smexplainer 0.0.2

A python library to explains molecular patterns (SMARTS)

👀 smarts-explainer

SMARTS explainer is a small wrapper around the [SMARTSview](https://smarts.plus/) tool developped at ZBH U. Hamburg for creating an easy to comprehend visualization for SMARTS expression. The concept was developed K. Schomburg and M. Rarey.

Installation

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smarts-explainer requires datamol and requests-toolbelt. You can install it as follows

pip install smarts-explainer

Alternatively, download, install the dependency then install it with:

git clone [e-mail]:maclandrol/smexplainer.git
cd smexplainer
mamba env create -f env.yml -n "smexplainer" && conda activate smexplainer
pip install -e . 

Usage

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import smexplainer

my_smarts = "c12c(n(C)c(=O)[nH,$(nC)]c(=O)1)ncn2C"
smexplainer.explain(my_smarts, filetype="png")

For a batch of smarts, you can use the smexplainer.batch_explain function instead

Input parameters:

• smarts: a smarts string (valid) to visualize
• comparesmarts: optional smarts to compare agains
• vmode: visualization Mode:
  • 0 = Complete visualization (default)
  • 1 = ID-Mapping
  • 2 = Element symbols
  • 3 = Structure Diagram-Like
• vbonds: Visualization of Default Bonds
  • 0 = "Single bonds"
  • 1 = "Single or Aromatic Bonds" (default)
• textdesc: Legend Option 1: Textual desciption
  • False = No
  • True = Yes (default)
• depsymbols: Legend Option 2: Depiction of SMARTS symbols
  • False = No
  • True = Yes (default)
• smartsheading: Legend Option 3: Write SMARTS as picture heading
  • False = No
  • True = Yes (default)
• trim: SMARTS trim active:
  • False = No
  • True = Yes (default)
• labels: Show Atom Labels
  • False = No
  • True = Yes (default)
• cmode: Compare Mode: This only affects compare images
  • 1 = Search for Identical Patterns
  • 2 = Subset search from smarts
  • 3 = subset search from comparesmarts
  • 4 = Similarity Search (default)
• detectarom: Detect Aromatic Bonds
  • False = No
  • True = Yes (default)
• smileslikearom: SMILES-Like Aromaticity Detection
  • False = No
  • True = Yes (default)
• filetype: Output File Type
  • png (default)
  • svg
  • pdf
• outfile: Optional Output file where to save the output image

Reference

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For more information about the explainer, see the corresponding paper:

@article{schomburg2010structure,
  title={From structure diagrams to visual chemical patterns},
  author={Schomburg, Karen and Ehrlich, Hans-Christian and Stierand, Katrin and Rarey, Matthias},
  journal={Journal of chemical information and modeling},
  volume={50},
  number={9},
  pages={1529--1535},
  year={2010},
  publisher={ACS Publications}
}

Changelogs

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See the latest changelogs at CHANGELOG.rst.

License

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The smexplainer is under the Apache-2.0 license. See LICENSE. But the original work is copyrighted by "SMARTSviewer smartsview.zbh.uni-hamburg.de, ZBH Center for Bioinformatics, University of Hamburg"

Authors

See AUTHORS.rst.