SCINE Art

Philosophy of SCINE Art

The exhaustive, brute-force exploration of vast chemical reaction networks is very demanding in terms of computational resources. Moreover, the analysis of such a huge network is far from trivial; one can easily drown in this information. With Art, you can extract reaction templates from complex chemical reaction networks in an automated fashion. These templates allow to group similar reactions together, thereby simplifying the analysis of a complex network. Moreover, the templates can be used to limit an exploration to certain desired reaction classes, greatly alleviating the computational burden.

Technical Details

Art is implemented as a (pure) Python module. It can be installed either from source or via PyPI. To work properly, Art needs the following two other SCINE modules:

  • SCINE Molassembler, which is a library to handle molecular structures as graphs,
    • (to be used by ReaDuct) for a range of semiempirical methods, and
  • SCINE Utilities, which is a library of common functionality used across all SCINE modules.
These components do not need to be installed manually; rather, they are automatically installed when installing Art.

Current Features

  • Four reaction template flavors (many features are only geared towards the first two):
    • 'minimal' and 'minimal' with shape dressing
    • 'minimal_shell' (the minimal template type with nearest neighbors added for each reactive atom)
    • 'fragment' (all atom of one molecule have to form a single graph)
    • 'fragment_shell' (all atom of one molecule have to form a single graph, neighbors are added)
  • Deduplication of reaction templates based on a template graph representation
  • A database to hold reaction templates
  • Automated template extraction from SCINE databases
  • Template application to new molecules
  • Incomplete atom mapping features for arbitrary molecules

Download

SCINE Art is distributed as an open source code. Visit our GitHub page to download it.

Future Releases

  • Template application to arbitrary molecular graphs including 3D alignment of structures
  • Enhanced atom mapping features, including auto completion of partial mappings

Documentation

Documentation is provided in the source code; you can also access it here.

Support

Despite intense testing of the program, questions may arise with respect to the usage of SCINE Art. Do not hesitate to contact the developers via scine@phys.chem.ethz.ch in case of any questions and suggestions.

References

  • Primary reference for Art 2.0.0:
    J. P. Unsleber, "qcscine/art: Release 2.0.0 (Version 2.0.0)", Zenodo, 2023. DOI
  • Please cite also the following paper when publishing results obtained with Art:
    J. P. Unsleber, "Accelerating Reaction Network Explorations with Automated Reaction Template Extraction and Application", J. Chem. Inf. Model., 2023, 63, 3392. DOI