Mapper

Mapper is an implementation of approximate structure-matching algorithm proposed by Lynch and Willett [1]. It applies the Morgan algorithm [2] with different stopping rule simultaneously to both reacting molecules to detect inter-molecular equivalences.

The authors of Ref. [1] are a bit vague as far as assigning initial extended connectivity indices is concerned. Thus, besides original Morgan's approach, two alternative methods [3,4] were implemented.

Requirements

Mapper depends on:

• Python (version 3.11+)
• numpy
• RDKit toolkit

Installation

Create a virtual environment with

python3 -m venv <ENV_DIR>

where <ENV_DIR> is any directory, for example $HOME/venvs/mapper.

Clone the package repository with

git clone https://github.com/mxk62/Mapper.git

Switch to the package directory and activate the virtual environment you created earlier

cd Mapper
source $HOME/venvs/mapper

and install the package using pip

pip install --user .

If you want to be able to generate package documentation, you need to install additional (optional) dependencies with

pip install --user .[docs]

instead. Then you can generate the documentation simply with

cd docs
make html

If building documentation finished successfully, open _build/html/index.html in your web browser.

Note

A fair warning though. At the moment the documentation is just an API reference. Having said that this should provide some insight how to use the package.

Misc

Other files you can find in the package directory are:

• demo.py: a (very) simple CLI for demonstration purposes.
• rxns.smi: example reactions from Ref. [1] encoded in SMILES format.

References

1. MF Lynch and P Willett, The Automatic Detection of Chemical Reaction Sites, J Chem Inf Comput Sci 18, 154-159 (1978)
2. HL Morgan, , The generation of a Unique Machine Description for Chemical Structures---A Technique Developed at Chemical Abstract Service, J Chem Doc 5, 107-113 (1965)
3. CA Shelley and ME Munk, Computer Perception of Topological Symmetry, J Chem Inf Mod 17, 110-113 (1977)
4. K Funatsu, T Endo, N Kotera, and SI Sasaki, Automatic Recognition of Reaction Site in Organic Chemnical Reactions, Tetrahedron Computer Methodology 1, 53-69 (1988)