DerivedProperty.h b/src/Database/Database/Objects/Impl/DerivedProperty.h
index 06b95b2..3341c06 100644
--- a/src/Database/Database/Objects/Impl/DerivedProperty.h
+++ b/src/Database/Database/Objects/Impl/DerivedProperty.h
@@ -13,6 +13,7 @@
 #include "Database/Id.h"
 #include "Database/Objects/Model.h"
 #include "Database/Objects/Property.h"
+#include "Fields.h"
 #include <Eigen/Core>
 #include <Eigen/Sparse>
 #include <boost/optional.hpp>
@@ -27,23 +28,6 @@
 namespace Scine {
 namespace Database {
 
-namespace {
-
-template<typename T>
-long getIntegerFromElement(T v) {
-  try {
-    return v.get_int64();
-  }
-  catch (const bsoncxx::exception&) {
-    return static_cast<long>(v.get_int32());
-  }
-}
-
-long getInteger(bsoncxx::document::view& view, const std::string& key) {
-  return getIntegerFromElement<bsoncxx::document::element>(view[key]);
-}
-} // namespace
-
 namespace Serialization {
 
 template<typename T>
@@ -146,7 +130,7 @@ struct Serializer<Eigen::VectorXd> {
   }
 
   static Eigen::VectorXd deserialize(bsoncxx::document::view view) {
-    const Eigen::Index size = getInteger(view, "size");
+    const Eigen::Index size = Fields::getInteger<long>(view, "size");
     Eigen::VectorXd ret(size);
     bsoncxx::array::view data = view["data"].get_array();
     Eigen::Index idx = 0;
@@ -181,8 +165,8 @@ struct Serializer<Eigen::MatrixXd> {
   }
 
   static Eigen::MatrixXd deserialize(bsoncxx::document::view view) {
-    const Eigen::Index cols = getInteger(view, "cols");
-    const Eigen::Index rows = getInteger(view, "rows");
+    const Eigen::Index cols = Fields::getInteger<long>(view, "cols");
+    const Eigen::Index rows = Fields::getInteger<long>(view, "rows");
     Eigen::MatrixXd ret(rows, cols);
     bsoncxx::array::view data = view["data"].get_array();
     Eigen::Index idx = 0;
@@ -230,9 +214,9 @@ struct Serializer<Eigen::SparseMatrix<double>> {
   }
 
   static Eigen::SparseMatrix<double> deserialize(bsoncxx::document::view view) {
-    const Eigen::Index cols = getInteger(view, "cols");
-    const Eigen::Index rows = getInteger(view, "rows");
-    const Eigen::Index size = getInteger(view, "size");
+    const Eigen::Index cols = Fields::getInteger<long>(view, "cols");
+    const Eigen::Index rows = Fields::getInteger<long>(view, "rows");
+    const Eigen::Index size = Fields::getInteger<long>(view, "size");
 
     // Read triplets
     std::vector<Eigen::Triplet<double>> triplets;
@@ -248,8 +232,8 @@ struct Serializer<Eigen::SparseMatrix<double>> {
       auto v = *values_it++;
       auto c = *col_it++;
       auto r = *row_it++;
-      triplets.emplace_back(getIntegerFromElement<bsoncxx::array::element>(r),
-                            getIntegerFromElement<bsoncxx::array::element>(c), v.get_double());
+      triplets.emplace_back(Fields::getIntegerFromElement<bsoncxx::array::element, long>(r),
+                            Fields::getIntegerFromElement<bsoncxx::array::element, long>(c), v.get_double());
     }
 
     Eigen::SparseMatrix<double> ret(rows, cols);
@@ -271,7 +255,7 @@ DerivedType create(std::shared_ptr<Collection> collection, const Model& model, c
     throw Exceptions::MissingCollectionException();
   }
 
-  document builder{};
+  bsoncxx::builder::basic::document builder{};
   const bsoncxx::types::b_date now{std::chrono::system_clock::now()};
   builder.append(kvp("_created", now));
   builder.append(kvp("_lastmodified", now));
@@ -292,8 +276,8 @@ DerivedType create(std::shared_ptr<Collection> collection, const Model& model, c
 
   auto doc = builder.extract();
   auto result = collection->mongocxx().insert_one(doc.view());
-  ID id{result->inserted_id().get_oid().value};
-  return DerivedType{std::move(id), collection};
+  const bsoncxx::v_noabi::oid oid = result->inserted_id().get_oid().value;
+  return DerivedType{ID(oid), collection};
 }
 
 template<typename DerivedProperty, typename T>
@@ -304,9 +288,9 @@ void updateData(DerivedProperty& derived, const T& data) {
     throw Exceptions::MissingLinkedCollectionException();
   }
   using namespace bsoncxx::builder::basic;
-  document selection{};
+  bsoncxx::builder::basic::document selection{};
   selection.append(kvp("_id", derived.id().bsoncxx()));
-  document update{};
+  bsoncxx::builder::basic::document update{};
   update.append(kvp("$set", [&data](sub_document updates) { Serialization::Serializer<T>::serialize(updates, data); }));
   update.append(kvp("$currentDate", [](sub_document dates) { dates.append(kvp("_lastmodified", true)); }));
   collection->mongocxx().find_one_and_update(selection.view(), update.view());
@@ -322,7 +306,7 @@ T getData(DerivedProperty& derived) {
   }
 
   using namespace bsoncxx::builder::basic;
-  document selection{};
+  bsoncxx::builder::basic::document selection{};
   selection.append(kvp("_id", derived.id().bsoncxx()));
   mongocxx::options::find options{};
   Serialization::Serializer<T>::project(options);
diff --git a/src/Database/Database/Objects/Impl/Fields.h b/src/Database/Database/Objects/Impl/Fields.h
index ec980eb..014a733 100644
--- a/src/Database/Database/Objects/Impl/Fields.h
+++ b/src/Database/Database/Objects/Impl/Fields.h
@@ -14,6 +14,7 @@
 #include "Database/Objects/Object.h"
 #include <bsoncxx/builder/stream/document.hpp>
 #include <bsoncxx/exception/exception.hpp>
+#include <iostream>
 #include <mongocxx/collection.hpp>
 #include <string>
 
@@ -229,7 +230,9 @@ void set(const Object& obj, const std::string& field, const T& value) {
                              << close_document
                            << finalize;
   // clang-format on
-  collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 /**
@@ -281,7 +284,9 @@ inline void unset(const Object& obj, const std::string& field) {
                              << close_document
                            << finalize;
   // clang-format on
-  collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 //! Check whether a field exists
@@ -324,10 +329,43 @@ inline bool nonNull(const Object& obj, const std::string& field) {
                               << close_array
                               << finalize;
   // clang-format on
-  auto optional = collection->mongocxx().find_one(selection.view());
+  auto options = mongocxx::options::find();
+  options.projection(document{} << "_id" << 1 << finalize);
+  auto optional = collection->mongocxx().find_one(selection.view(), options);
   return static_cast<bool>(optional);
 }
 
+template<typename T, typename R>
+inline R getIntegerFromElement(T v) {
+  if (v.type() == bsoncxx::type::k_int64) {
+    return static_cast<R>(v.get_int64());
+  }
+  if (v.type() == bsoncxx::type::k_int32) {
+    return static_cast<R>(v.get_int32());
+  }
+  if (v.type() == bsoncxx::type::k_double) {
+    std::cerr << "Warning: The database contains a double value for an integer field." << std::endl;
+    return static_cast<R>(v.get_double());
+  }
+  throw std::runtime_error("The database contains a non-integer value for an integer field.");
+}
+
+template<typename R>
+inline R getInteger(bsoncxx::document::view& view, const std::string& key) {
+  return getIntegerFromElement<bsoncxx::document::element, R>(view[key]);
+}
+
+// define template of getInteger explicitly for int return type to include check for overflow
+template<>
+inline int getInteger<int>(bsoncxx::document::view& view, const std::string& key) {
+  const long x = getInteger<long>(view, key);
+  if (x > std::numeric_limits<int>::max() || x < std::numeric_limits<int>::min()) {
+    throw std::runtime_error("The database contains an 64bit integer that cannot be represented as 32bit integer "
+                             "as defined in our database schema.");
+  }
+  return getIntegerFromElement<bsoncxx::document::element, int>(view[key]);
+}
+
 } /* namespace Fields */
 } /* namespace Database */
 } /* namespace Scine */
diff --git a/src/Database/Database/Objects/Model.cpp b/src/Database/Database/Objects/Model.cpp
index 3b2cc71..4e4961c 100644
--- a/src/Database/Database/Objects/Model.cpp
+++ b/src/Database/Database/Objects/Model.cpp
@@ -197,6 +197,14 @@ const std::vector<std::string>& Model::skipFields() {
 }
 
 bool Model::operator==(const Model& rhs) const {
+  return equality(rhs, true);
+}
+
+bool Model::equalWithoutPeriodicBoundaryCheck(const Model& rhs) const {
+  return equality(rhs, false);
+}
+
+bool Model::equality(const Model& rhs, bool comparePbc) const {
   auto lhsPairs = this->getConstSettingsModelPairs(); // necessary to call here because of pybind
   auto rhsPairs = rhs.getConstSettingsModelPairs();
   auto rhsIterator = rhsPairs.begin();
@@ -234,6 +242,10 @@ bool Model::operator==(const Model& rhs) const {
       }
       // make sure we don't have equivalent periodic boundaries
       else if (name == Utils::SettingsNames::periodicBoundaries) {
+        if (!comparePbc) {
+          rhsIterator++;
+          continue;
+        }
         try {
           auto lhsPbc = Utils::PeriodicBoundaries(lhsModelEntryRef.get());
           auto rhsPbc = Utils::PeriodicBoundaries(rhsModelEntryRef.get());
diff --git a/src/Database/Database/Objects/Model.h b/src/Database/Database/Objects/Model.h
index ed7c10d..4ba9f90 100644
--- a/src/Database/Database/Objects/Model.h
+++ b/src/Database/Database/Objects/Model.h
@@ -113,6 +113,7 @@ class Model {
    */
   bool operator==(const Model& rhs) const;
   bool operator!=(const Model& rhs) const;
+  bool equalWithoutPeriodicBoundaryCheck(const Model& rhs) const;
 
   /**
    * @brief If the given entry is interpreted as None, i.e., and empty string or case insensitive 'none'
@@ -136,6 +137,8 @@ class Model {
  private:
   static const std::vector<std::string>& skipFields();
 
+  bool equality(const Model& rhs, bool comparePbc) const;
+
   std::map<std::string, std::reference_wrapper<std::string>> getSettingsModelPairs() {
     // reference wrapper instead of unique ptr because of std::pair
     std::map<std::string, std::reference_wrapper<std::string>> settingsModelPairs;
diff --git a/src/Database/Database/Objects/Object.cpp b/src/Database/Database/Objects/Object.cpp
index 5654184..a8ab440 100644
--- a/src/Database/Database/Objects/Object.cpp
+++ b/src/Database/Database/Objects/Object.cpp
@@ -87,6 +87,7 @@ bsoncxx::document::value Object::getRawContent() const {
   if (!_collection)
     throw Exceptions::MissingLinkedCollectionException();
   auto selection = document{} << "_id" << this->id().bsoncxx() << finalize;
+  // do not add projection here, because we want the whole document
   auto optional = _collection->mongocxx().find_one(selection.view());
   if (!optional)
     throw Exceptions::IDNotFoundException();
@@ -125,7 +126,9 @@ void Object::wipe(bool expectPresence) {
     throw Exceptions::MissingLinkedCollectionException();
   auto selection = document{} << "_id" << this->id().bsoncxx() << finalize;
   if (expectPresence) {
-    auto optional = _collection->mongocxx().find_one(selection.view());
+    auto options = mongocxx::options::find();
+    options.projection(document{} << "_id" << 1 << finalize);
+    auto optional = _collection->mongocxx().find_one(selection.view(), options);
     if (!optional)
       throw Exceptions::IDNotFoundException();
   }
@@ -187,7 +190,9 @@ void Object::touch() const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Object::enable_analysis() {
@@ -203,7 +208,9 @@ void Object::enable_analysis() {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Object::enable_exploration() {
@@ -219,7 +226,9 @@ void Object::enable_exploration() {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Object::disable_analysis() {
@@ -235,7 +244,9 @@ void Object::disable_analysis() {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Object::disable_exploration() {
@@ -251,7 +262,9 @@ void Object::disable_exploration() {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 bool Object::analyze() {
diff --git a/src/Database/Database/Objects/Property.cpp b/src/Database/Database/Objects/Property.cpp
index 85d9361..b6285ef 100644
--- a/src/Database/Database/Objects/Property.cpp
+++ b/src/Database/Database/Objects/Property.cpp
@@ -81,7 +81,9 @@ void Property::setPropertyName(const std::string& name) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 Model Property::getModel() const {
diff --git a/src/Database/Database/Objects/Reaction.cpp b/src/Database/Database/Objects/Reaction.cpp
index 8ea9245..c30af5c 100644
--- a/src/Database/Database/Objects/Reaction.cpp
+++ b/src/Database/Database/Objects/Reaction.cpp
@@ -129,7 +129,9 @@ void Reaction::addElementaryStep(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Reaction::removeElementaryStep(const ID& id) const {
@@ -145,7 +147,9 @@ void Reaction::removeElementaryStep(const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 int Reaction::hasElementarySteps() const {
@@ -223,7 +227,9 @@ void Reaction::addReactant(const ID& id, const SIDE side, COMPOUND_OR_FLASK type
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
   if (side == SIDE::BOTH || side == SIDE::RHS) {
     auto selection = document{} << "_id" << this->id().bsoncxx() << finalize;
@@ -239,7 +245,9 @@ void Reaction::addReactant(const ID& id, const SIDE side, COMPOUND_OR_FLASK type
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
 }
 
@@ -257,7 +265,9 @@ void Reaction::removeReactant(const ID& id, const SIDE side) const {
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
   if (side == SIDE::BOTH || side == SIDE::RHS) {
     auto selection = document{} << "_id" << this->id().bsoncxx() << finalize;
@@ -270,7 +280,9 @@ void Reaction::removeReactant(const ID& id, const SIDE side) const {
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
 }
 
@@ -307,7 +319,9 @@ void Reaction::setReactants(const std::vector<ID>& ids, const SIDE side, const s
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
   if (side == SIDE::BOTH || side == SIDE::RHS) {
     auto selection = document{} << "_id" << this->id().bsoncxx() << finalize;
@@ -320,7 +334,9 @@ void Reaction::setReactants(const std::vector<ID>& ids, const SIDE side, const s
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
 }
 
@@ -415,7 +431,7 @@ COMPOUND_OR_FLASK Reaction::getReactantType(const ID& id) const {
   // clang-format on
   mongocxx::options::find options{};
   options.projection(document{} << "lhs" << 1 << "rhs" << 1 << finalize);
-  auto optional = _collection->mongocxx().find_one(selection.view());
+  auto optional = _collection->mongocxx().find_one(selection.view(), options);
   if (!optional)
     throw Exceptions::MissingIdOrField();
   auto view = optional.value().view();
@@ -454,7 +470,9 @@ void Reaction::clearReactants(const SIDE side) const {
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
   if (side == SIDE::BOTH || side == SIDE::RHS) {
     auto selection = document{} << "_id" << this->id().bsoncxx() << finalize;
@@ -467,7 +485,9 @@ void Reaction::clearReactants(const SIDE side) const {
                                << close_document
                              << finalize;
     // clang-format on
-    _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+    auto options = mongocxx::options::find_one_and_update();
+    options.projection(document{} << "_id" << 1 << finalize);
+    _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
   }
 }
 
diff --git a/src/Database/Database/Objects/Structure.cpp b/src/Database/Database/Objects/Structure.cpp
index abde495..3b17d29 100644
--- a/src/Database/Database/Objects/Structure.cpp
+++ b/src/Database/Database/Objects/Structure.cpp
@@ -132,21 +132,36 @@ Utils::AtomCollection Structure::getAtoms() const {
     throw Exceptions::MissingIdOrField();
   auto view = optional.value().view();
   // Read number of atoms
-  auto nAtoms = view["nAtoms"].get_int32();
-  // Read atoms in AtomCollection
-  Utils::AtomCollection atoms;
-  atoms.resize(nAtoms);
+  auto nAtoms = Fields::getInteger<int>(view, "nAtoms");
   bsoncxx::array::view atomsView = view["atoms"].get_array();
-  for (int i = 0; i < nAtoms; i++) {
-    const auto atom = atomsView[i];
-    std::string symbol = atom["element"].get_utf8().value.to_string();
-    const auto e = Utils::ElementInfo::elementTypeForSymbol(symbol);
-    const double x = atom["x"].get_double();
-    const double y = atom["y"].get_double();
-    const double z = atom["z"].get_double();
-    atoms.setElement(i, e);
-    atoms.setPosition(i, Eigen::Vector3d(x, y, z));
-  }
+  // Read atoms in AtomCollection
+  std::vector<Utils::ElementType> elements;
+  Eigen::Matrix<double, Eigen::Dynamic, 3, Eigen::RowMajor> coordinates =
+      Eigen::Matrix<double, Eigen::Dynamic, 3, Eigen::RowMajor>::Zero(nAtoms, 3);
+  /*
+   * Note that the loop
+   * for(const auto& atom : atomsView) {
+   *   ...
+   * }
+   * is significantly faster than its index-based equivalent
+   * for (int i = 0; i < nAtoms; i++) {
+   *   const auto atom = atomsView[i];
+   *   ...
+   * }
+   * Therefore, we use a somewhat awkward counter for the atom index.
+   *
+   */
+  unsigned int iAtom = 0;
+  for (const auto& atom : atomsView) {
+    const std::string symbol = atom["element"].get_utf8().value.to_string();
+    elements.push_back(Utils::ElementInfo::elementTypeForSymbol(symbol));
+    coordinates(iAtom, 0) = atom["x"].get_double();
+    coordinates(iAtom, 1) = atom["y"].get_double();
+    coordinates(iAtom, 2) = atom["z"].get_double();
+    iAtom++;
+  }
+
+  Utils::AtomCollection atoms(elements, coordinates);
   return atoms;
 }
 
@@ -178,7 +193,9 @@ void Structure::setAtoms(const Utils::AtomCollection& atoms) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto projection = document{} << "_id" << 1 << "_objecttype" << 1 << finalize;
+  auto options = mongocxx::options::find_one_and_update();
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 int Structure::hasAtoms() const {
@@ -193,9 +210,7 @@ int Structure::hasAtoms() const {
   if (!optional)
     throw Exceptions::MissingIdOrField();
   auto view = optional.value().view();
-  if (view["nAtoms"].type() != bsoncxx::types::b_int32::type_id)
-    throw Exceptions::MissingIdOrField();
-  return view["nAtoms"].get_int32();
+  return Fields::getInteger<int>(view, "nAtoms");
 }
 
 void Structure::clearAtoms() const {
@@ -212,7 +227,9 @@ void Structure::clearAtoms() const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 /*=========*
@@ -348,7 +365,9 @@ void Structure::addProperty(const std::string& key, const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Structure::removeProperty(const std::string& key, const ID& id) const {
@@ -364,7 +383,9 @@ void Structure::removeProperty(const std::string& key, const ID& id) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Structure::setProperties(const std::string& key, const std::vector<ID>& ids) const {
@@ -384,7 +405,9 @@ void Structure::setProperties(const std::string& key, const std::vector<ID>& ids
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 std::vector<ID> Structure::getProperties(const std::string& key) const {
@@ -419,11 +442,13 @@ std::vector<ID> Structure::queryProperties(const std::string& key, const Model&
     return {};
   const auto& ids = it->second;
 
+  mongocxx::options::find options{};
+  options.projection(document{} << "model" << 1 << finalize);
   // Setup selection for query in properties
   std::vector<ID> ret;
   for (const auto& id : ids) {
     auto selection = document{} << "_id" << id.bsoncxx() << finalize;
-    auto optional = collection->mongocxx().find_one(selection.view());
+    auto optional = collection->mongocxx().find_one(selection.view(), options);
     if (!optional)
       throw Exceptions::MissingIdOrField();
     auto doc = optional.value().view();
@@ -457,7 +482,9 @@ void Structure::clearProperties(const std::string& key) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 std::map<std::string, std::vector<ID>> Structure::getAllProperties() const {
@@ -504,7 +531,9 @@ void Structure::setAllProperties(const std::map<std::string, std::vector<ID>>& p
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Structure::clearAllProperties() const {
@@ -520,7 +549,9 @@ void Structure::clearAllProperties() const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 /*================*
@@ -568,7 +599,9 @@ void Structure::addCalculation(const std::string& key, const ID& id) const {
                            << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Structure::addCalculations(const std::string& key, const std::vector<ID>& ids) const {
@@ -588,7 +621,9 @@ void Structure::addCalculations(const std::string& key, const std::vector<ID>& i
                            << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Structure::removeCalculation(const std::string& key, const ID& id) const {
@@ -604,7 +639,9 @@ void Structure::removeCalculation(const std::string& key, const ID& id) const {
                            << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Structure::setCalculations(const std::string& key, const std::vector<ID>& ids) const {
@@ -624,7 +661,9 @@ void Structure::setCalculations(const std::string& key, const std::vector<ID>& i
                            << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 std::vector<ID> Structure::getCalculations(const std::string& key) const {
@@ -666,7 +705,9 @@ std::vector<ID> Structure::queryCalculations(const std::string& key, const Model
   }
 
   auto selection = document{} << "_id" << open_document << "$in" << array << close_document << finalize;
-  auto cursor = collection->mongocxx().find(selection.view());
+  mongocxx::options::find options{};
+  options.projection(document{} << "model" << 1 << finalize);
+  auto cursor = collection->mongocxx().find(selection.view(), options);
   std::vector<ID> ret;
   for (const auto& doc : cursor) {
     Model docModel(doc["model"].get_document().view());
@@ -699,7 +740,9 @@ void Structure::clearCalculations(const std::string& key) const {
                            << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 std::map<std::string, std::vector<ID>> Structure::getAllCalculations() const {
@@ -746,7 +789,9 @@ void Structure::setAllCalculations(const std::map<std::string, std::vector<ID>>&
                            << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Structure::clearAllCalculations() const {
@@ -762,7 +807,9 @@ void Structure::clearAllCalculations() const {
                            << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 /*===================*
@@ -800,7 +847,9 @@ void Structure::setGraph(const std::string& key, const std::string& graph) const
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 void Structure::removeGraph(const std::string& key) const {
@@ -816,7 +865,9 @@ void Structure::removeGraph(const std::string& key) const {
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 bool Structure::hasGraph(const std::string& key) const {
@@ -869,7 +920,9 @@ void Structure::setGraphs(const std::map<std::string, std::string>& graphs) cons
                              << close_document
                            << finalize;
   // clang-format on
-  _collection->mongocxx().find_one_and_update(selection.view(), update.view());
+  auto options = mongocxx::options::find_one_and_update();
+  options.projection(document{} << "_id" << 1 << finalize);
+  _collection->mongocxx().find_one_and_update(selection.view(), update.view(), options);
 }
 
 /*===========*
@@ -910,6 +963,9 @@ ID Structure::getOriginal() const {
   if (!this->hasOriginal()) {
     throw Exceptions::MissingIdOrField();
   }
+  if (*this->_id == Fields::get<ID>(*this, "duplicate_of")) {
+    throw Exceptions::SelfDuplicateException();
+  }
   return Fields::get<ID>(*this, "duplicate_of");
 }
 
diff --git a/src/Database/Database/Objects/ValueCollection.cpp b/src/Database/Database/Objects/ValueCollection.cpp
index 020ff5a..b6a54bb 100644
--- a/src/Database/Database/Objects/ValueCollection.cpp
+++ b/src/Database/Database/Objects/ValueCollection.cpp
@@ -7,10 +7,10 @@
 
 #include "Database/Objects/ValueCollection.h"
 #include "Database/Exceptions.h"
+#include "Database/Objects/Impl/Fields.h"
 #include "Utils/UniversalSettings/GenericValueVariant.h"
 #include <bsoncxx/builder/basic/array.hpp>
 #include <bsoncxx/types/value.hpp>
-#include <map>
 #include <tuple>
 
 namespace Scine {
@@ -63,6 +63,15 @@ void array_append(bsoncxx::builder::basic::array& array, const std::string& v) {
 void array_append(bsoncxx::builder::basic::array& array, const Utils::UniversalSettings::ValueCollection& v) {
   array.append(ValueCollection::serialize(v));
 }
+void array_append(bsoncxx::builder::basic::array& array, const std::vector<int>& v) {
+  /*
+   * MongoDB does not support arrays of arrays. Therefore, we construct an array of value collections.
+   * These value collections then contain exactly one array which is the inner array.
+   */
+  Utils::UniversalSettings::ValueCollection newValueCollection;
+  newValueCollection.addIntList(subListKey, v);
+  array.append(ValueCollection::serialize(newValueCollection));
+}
 
 // Blanket impl for IntList, DoubleList, StringList and CollectionList
 template<typename T>
@@ -103,6 +112,13 @@ struct ListTypeHint<Utils::UniversalSettings::ValueCollection> {
   }
 };
 
+template<>
+struct ListTypeHint<std::vector<int>> {
+  static std::string value() {
+    return "list_of_lists";
+  }
+};
+
 template<typename T>
 void anon_serialize(bsoncxx::builder::basic::document& document, const std::string& key, const std::vector<T>& v) {
   bsoncxx::builder::basic::document builder{};
@@ -133,16 +149,16 @@ Utils::UniversalSettings::GenericValue GenericValue::deserialize(const BsonValue
   if (type == bsoncxx::type::k_bool) {
     return Utils::UniversalSettings::GenericValue::fromBool(value.get_bool());
   }
-  else if (type == bsoncxx::type::k_int32) {
-    return Utils::UniversalSettings::GenericValue::fromInt(value.get_int32());
+  if (type == bsoncxx::type::k_int32) {
+    return Utils::UniversalSettings::GenericValue::fromInt(Fields::getIntegerFromElement<BsonValueType, int>(value));
   }
-  else if (type == bsoncxx::type::k_double) {
+  if (type == bsoncxx::type::k_double) {
     return Utils::UniversalSettings::GenericValue::fromDouble(value.get_double());
   }
-  else if (type == bsoncxx::type::k_utf8) {
+  if (type == bsoncxx::type::k_utf8) {
     return Utils::UniversalSettings::GenericValue::fromString(value.get_utf8().value.to_string());
   }
-  else if (type == bsoncxx::type::k_document) {
+  if (type == bsoncxx::type::k_document) {
     /* Possible types:
      * - IntList, DoubleList, StringList, CollectionList (has type and list elements)
      * - ParametrizedOptionValue (has selectedOption member)
@@ -156,45 +172,50 @@ Utils::UniversalSettings::GenericValue GenericValue::deserialize(const BsonValue
       auto array = document.view()["list"].get_array();
       if (typeString == ListTypeHint<int>::value()) {
         std::vector<int> vs;
-        for (auto v : array.value) {
-          vs.push_back(v.get_int32());
+        for (const auto v : array.value) {
+          vs.push_back(Fields::getIntegerFromElement<bsoncxx::array::element, int>(v));
         }
         return Utils::UniversalSettings::GenericValue::fromIntList(std::move(vs));
       }
-      else if (typeString == ListTypeHint<double>::value()) {
+      if (typeString == ListTypeHint<double>::value()) {
         std::vector<double> vs;
-        for (auto v : array.value) {
+        for (const auto v : array.value) {
           vs.push_back(v.get_double());
         }
         return Utils::UniversalSettings::GenericValue::fromDoubleList(std::move(vs));
       }
-      else if (typeString == ListTypeHint<std::string>::value()) {
+      if (typeString == ListTypeHint<std::string>::value()) {
         std::vector<std::string> vs;
-        for (auto v : array.value) {
+        for (const auto v : array.value) {
           vs.push_back(v.get_utf8().value.to_string());
         }
         return Utils::UniversalSettings::GenericValue::fromStringList(std::move(vs));
       }
-      else if (typeString == ListTypeHint<Utils::UniversalSettings::ValueCollection>::value()) {
+      if (typeString == ListTypeHint<Utils::UniversalSettings::ValueCollection>::value()) {
         std::vector<Utils::UniversalSettings::ValueCollection> vs;
         for (auto v : array.value) {
           vs.push_back(ValueCollection::deserialize(v.get_document()));
         }
         return Utils::UniversalSettings::GenericValue::fromCollectionList(std::move(vs));
       }
-      else {
-        throw Exceptions::MissingIdOrField();
+      if (typeString == ListTypeHint<std::vector<int>>::value()) {
+        std::vector<std::vector<int>> listOfLists;
+        for (auto v : array.value) {
+          auto collection = ValueCollection::deserialize(v.get_document());
+          listOfLists.push_back(collection.getIntList(subListKey));
+        }
+        return Utils::UniversalSettings::GenericValue::fromIntListList(std::move(listOfLists));
       }
+
+      throw Exceptions::MissingIdOrField();
     }
-    else if (document.view().find("selectedOption") != document.view().end()) {
+    if (document.view().find("selectedOption") != document.view().end()) {
       Utils::UniversalSettings::ParametrizedOptionValue option{
           document.view()["selectedOption"].get_utf8().value.to_string(),
           ValueCollection::deserialize(document.view()["optionSettings"].get_document())};
       return Utils::UniversalSettings::GenericValue::fromOptionWithSettings(std::move(option));
     }
-    else {
-      return Utils::UniversalSettings::GenericValue::fromCollection(ValueCollection::deserialize(document));
-    }
+    return Utils::UniversalSettings::GenericValue::fromCollection(ValueCollection::deserialize(document));
   }
 
   throw Exceptions::MissingIdOrField();
diff --git a/src/Database/Database/Objects/ValueCollection.h b/src/Database/Database/Objects/ValueCollection.h
index f4779fd..9f4bd34 100644
--- a/src/Database/Database/Objects/ValueCollection.h
+++ b/src/Database/Database/Objects/ValueCollection.h
@@ -13,6 +13,7 @@
 #include "boost/optional.hpp"
 #include <bsoncxx/builder/basic/document.hpp>
 #include <bsoncxx/types.hpp>
+#include <string>
 
 namespace Scine {
 namespace Database {
@@ -29,6 +30,7 @@ struct GenericValue {
                         const Utils::UniversalSettings::GenericValue& value);
   static Utils::UniversalSettings::GenericValue deserialize(const BsonValueType& value);
 };
+const static std::string subListKey = "sub_list";
 
 struct ValueCollection {
   static bsoncxx::v_noabi::document::value serialize(const Utils::UniversalSettings::ValueCollection& collection);
diff --git a/src/Database/Database/Version.h b/src/Database/Database/Version.h
index 24090c7..909d333 100644
--- a/src/Database/Database/Version.h
+++ b/src/Database/Database/Version.h
@@ -16,7 +16,7 @@ namespace Database {
 namespace Version {
 
 constexpr static const int major = 1;
-constexpr static const int minor = 2;
+constexpr static const int minor = 3;
 constexpr static const int patch = 0;
 
 } // namespace Version
diff --git a/src/Database/Python/CompoundPython.cpp b/src/Database/Python/CompoundPython.cpp
index 0288752..7686d7e 100644
--- a/src/Database/Python/CompoundPython.cpp
+++ b/src/Database/Python/CompoundPython.cpp
@@ -25,10 +25,12 @@ void init_compound(pybind11::class_<Compound, Object>& compound) {
     )delim");
   compound.def(pybind11::init<const ID&, const Object::CollectionPtr&>(), pybind11::arg("id"), pybind11::arg("collection"));
 
-  compound.def_static("make", pybind11::overload_cast<const std::vector<ID>&, const Object::CollectionPtr&>(&Compound::create),
-                      pybind11::arg("structure_ids"), pybind11::arg("collection"));
+  compound.def_static(
+      "make", pybind11::overload_cast<const std::vector<ID>&, const Object::CollectionPtr&, bool>(&Compound::create),
+      pybind11::arg("structure_ids"), pybind11::arg("collection"), pybind11::arg("exploration_disabled") = false);
 
-  compound.def("create", pybind11::overload_cast<const std::vector<ID>&>(&Compound::create), pybind11::arg("structure_ids"),
+  compound.def("create", pybind11::overload_cast<const std::vector<ID>&, bool>(&Compound::create),
+               pybind11::arg("structure_ids"), pybind11::arg("exploration_disabled") = false,
                R"delim(
       Generates a new compound in the linked collection from a list of
       structure IDs.
diff --git a/src/Database/Python/ElementaryStepPython.cpp b/src/Database/Python/ElementaryStepPython.cpp
index 87ecb81..ddfecb5 100644
--- a/src/Database/Python/ElementaryStepPython.cpp
+++ b/src/Database/Python/ElementaryStepPython.cpp
@@ -131,9 +131,6 @@ void init_elementary_step(pybind11::module& m) {
   pybind11::enum_<ElementaryStepType> estype(m, "ElementaryStepType");
   estype.value("REGULAR", ElementaryStepType::REGULAR, "A regular elementary step that involves exactly one transition state.");
   estype.value("BARRIERLESS", ElementaryStepType::BARRIERLESS, "An elementary step that has no barrier/ transition state");
-  estype.value("MODEL_TRANSFORMATION", ElementaryStepType::MODEL_TRANSFORMATION,
-               "An elementary step that describes the transformation between"
-               "electronic structure models.");
   elementaryStep.def("get_type", &ElementaryStep::getType);
   elementaryStep.def("set_type", &ElementaryStep::setType);
   elementaryStep.def("get_barrier_from_spline", &ElementaryStep::getBarrierFromSpline, R"delim(
diff --git a/src/Database/Python/FlaskPython.cpp b/src/Database/Python/FlaskPython.cpp
index 86557dd..3cd03f9 100644
--- a/src/Database/Python/FlaskPython.cpp
+++ b/src/Database/Python/FlaskPython.cpp
@@ -26,18 +26,19 @@ void init_flask(pybind11::class_<Flask, Object>& flask) {
     )delim");
   flask.def(pybind11::init<const ID&, const Object::CollectionPtr&>(), pybind11::arg("id"), pybind11::arg("collection"));
 
-  flask.def_static(
-      "make",
-      pybind11::overload_cast<const std::vector<ID>&, const std::vector<ID>&, const Object::CollectionPtr&>(&Flask::create),
-      pybind11::arg("structure_ids"), pybind11::arg("compound_ids"), pybind11::arg("collection"),
-      R"delim(
+  flask.def_static("make",
+                   pybind11::overload_cast<const std::vector<ID>&, const std::vector<ID>&, const Object::CollectionPtr&, bool>(
+                       &Flask::create),
+                   pybind11::arg("structure_ids"), pybind11::arg("compound_ids"), pybind11::arg("collection"),
+                   pybind11::arg("exploration_disabled") = false,
+                   R"delim(
       Create a new flask with a database ID.
 
       :returns: A Flask object linked to the given collection.
     )delim");
 
-  flask.def("create", pybind11::overload_cast<const std::vector<ID>&, const std::vector<ID>&>(&Flask::create),
-            pybind11::arg("structure_ids"), pybind11::arg("compound_ids"),
+  flask.def("create", pybind11::overload_cast<const std::vector<ID>&, const std::vector<ID>&, bool>(&Flask::create),
+            pybind11::arg("structure_ids"), pybind11::arg("compound_ids"), pybind11::arg("exploration_disabled") = false,
             R"delim(
       Generates a new flask in the linked collection from a list of
       structure IDs and compoud IDs. Stores the generated ID in the
diff --git a/src/Database/Python/ModelPython.cpp b/src/Database/Python/ModelPython.cpp
index b995d27..be6d3db 100644
--- a/src/Database/Python/ModelPython.cpp
+++ b/src/Database/Python/ModelPython.cpp
@@ -121,6 +121,8 @@ void init_model(pybind11::module& m) {
   model.def("__copy__", [](const Model& self) -> Model { return Model(self); });
   model.def("__deepcopy__", [](const Model& self, pybind11::dict /* memo */) -> Model { return Model(self); });
   // Comparison operators
+  model.def("equal_without_periodic_boundary_check", &Model::equalWithoutPeriodicBoundaryCheck, pybind11::arg("rhs"),
+            "Compares to another model without checking for equal periodic boundaries");
   model.def(pybind11::self == pybind11::self);
   model.def(pybind11::self != pybind11::self);
   model.def(pybind11::pickle(
diff --git a/src/Database/Python/Tests/elementary_step_test.py b/src/Database/Python/Tests/elementary_step_test.py
index e9b1405..236fd56 100644
--- a/src/Database/Python/Tests/elementary_step_test.py
+++ b/src/Database/Python/Tests/elementary_step_test.py
@@ -183,10 +183,6 @@ def test_type(self):
         step.set_type(db.ElementaryStepType.BARRIERLESS)
         assert db.ElementaryStepType.BARRIERLESS == step.get_type()
         assert db.ElementaryStepType.REGULAR != step.get_type()
-        step.set_type(db.ElementaryStepType.MODEL_TRANSFORMATION)
-        assert db.ElementaryStepType.MODEL_TRANSFORMATION == step.get_type()
-        assert db.ElementaryStepType.BARRIERLESS != step.get_type()
-        assert db.ElementaryStepType.REGULAR != step.get_type()
 
     def test_type_fails_collection(self):
         step = db.ElementaryStep(db.ID())
diff --git a/src/Database/Python/Tests/model_test.py b/src/Database/Python/Tests/model_test.py
index acb10ad..06ad4cb 100644
--- a/src/Database/Python/Tests/model_test.py
+++ b/src/Database/Python/Tests/model_test.py
@@ -9,6 +9,7 @@
 import unittest
 import os
 import pickle
+from copy import deepcopy
 
 
 class ModelTest(unittest.TestCase):
@@ -118,11 +119,14 @@ def test_equality_works(self):
         lhs = db.Model("dft", "any", "none", "none")
         rhs = db.Model("dft", "something", "", "none")
         assert lhs == rhs
+        assert lhs.equal_without_periodic_boundary_check(rhs)
         lhs.program = "sparrow"
         rhs.program = "sparrow"
         assert lhs == rhs
+        assert lhs.equal_without_periodic_boundary_check(rhs)
         rhs.program = "something_different"
         assert lhs != rhs
+        assert not lhs.equal_without_periodic_boundary_check(rhs)
         lhs.program = "any"
         rhs.program = "something"
         assert lhs == rhs
@@ -130,6 +134,11 @@ def test_equality_works(self):
         assert lhs != rhs
         rhs.program = ""
         assert lhs != rhs
+        another = deepcopy(rhs)
+        assert another.equal_without_periodic_boundary_check(rhs)
+        another.periodic_boundaries = "5.0,5.0,5.0,90.0,90.0,90.0,xyz"
+        assert another != rhs
+        assert another.equal_without_periodic_boundary_check(rhs)
 
     def test_model_output_string(self):
         m = db.Model("any", "any", "any", "any")
diff --git a/src/Database/Python/Tests/test_database_setup.py b/src/Database/Python/Tests/test_database_setup.py
index 945d2f7..955a9b5 100644
--- a/src/Database/Python/Tests/test_database_setup.py
+++ b/src/Database/Python/Tests/test_database_setup.py
@@ -34,6 +34,18 @@ def _water() -> utils.AtomCollection:
     return utils.AtomCollection(elements, positions)
 
 
+def _water_cbor() -> str:
+    return "pGFhg6VhYQBhYwBhb4GCAAFhcqRhbIKBAYECY2xua4GiYXCCAAFjc2Vxgw" + \
+           "ABAmJscoKBAIEBYXOCgQGBAmFzAaVhYQBhYwFhb4GCAAFhcqRhbIKBAIEC" + \
+           "Y2xua4GiYXCCAAFjc2VxgwEAAmJscoKBAIEBYXOCgQCBAmFzAaVhYQBhYw" + \
+           "Jhb4GCAAFhcqRhbIKBAIEBY2xua4GiYXCCAAFjc2VxgwIAAWJscoGCAAFh" + \
+           "c4GCAAFhcwFhYw9hZ6JhRYODAAEAgwACAIMBAgBhWoMBAQhhdoMCAAA="
+
+
+def _water_split_cbor() -> str:
+    return "o2FjD2FnomFFgYMAAQBhWoIBCGF2gwIAAA==;o2FjD2FnomFFgGFagQFhdoMCAAA="
+
+
 def get_test_db_credentials(name: str = "chemoton_unittests") -> db.Credentials:
     """
     Generate a set of credentials pointing to a database and server.
@@ -261,6 +273,7 @@ def _insert_flask(
     complex = db.Structure()
     complex.link(structures)
     complex.create(_water(), 0, 1)
+    complex.set_graph("masm_cbor_graph", _water_split_cbor())
     complex.set_label(db.Label.COMPLEX_OPTIMIZED)
     complex.set_aggregate(flask.get_id())
     complex.set_model(db.Model("FAKE", "FAKE", "F-AKE"))
@@ -355,6 +368,7 @@ def _fake_structure(
         structure.set_label(db.Label.USER_OPTIMIZED)
     else:
         structure.set_label(db.Label.MINIMUM_OPTIMIZED)
+    structure.set_graph("masm_cbor_graph", _water_cbor())
     structure.set_aggregate(compound.get_id())
     structure.set_model(model)
     add_random_energy(structure, energy_limits, properties, model)
@@ -579,8 +593,10 @@ def insert_single_empty_structure_aggregate(manager: db.Manager, label: db.Label
     aggregate.link(aggregates)
     if build_flask:
         aggregate.create([structure.get_id()], [])  # type: ignore
+        structure.set_graph("masm_cbor_graph", _water_split_cbor())
     else:
         aggregate.create([structure.get_id()])  # type: ignore
+        structure.set_graph("masm_cbor_graph", _water_cbor())
     aggregate.disable_exploration()
     structure.set_aggregate(aggregate.get_id())
     structure.set_label(label)
@@ -613,6 +629,7 @@ def insert_single_empty_structure_flask(manager: db.Manager, label: db.Label) ->
     flask.create([structure.get_id()], [])
     flask.disable_exploration()
     structure.set_aggregate(flask.get_id())
+    structure.set_graph("masm_cbor_graph", _water_split_cbor())
     structure.set_label(label)
     structure.set_model(db.Model("FAKE", "FAKE", "F-AKE"))
 
diff --git a/src/Database/Python/Tests/test_energy_query_functions.py b/src/Database/Python/Tests/test_energy_query_functions.py
index f82955c..572778a 100644
--- a/src/Database/Python/Tests/test_energy_query_functions.py
+++ b/src/Database/Python/Tests/test_energy_query_functions.py
@@ -10,7 +10,9 @@
 import scine_database as db
 import test_database_setup as db_setup
 from scine_database.energy_query_functions import (
-    get_min_free_energy_for_aggregate
+    get_min_free_energy_for_aggregate,
+    barrier_from_rate_constant,
+    rate_constant_from_barrier
 )
 
 
@@ -77,3 +79,10 @@ def test_get_min_free_energy_for_aggregate(self):
                    - (energies[len(energies) - 2] + gibbs_correction_2[len(gibbs_correction_2) - 2])) < 1e-12
 
         manager.wipe()
+
+    def test_barrier_to_rate_transformation(self):
+        temperature = 298.15
+        barrier = 42.0  # in kJ / mol
+
+        rate = rate_constant_from_barrier(barrier, temperature)
+        assert abs(barrier_from_rate_constant(rate, temperature) / 1000 - barrier) < 1e-12
diff --git a/src/Database/Python/energy_query_functions.py b/src/Database/Python/energy_query_functions.py
index c306dcd..8024cd9 100644
--- a/src/Database/Python/energy_query_functions.py
+++ b/src/Database/Python/energy_query_functions.py
@@ -6,13 +6,15 @@
 """
 
 # Standard library imports
-from typing import Union, Tuple, List, Optional
+from typing import Union, Tuple, List, Optional, TypeVar
 import math
 
 # Third party imports
 import numpy as np
 import scine_database as db
 import scine_utilities as utils
+# Type hint for float or numpy array
+float_or_ndarray = TypeVar('float_or_ndarray', float, np.ndarray)
 
 
 def get_elementary_step_with_min_ts_energy(reaction: db.Reaction,
@@ -62,13 +64,15 @@ def get_elementary_step_with_min_ts_energy(reaction: db.Reaction,
         es = db.ElementaryStep(es_id, elementary_steps)
         # # # Type check elementary step and break if barrierless
         if not es.has_transition_state():
-            first_structure_lhs = db.Structure(es.get_reactants()[0][0], structures)
-            if structure_model is not None and first_structure_lhs.get_model() != structure_model:
+            es_structures = [db.Structure(s_id, structures) for s_id in es.get_reactants()[0]] +\
+                            [db.Structure(s_id, structures) for s_id in es.get_reactants()[1]]
+            # # # Check all models of the structures
+            if structure_model is not None and\
+               any(es_struct.get_model() != structure_model for es_struct in es_structures):
                 continue
-            # # # Energy Check for minima
-            first_structure_lhs_energy = get_energy_for_structure(first_structure_lhs, energy_type, model,
-                                                                  structures, properties)
-            if first_structure_lhs_energy is None:
+            # # # Check all energies of the structures
+            if any(get_energy_for_structure(es_struct, energy_type, model, structures, properties) is None
+                   for es_struct in es_structures):
                 continue
             es_id_with_lowest_ts = es_id
             break
@@ -211,16 +215,16 @@ def get_energy_for_structure(structure: db.Structure, prop_name: str, model: db.
     return prop.get_data()
 
 
-def rate_constant_from_barrier(barrier: float, temperature: float) -> float:
+def rate_constant_from_barrier(barrier: float_or_ndarray, temperature: float) -> float_or_ndarray:
     """
     Calculate a rate constant from its energy [kJ / mol] and temperature according to transition state theory:
     rate-constant = k_B T / h exp[-barrier/(R T)]
 
     Parameters
     ----------
-    barrier :: float
+    barrier : float_or_ndarray
         The reaction barrier in kJ/mol.
-    temperature :: flaot
+    temperature : float
         The temperature in K.
 
     Returns
@@ -235,6 +239,29 @@ def rate_constant_from_barrier(barrier: float, temperature: float) -> float:
     return factor * np.exp(- beta_in_mol_per_j * barrier_j_per_mol)
 
 
+def barrier_from_rate_constant(rate_constant: float_or_ndarray, temperature: float) -> float_or_ndarray:
+    """
+    Calculate a barrier [J / mol] from a rate konstant [s^-1] and temperature [K] according to transition state theory:
+    barrier = log(rate-constant * h / (k_B * T)) * -1 * (R * T)
+
+    Parameters
+    ----------
+    rate_constant : float_or_ndarray
+        The rate constant in s^-1.
+    temperature : float
+        The temperature in K.
+
+    Returns
+    -------
+    The barrier in J/mol.
+    """
+    kbt_in_j = utils.BOLTZMANN_CONSTANT * temperature  # k_B T
+    factor = utils.PLANCK_CONSTANT / kbt_in_j  # h / k_B T
+    rt_in_j_per_mol = utils.MOLAR_GAS_CONSTANT * temperature  # R T
+
+    return -1.0 * rt_in_j_per_mol * np.log(rate_constant * factor)
+
+
 def get_all_energies_for_aggregate(aggregate: Union[db.Compound, db.Flask], model: db.Model, energy_label: str,
                                    structures: db.Collection, properties: db.Collection) -> List[Union[float, None]]:
     all_energies = []
@@ -246,6 +273,28 @@ def get_all_energies_for_aggregate(aggregate: Union[db.Compound, db.Flask], mode
 
 def get_min_energy_for_aggregate(aggregate: Union[db.Compound, db.Flask], model: db.Model, energy_label: str,
                                  structures: db.Collection, properties: db.Collection) -> Optional[float]:
+    """
+    Get the minimum energy for a given aggregate.
+
+    Parameters
+    ----------
+    aggregate : Union[db.Compound, db.Flask]
+        The aggregate for which to retrieve the minimum energy.
+    model : db.Model
+        The database model.
+    energy_label : str
+        The label of the energy property.
+    structures : db.Collection
+        The collection of structures.
+    properties : db.Collection
+        The collection of properties.
+
+    Returns
+    -------
+    Optional[float]
+        The minimum energy value for the aggregate,
+        or None if no energy values are available.
+    """
     all_energies = get_all_energies_for_aggregate(aggregate, model, energy_label, structures, properties)
     if len(all_energies) < 1:
         return None
@@ -261,6 +310,28 @@ def get_min_energy_for_aggregate(aggregate: Union[db.Compound, db.Flask], model:
 def get_min_free_energy_for_aggregate(aggregate: Union[db.Compound, db.Flask], electronic_model: db.Model,
                                       correction_model: db.Model, structures: db.Collection,
                                       properties: db.Collection) -> Optional[float]:
+    """
+    Calculate the minimum free energy for an aggregate.
+    The free energy correction can have a different model than the electronic model.
+
+    Parameters
+    ----------
+    aggregate : Union[db.Compound, db.Flask]
+        The aggregate for which to retrieve the minimum free energy.
+    electronic_model : db.Model
+        The electronic model used for energy calculations.
+    correction_model : db.Model
+        The correction model used for energy calculations.
+    structures : db.Collection
+        The collection of structures.
+    properties : db.Collection
+        The collection of properties.
+
+    Returns
+    -------
+    Optional[float]
+        The minimum free energy of the aggregate, or None if the energy calculation is not possible.
+    """
     equal_models = electronic_model == correction_model
     if equal_models:
         return get_min_energy_for_aggregate(aggregate, electronic_model, "gibbs_free_energy", structures, properties)
diff --git a/src/Database/Python/insert_concentration.py b/src/Database/Python/insert_concentration.py
index 724879a..fb5174c 100644
--- a/src/Database/Python/insert_concentration.py
+++ b/src/Database/Python/insert_concentration.py
@@ -33,7 +33,7 @@ def insert_concentration_for_structure(
         label: str = "start_concentration"):
     concentration_options = ["start_concentration", "max_concentration", "final_concentration", "concentration_flux",
                              "manual_activation"]
-    if label not in concentration_options and "_concentration_flux" not in label:
+    if label not in concentration_options and "_concentration_flux" not in label and "sensitivity" not in label:
         warn(f"Your concentration label is not within the suggested labels {str(concentration_options)}."
              f"This may lead to problems recognizing the concentrations in the individual gears!")
 
diff --git a/src/Database/Python/queries.py b/src/Database/Python/queries.py
index 29868bf..1912333 100644
--- a/src/Database/Python/queries.py
+++ b/src/Database/Python/queries.py
@@ -269,15 +269,17 @@ def calculation_exists_in_structure(job_order: str, structure_id_list: List[db.I
 def calculation_exists_in_id_set(id_selection: Set[str], n_structures: int, calculations: db.Collection,
                                  specific_structures: Optional[List[db.ID]] = None,
                                  settings: Optional[Union[utils.ValueCollection, Dict[str, Any]]] = None,
-                                 auxiliaries: Optional[Dict[str, Any]] = None) -> bool:
+                                 auxiliaries: Optional[Dict[str, Any]] = None,
+                                 job_order: Optional[str] = None) -> bool:
     return query_calculation_in_id_set(id_selection, n_structures, calculations, specific_structures,
-                                       settings, auxiliaries) is not None
+                                       settings, auxiliaries, job_order) is not None
 
 
 def query_calculation_in_id_set(id_selection: Set[str], n_structures: int, calculations: db.Collection,
                                 specific_structures: Optional[List[db.ID]] = None,
                                 settings: Optional[Union[utils.ValueCollection, Dict[str, Any]]] = None,
-                                auxiliaries: Optional[Dict[str, Any]] = None) -> Union[db.ID, None]:
+                                auxiliaries: Optional[Dict[str, Any]] = None,
+                                job_order: Optional[str] = None) -> Union[db.ID, None]:
     """
     Check if a calculation exists that corresponds to the given structures, mode, settings, etc.
 
@@ -300,6 +302,8 @@ def query_calculation_in_id_set(id_selection: Set[str], n_structures: int, calcu
         The settings of the calculation.
     auxiliaries : Optional[Dict[str, Any]]
         The auxiliaries of the calculation.
+    job_order : Optional[str]
+        The job order of the calculation.
 
     Returns
     -------
@@ -340,6 +344,9 @@ def query_calculation_in_id_set(id_selection: Set[str], n_structures: int, calcu
         if auxiliaries is not None:
             if auxiliaries != calculation.get_auxiliaries():
                 continue
+        if job_order is not None:
+            if job_order != calculation.get_job().order:
+                continue
         return calculation.id()
     return None
 
@@ -377,7 +384,7 @@ def get_calculation_id_from_structure(job_order: str, structure_id_list: List[db
     if not calc_id_set:
         return None
     return query_calculation_in_id_set(calc_id_set, len(structure_id_list), calculations, structure_id_list,
-                                       settings, auxiliaries)
+                                       settings, auxiliaries, job_order)
 
 
 def get_calculation_id(job_order: str, structure_id_list: List[db.ID], model: db.Model,
diff --git a/src/Database/Python/setup.py b/src/Database/Python/setup.py
index b8f57f7..a3d37a5 100644
--- a/src/Database/Python/setup.py
+++ b/src/Database/Python/setup.py
@@ -9,7 +9,7 @@
 import os
 
 # Read README.rst for the long description
-with open("README.rst", "r") as fh:
+with open("README.rst", "r", encoding="utf-8") as fh:
     long_description = fh.read()
 
 
diff --git a/src/Database/Tests/CalculationTest.cpp b/src/Database/Tests/CalculationTest.cpp
index d582b04..7ded532 100644
--- a/src/Database/Tests/CalculationTest.cpp
+++ b/src/Database/Tests/CalculationTest.cpp
@@ -314,13 +314,25 @@ TEST_F(CalculationTest, Settings) {
   auto settings = calc.getSettings();
   ASSERT_EQ(settings.size(), 0);
 
+  const std::vector<std::vector<int>> listOfLists = {{0, 1, 2}, {3, 4, 5}, {-1, -2, 9}};
   calc.setSetting("foo", Utils::UniversalSettings::GenericValue::fromString("bar"));
   calc.setSetting("spam", Utils::UniversalSettings::GenericValue::fromInt(4));
+  calc.setSetting("spam_with_eggs", Utils::UniversalSettings::GenericValue::fromIntListList(listOfLists));
   auto settings_db = calc.getSettings();
   ASSERT_EQ(settings_db.getString("foo"), "bar");
   ASSERT_EQ(settings_db.getInt("spam"), 4);
   ASSERT_EQ(calc.getSetting("foo").toString(), "bar");
   ASSERT_EQ(calc.getSetting("spam").toInt(), 4);
+  const std::vector<std::vector<int>> listOfListsFromSettings = calc.getSetting("spam_with_eggs").toIntListList();
+  ASSERT_EQ(listOfListsFromSettings.size(), listOfLists.size());
+  for (unsigned int i = 0; i < listOfListsFromSettings.size(); ++i) {
+    const std::vector<int> sublist = listOfListsFromSettings[i];
+    const std::vector<int> sublistRef = listOfLists[i];
+    ASSERT_EQ(sublist.size(), sublistRef.size());
+    for (unsigned int j = 0; j < sublist.size(); ++j) {
+      ASSERT_EQ(sublist[j], sublistRef[j]);
+    }
+  }
 
   calc.removeSetting("foo");
   settings_db = calc.getSettings();
diff --git a/src/Database/Tests/ElementaryStepTest.cpp b/src/Database/Tests/ElementaryStepTest.cpp
index 9e78c27..4ab59de 100644
--- a/src/Database/Tests/ElementaryStepTest.cpp
+++ b/src/Database/Tests/ElementaryStepTest.cpp
@@ -171,10 +171,6 @@ TEST_F(ElementaryStepTest, Type) {
   step.setType(ElementaryStepType::BARRIERLESS);
   ASSERT_EQ(ElementaryStepType::BARRIERLESS, step.getType());
   ASSERT_NE(ElementaryStepType::REGULAR, step.getType());
-  step.setType(ElementaryStepType::MODEL_TRANSFORMATION);
-  ASSERT_EQ(ElementaryStepType::MODEL_TRANSFORMATION, step.getType());
-  ASSERT_NE(ElementaryStepType::REGULAR, step.getType());
-  ASSERT_NE(ElementaryStepType::BARRIERLESS, step.getType());
 }
 
 TEST_F(ElementaryStepTest, TypeFails1) {
diff --git a/src/Database/Tests/ModelTest.cpp b/src/Database/Tests/ModelTest.cpp
index 9477070..3e89da5 100644
--- a/src/Database/Tests/ModelTest.cpp
+++ b/src/Database/Tests/ModelTest.cpp
@@ -186,11 +186,14 @@ TEST_F(ModelTest, EqualityWorks) {
   Model lhs("dft", "any", "none", "none");
   Model rhs("dft", "something", "", "none");
   ASSERT_TRUE(lhs == rhs);
+  ASSERT_TRUE(lhs.equalWithoutPeriodicBoundaryCheck(rhs));
   lhs.program = "sparrow";
   rhs.program = "Sparrow";
   ASSERT_TRUE(lhs == rhs);
+  ASSERT_TRUE(lhs.equalWithoutPeriodicBoundaryCheck(rhs));
   rhs.program = "something_different";
   ASSERT_FALSE(lhs == rhs);
+  ASSERT_FALSE(lhs.equalWithoutPeriodicBoundaryCheck(rhs));
   lhs.program = "any";
   rhs.program = "something";
   ASSERT_TRUE(lhs == rhs);
@@ -212,7 +215,9 @@ TEST_F(ModelTest, EqualityWorks) {
   lhs.periodicBoundaries = "any";
   rhs.periodicBoundaries = "ANY";
   ASSERT_TRUE(lhs == rhs);
+  ASSERT_TRUE(lhs.equalWithoutPeriodicBoundaryCheck(rhs));
   rhs.periodicBoundaries = "none";
+  ASSERT_TRUE(lhs.equalWithoutPeriodicBoundaryCheck(rhs));
   ASSERT_FALSE(lhs == rhs);
   rhs.periodicBoundaries = "8.0,10.0,10.0,45.0,90.0,90.0,xyz";
   ASSERT_TRUE(lhs == rhs);
@@ -220,8 +225,10 @@ TEST_F(ModelTest, EqualityWorks) {
   ASSERT_TRUE(lhs == rhs);
   rhs.periodicBoundaries = "8.00,10.0,10.0,45.0,90.0,90.00,xyz";
   ASSERT_TRUE(lhs == rhs);
+  ASSERT_TRUE(lhs.equalWithoutPeriodicBoundaryCheck(rhs));
   rhs.periodicBoundaries = "8.00,10.1,10.0,45.0,90.0,90.00,xyz";
   ASSERT_FALSE(lhs == rhs);
+  ASSERT_TRUE(lhs.equalWithoutPeriodicBoundaryCheck(rhs));
 }
 
 TEST_F(ModelTest, EntryNoneAndAnyChecksWork) {
diff --git a/updates/0_0_x_to_1_0_0.py b/updates/0_0_x_to_1_0_0.py
index 3890351..7376d51 100644
--- a/updates/0_0_x_to_1_0_0.py
+++ b/updates/0_0_x_to_1_0_0.py
@@ -1,3 +1,9 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+__copyright__ = """ This code is licensed under the 3-clause BSD license.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
+See LICENSE.txt for details.
+"""
 from pymongo import MongoClient
 import datetime
 import argparse
@@ -17,13 +23,14 @@
 db_name = args.db_name
 
 
-client = MongoClient(ip, port)
+client: MongoClient = MongoClient(ip, port)
 db = client[db_name]
 
 # Check version
 is_correct_old_version = False
 if "_db_meta_data" in db.list_collection_names():
     meta_data = db["_db_meta_data"].find_one({})
+    assert meta_data
     version = meta_data["version"]
     if version["major"] == 0 and version["minor"] == 0:
         is_correct_old_version = True
@@ -42,6 +49,7 @@
 if "_db_meta_data" in db.list_collection_names():
     _db_meta_data = db["_db_meta_data"]
     meta_data = db["_db_meta_data"].find_one({})
+    assert meta_data
     date = meta_data["_created"]
     db["_db_meta_data"].delete_many({})
 else:
diff --git a/updates/1_0_0_to_1_1_0.py b/updates/1_0_0_to_1_1_0.py
index c3dc4f9..fe7f39f 100644
--- a/updates/1_0_0_to_1_1_0.py
+++ b/updates/1_0_0_to_1_1_0.py
@@ -1,4 +1,11 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+__copyright__ = """ This code is licensed under the 3-clause BSD license.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
+See LICENSE.txt for details.
+"""
 from pymongo import MongoClient
+from typing import Any, List, Dict
 from bson.objectid import ObjectId
 import datetime
 import argparse
@@ -20,13 +27,14 @@
 db_name = args.db_name
 extract_duplicates = args.duplicates
 
-client = MongoClient(ip, port)
+client: MongoClient = MongoClient(ip, port)
 db = client[db_name]
 
 # Check version
 is_correct_old_version = False
 if "_db_meta_data" in db.list_collection_names():
     meta_data = db["_db_meta_data"].find_one({})
+    assert meta_data
     version = meta_data["version"]
     if version["major"] == 1 and version["minor"] == 0:
         is_correct_old_version = True
@@ -44,6 +52,7 @@
     flasks = db["flasks"]
     flasks.create_index("flasks")
 # Add type to reactants of reaction
+reaction: Dict[str, List[Dict[str, Any]]]
 for reaction in db["reactions"].find():
     if len(reaction['lhs']) == 0 and len(reaction['rhs']) == 0:
         continue
@@ -53,7 +62,7 @@
                 continue
     elif len(reaction['rhs']) != 0:
         if isinstance(reaction['rhs'][0], type(dict)):
-            if 'type' in reaction['rhs'][0]:
+            if 'type' in reaction['rhs'][0].keys():
                 continue
     lids = [lid for lid in reaction['lhs']]
     new_lhs = []
@@ -89,6 +98,7 @@
 if "_db_meta_data" in db.list_collection_names():
     _db_meta_data = db["_db_meta_data"]
     meta_data = db["_db_meta_data"].find_one({})
+    assert meta_data
     date = meta_data["_created"]
     db["_db_meta_data"].delete_many({})
 else:
diff --git a/updates/1_1_0_to_1_2_0.py b/updates/1_1_0_to_1_2_0.py
index 001457b..1b3e32b 100644
--- a/updates/1_1_0_to_1_2_0.py
+++ b/updates/1_1_0_to_1_2_0.py
@@ -1,5 +1,10 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+__copyright__ = """ This code is licensed under the 3-clause BSD license.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
+See LICENSE.txt for details.
+"""
 from pymongo import MongoClient
-from bson.objectid import ObjectId
 import datetime
 import argparse
 
@@ -17,13 +22,14 @@
 port = args.port
 db_name = args.db_name
 
-client = MongoClient(ip, port)
+client: MongoClient = MongoClient(ip, port)
 db = client[db_name]
 
 # Check version
 is_correct_old_version = False
 if "_db_meta_data" in db.list_collection_names():
     meta_data = db["_db_meta_data"].find_one({})
+    assert meta_data
     version = meta_data["version"]
     if version["major"] == 1 and version["minor"] == 1:
         is_correct_old_version = True
@@ -49,6 +55,7 @@
 if "_db_meta_data" in db.list_collection_names():
     _db_meta_data = db["_db_meta_data"]
     meta_data = db["_db_meta_data"].find_one({})
+    assert meta_data
     date = meta_data["_created"]
     db["_db_meta_data"].delete_many({})
 else:
diff --git a/updates/1_2_0_to_1_3_0.py b/updates/1_2_0_to_1_3_0.py
new file mode 100644
index 0000000..b974f53
--- /dev/null
+++ b/updates/1_2_0_to_1_3_0.py
@@ -0,0 +1,69 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+__copyright__ = """ This code is licensed under the 3-clause BSD license.
+Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
+See LICENSE.txt for details.
+"""
+from pymongo import MongoClient
+import datetime
+import argparse
+
+
+parser = argparse.ArgumentParser(description='SCINE Database Update 1.2.X to 1.3.0.')
+parser.add_argument('--ip', dest='ip', type=str, default='localhost',
+                    help='The database server IP or hostname. [default = localhost]')
+parser.add_argument('--port', dest='port', type=int, default=27017,
+                    help='The database server port. [default = 27017]')
+parser.add_argument('--name', dest='db_name', type=str, default='my_awesome_database',
+                    help='The database name. [default = my_awesome_database]')
+args = parser.parse_args()
+
+ip = args.ip
+port = args.port
+db_name = args.db_name
+
+client: MongoClient = MongoClient(ip, port)
+db = client[db_name]
+
+# Check version
+is_correct_old_version = False
+if "_db_meta_data" in db.list_collection_names():
+    meta_data = db["_db_meta_data"].find_one({})
+    assert meta_data
+    version = meta_data["version"]
+    if version["major"] == 1 and version["minor"] == 2:
+        is_correct_old_version = True
+else:
+    is_correct_old_version = False
+
+if not is_correct_old_version:
+    print("The database does not have the correct old version for this update.")
+    print("Exiting!")
+    exit(1)
+
+# Check for model_transformation steps
+step = db["elementary_steps"].find_one({"type": "model_transformation"})
+if step is not None:
+    print("The database contains outdated elementary steps of type model_transformation.")
+    print("These steps must be removed manually before updating")
+    exit(1)
+
+# Update version
+if "_db_meta_data" in db.list_collection_names():
+    _db_meta_data = db["_db_meta_data"]
+    meta_data = db["_db_meta_data"].find_one({})
+    assert meta_data
+    date = meta_data["_created"]
+    db["_db_meta_data"].delete_many({})
+else:
+    date = datetime.datetime.utcnow()
+    _db_meta_data = db["_db_meta_data"]
+post = {
+    "version": {
+        "major": 1,
+        "minor": 3,
+        "patch": 0
+    },
+    "_created": date
+}
+_db_meta_data.insert_one(post)
diff --git a/updates/requirements.txt b/updates/requirements.txt
new file mode 100644
index 0000000..de4887b
--- /dev/null
+++ b/updates/requirements.txt
@@ -0,0 +1 @@
+pymongo