LWReg: a lightweight chemical registration system

This provides a basic registration system which can be used either as a python library or via a command-line interface.

Basic operations: - initdb: resets the database. Note that this destroys any information which is already in the database, so be careful with it. - register: standardize the input molecule, calculates a hash for it, and adds them molecule to the database if it's not already there. returns the molregno (registry ID) of the newly registered molecule. - query: takes a molecule as input and checks whether or not a matching molecule is registered. returns molregnos (registry IDs) of the matching molecule(s), if any - retrieve: takes one or more IDs and returns the registered structures for them

Publications

[1] J. Chem. Inf. Model. 2024, 64, 16, 6247–6252 : https://pubs.acs.org/doi/10.1021/acs.jcim.4c01133

Documentation

Our full documentation: https://lightweight-registration.readthedocs.io/en/

Quick-start

Assuming that you have conda (or mamba or something equivalent) installed you can install lwreg directly from this github repo by first creating a conda environment with all the dependencies installed: % conda env create --name py313_lwreg --file=https://raw.githubusercontent.com/rinikerlab/lightweight-registration/main/environment.yml If you have mamba installed, you can run this instead (it will run faster): % mamba env create --name py313_lwreg --file=https://raw.githubusercontent.com/rinikerlab/lightweight-registration/main/environment.yml

You can then activate the new environment and install lwreg: % conda activate py313_lwreg % python -m pip install git+https://github.com/rinikerlab/lightweight-registration

You can then verify that the install worked by doing: % lwreg --help

If you want to use PostgreSQL as the database for lwreg, then you will also need to install the python connector for PostgreSQL: % conda install -c conda-forge psycopg2

For further information, consult the INSTALL.md file.

Very basic usage demo

Command line

% lwreg initdb --confirm=yes % lwreg register --smiles CCOCC % lwreg query --smiles CCOCCC % lwreg retrieve --id 2

Python

```

import lwreg

from lwreg import utils

lwreg.setdefaultconfig(utils.defaultConfig()) # you generally will want to provide more information about the database

lwreg.initdb() This will destroy any existing information in the registration database. are you sure? [yes/no]: yes True

lwreg.register(smiles='CCO') 1

from rdkit import Chem

m = Chem.MolFromSmiles('CCOCC')

lwreg.register(mol=m) 2

lwreg.query(smiles='CCO') [1]

lwreg.retrieve(id=2) {2: ('\n RDKit 2D\n\n 0 0 0 0 0 0 0 0 0 0999 V3000\nM V30 BEGIN CTAB\nM V30 COUNTS 5 4 0 0 0\nM V30 BEGIN ATOM\nM V30 1 C 0.000000 0.000000 0.000000 0\nM V30 2 C 1.299038 0.750000 0.000000 0\nM V30 3 O 2.598076 -0.000000 0.000000 0\nM V30 4 C 3.897114 0.750000 0.000000 0\nM V30 5 C 5.196152 -0.000000 0.000000 0\nM V30 END ATOM\nM V30 BEGIN BOND\nM V30 1 1 1 2\nM V30 2 1 2 3\nM V30 3 1 3 4\nM V30 4 1 4 5\nM V30 END BOND\nM V30 END CTAB\nM END\n', 'mol')}

```