/TUCAN

A molecular identifier and descriptor for all domains of chemistry.

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

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TUCAN1 is a molecular identifier and descriptor for all domains of chemistry.

When you give TUCAN a molfile:

HOAc.mol
 OpenBabel02172217462D

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 8 7 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C -0.357235 0 0 0
M  V30 2 C 0.357235 0.4125 0 0
M  V30 3 H 1.07171 0 0 0
M  V30 4 H 0.357235 1.2375 0 0
M  V30 5 H 1.07171 0.825 0 0
M  V30 6 O -1.07171 0.4125 0 0
M  V30 7 O -0.357235 -0.825 0 0
M  V30 8 H 0.357235 -1.2375 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 2 1 6
M  V30 3 1 1 7
M  V30 4 1 2 3
M  V30 5 1 2 4
M  V30 6 1 2 5
M  V30 7 1 7 8
M  V30 END BOND
M  V30 END CTAB
M  END

it computes a serialized, canonical representation of your molecule:

from tucan.io.molfile_reader import graph_from_file
from tucan.canonicalization import canonicalize_molecule
from tucan.serialization import serialize_molecule

molecule = graph_from_file("HOAc.mol")
canonical_molecule = canonicalize_molecule(molecule)
tucan_string = serialize_molecule(canonical_molecule)

print(tucan_string)
C2H4O2/(1-5)(2-5)(3-5)(4-8)(5-6)(6-7)(6-8)

Have a look at our demo notebook to see TUCAN at work.

You can explore TUCAN interactively on our website,

and find details on TUCAN's scientific background in our paper.

Installation

TUCAN requires a Python installation (>=3.10), and preferably you install the package in a virtual environment (e.g., venv).

You can install TUCAN locally using pip by first cloning the repository, and then running

pip install .

in the root of the repository. Alternatively, you can skip cloning by running

pip install git+https://github.com/TUCAN-nest/TUCAN.git

In order to install an editable development version run

pip install -e .

The commands above will only install the minimal set of dependencies that is necessary to use TUCAN. If you want to install the additional development dependencies (testing, linting, support for notebooks), run

pip install .[dev,drawing]

or

pip install git+https://github.com/TUCAN-nest/TUCAN.git#egg=tucan[dev,drawing]

Have a look at the pyproject.toml for details regarding the optional dependencies.

Contributors

  • Claudia Kellner (Universität Würzburg) - molecule test set
  • Alexander Hoffmann (RWTH Aachen) - molecule test set
  • Sonja Herres-Pawlis (RWTH Aachen) - concept
  • Ulrich Schatzschneider (Universität Würzburg) - concept, documentation, and software development
  • Jan C. Brammer (RWTH Aachen) - software development and documentation
  • Frank Lange (IPB Halle) - software development

Acknowledgments

Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI4Chem – Projektnummer 441958208.

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Footnotes

  1. TUCAN stands for tuple canonicalization, since we're using 2-tuples to represent the bonds of our canonicalized molecules. Besides, Wikipedia informs us that in the tucán's native parlance, "tu canonicalización" expresses our hope that this software will help canonicalize your molecules. ↩