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https://github.com/qcscine/molassembler

Chemoinformatics toolkit with support for inorganic molecules
https://github.com/qcscine/molassembler

chemistry chemoinformatics conformer-generator data-structures graph-algorithms molecule molecule-builder stereochemistry

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Chemoinformatics toolkit with support for inorganic molecules

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README 

        
SCINE - Molassembler

====================



Overview

--------



Molassembler is a C++ library that aims to facilitate conversions between

Cartesian and graph representations of molecules. It provides the necessary

functionality to represent a molecule as a graph, modify it in graph space, and

generate new coordinates from graphs. It can capture the absolute configuration

of inorganic molecules with multidentate and haptic ligands from Cartesian

coordinates and enumerate non-superposable stereopermutations at non-terminal

atoms and non-isotropic bonds at arbitrary local shapes ranging up to the

icosahedron and cuboctahedron.



Features

--------



- Molecules can be constructed from many types of information.

- Stereocenters are treated in shapes ranging from monovacant tetrahedron all

  the way up to the icosahedron and cuboctahedron.

- A high-temperature approximation is invoked by default to avoid considering

  inverting nitrogen centers as stereocenters, but this is optional. Even in

  the high-temperature approximation, nitrogen centers whose substituents

  form a strained cycle and hence do not invert rapidly are considered a

  stereocenter.

- All stereocenter permutations are generated with relative statistical

  occurrence weights. Linking of ligands (denticity) is properly considered.

  Several classes of haptic ligands are supported.

- Editing of molecules preserves chiral information by default, and is highly

  configurable.

- Molecules can be canonicalized for fast isomorphism tests. Canonicalization

  can be customized to use subsets of the available information for vertex

  coloring if desired.

- Ranking algorithms are nearly fully IUPAC Blue Book 2013 compliant,

  generalized to larger coordination polyhedra.

- Stochastic conformer generation with Distance Geometry

- Directed conformer generation through enumeration of rotamers



License

-------



Molassembler is licensed under the BSD 3-clause "New" or "Revised" license. See

also the ``LICENSE.txt`` file.



Integrating

-----------



This library requires the C++17 standard.



Dependencies:



- `SCINE Utilities `_ (BSD-3 license) >= 3.0.0

- `Boost `_ (Boost license) >= 1.65 (lowest tested, prefer newest)

- `Eigen `_ (MPL 2.0 license) >= 3.3.2

- `RingDecomposerLib `_ [1]_ (BSD-3 license): Unique Ring Family [2]_ cycle detection

- `Outcome `_ single-header (Boost license): Enforce error handling requirement in type system

- `JSON For Modern C++ `_ (MIT license): JSON serialization

- `nauty `_ [3]_ (Apache 2.0 license): Graph automorphism determination and canonical labeling

- (MKL/LAPACK/BLAS libraries, added if detected during compilation)



Can currently be compiled with:



- GCC >= 7

- Clang >= 4

- MinGW-w64 (latest)



MSVC is currently untested. Last attempts failed because of compiler standard

compliance issues with ``constexpr`` code.



How to Cite

-----------



When publishing results obtained with Molassembler, please cite the

corresponding release as archived on `Zenodo `_.



In addition, we kindly request you cite the following article when using

Molassembler:



J.-G. Sobez, M. Reiher, "Molassembler: Molecular Graph Construction,

Modification, and Conformer Generation for Inorganic and Organic

Molecules", *J. Chem. Inf. Model*, **2020**, *60*, 3884.



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 `_).



Installation

------------



CMake

.....



When building with CMake, Boost and Eigen must be installed and available via

CMake's ``find_package`` (e.g. via ``CMAKE_PREFIX_PATH``). Any of the other

libraries can be available, but are downloaded dynamically if missing. 



Clone the repository, then enter the following commands::



    git submodule update --init

    mkdir build-release

    cd build-release

    cmake -DCMAKE_BUILD_TYPE=Release ..

    make



You may want to peruse the CMake options to disable building the tests or

activating the Python binding builds. Run ``cmake -L ..`` to list options

affecting the build. Look for options with the ``SCINE_`` prefix.



Conan

.....



No dependencies must be preinstalled, and you do not need to download the

sources. To install/build with Conan::



    conan remote add scine https://scine-artifactory.ethz.ch/artifactory/api/conan/public

    conan install -r scine --build=missing scine_molassembler/3.0.0@



Should you want Python bindings, add ``-o scine_molassembler:python=True`` before

the last argument.



PyPI

....



``manylinux`` packages of thie Python bindings are available from PyPI and can be

installed with::



    python3 -m pip install scine_molassembler



Documentation

-------------



Built documentation for releases is available for the `C++ library`_ and `Python bindings`_.



If ``doxygen`` is found, the C++ library documentation is built. If the Python

bindings are built and the ``sphinx`` Python module is available, the Python

binding documentation is generated too.



.. _C++ library: https://scine.ethz.ch/static/download/documentation/molassembler/v3.0.0/cpp/index.html



.. _Python bindings: https://scine.ethz.ch/static/download/documentation/molassembler/v3.0.0/py/index.html



References

----------



.. [1] Flachsenberg, F.; Andresen, N.; Rarey, M. RingDecomposerLib: An

       Open-Source implementation of Unique Ring Families and Other Cycle Bases. J.

       Chem. Inf. Model., 2017, 57 (2), pp 122–126



.. [2] Kolodzik, A.; Urbaczek, S.; Rarey, M. Unique Ring Families: A Chemically

       Meaningful Description of Molecular Ring Topologies. J. Chem. Inf. Model.,

       2012, 52 (8), pp 2013–2021



.. [3] McKay, Brendan D.; Adolfo Piperno. Practical graph isomorphism, II.

       J. Symb. Comput., 2014, 60, pp 94-112.