👀 smarts-explainer

SMARTS explainer is a small wrapper around the SMARTSview tool developped at ZBH U. Hamburg for creating an easy to comprehend visualization for SMARTS expression. The concept was developed by 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 smexplainer

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

git clone git@github.com: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.