SCINE - Database

Introduction

The SCINE database module is a database wrapper for a MongoDB encoding reaction networks.

License and Copyright Information

For license and copyright information, see the file LICENSE.txt in this directory.

Installation and Usage

The following software packages are required in order to compile the SCINE Database:

A C++ compiler supporting the C++17 standard (GCC at least 7.3.0 or later)
CMake (at least version 3.9.0)
Eigen3 (at least version 3.3.2 or later)
MongoDB C++ Driver (at least version 3.4.0)
Boost (recommended: version 1.65.0 or later)

Furthermore the database compilation will require the SCINE Utilities module, and download it automatically if it is not present.

The SCINE database repository includes a Git submodule; either clone the repository recursively::

git clone --recurse-submodules https://github.com/qcscine/database.git

or initialize and update the submodules after a regular clone::

git clone https://github.com/qcscine/database.git scine_database
cd scine_database
git submodule update --init

The SCINE database module can be built using a standard CMake/make setup::

mkdir build
cd build
cmake -DSCINE_BUILD_PYTHON_BINDINGS=ON ..
make
make test
make install

Note that the tests, by default, require a MongoDB to be running on the local host. Alternatively the -DTEST_MONGO_DB_IP=XXX flag can be set in the CMake configure step to route the test executable to another database. For MongoDB, use at least version 4.2.0.

For minimal usage examples please see the user manual provided in this repository or check the latest online version on the SCINE web page <https://scine.ethz.ch>_.

How to Cite

When publishing results obtained with the SCINE database wrapper, please cite the corresponding release as archived on Zenodo <https://zenodo.org/record/6695495>_ (DOI 10.5281/zenodo.6695495; please use the DOI of the respective release).

In addition, we kindly request you to cite the following article when using the SCINE database wrapper: 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

In case you should encounter problems or bugs, please write a short message to scine@phys.chem.ethz.ch.

Third-Party Libraries Used

SCINE Database makes use of the following third-party libraries:

Boost <https://www.boost.org/>_
Eigen <http://eigen.tuxfamily.org>_
Google Test <https://github.com/google/googletest>_
MongoDB C++ Driver <https://github.com/mongodb/mongo-cxx-driver>_
pybind11 <https://github.com/pybind/pybind11>_

qcscine / database

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