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lightweight-registration

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lwreg is a lightweight registration system for chemical registration and data storage.

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- - deploy_docker.yaml
  - test.yml
- Dockerfile
- README.md
- - lwreg_schema.png
  - ml_experimental_schema.png
  - simple_experimental_schema.png
- - additionalfunctionality.rst
  - basicfunctionality.rst
  - bestpracticeguide.rst
  - conf.py
  - examples.rst
  - gettingstarted.rst
  - index.rst
  - registrationdetails.rst
  - technicaldetails.rst
  - tutorials.rst
- Database_layout.md
- make.bat
- Makefile
- requirements.txt
- __init__.py
- db_utils.py
- helpers.py
- lwreg.py
- standardization_lib.py
- test_cli.py
- test_dbutils.py
- test_lwreg.py
- utils.py
- test_molecules.sdf
- test_molecules_hs.sdf
- test_smiles.smi
- test_smiles_no_delim.smi
- test_smiles_no_delim_with_header.smi
- test_smiles_with_header.smi
- - mols_with_confs.sdf
  - S1P1_data.csv
- 01_registration_basics.ipynb
- 02_querying_existing_database.ipynb
- 03_registering_conformers.ipynb
- 04_registering_molecules_and_data.ipynb
- 100_computational_experiment_1.ipynb
- 101_computational_experiment_2.ipynb
.gitignore
.readthedocs.yaml
CITATION.cff
Dockerfile
environment.yml
environment_dev.yml
INSTALL.md
LICENSE
Lwreg.png
pyproject.toml
README.md

# Installation Guide

1. Get the code

git clone https://github.com/rinikerlab/lightweight-registration

Downloads the entire project code from GitHub to your computer.

cd lightweight-registration

Moves into the project folder you just downloaded.

2. Docker

Easy Recommended

Prerequisites

Git Needed to download the project code from GitHub.
Docker Desktop Needed to build and run containers. Install it and keep it running in the background.

docker build -t lightweight-registration .

Builds a runnable image based on the Dockerfile.

docker run -p 8080:80 lightweight-registration

Runs the built image as an actual container.

✅ Run docker compose ps to check the containers are Up. If the README mentions a port, open http://localhost:PORT in your browser.

3. Python

Easy

Prerequisites

Git Needed to download the project code from GitHub.
Python 3 On Windows, be sure to check 'Add Python to PATH' during installation.

% python -m pip install git+https://github.com/rinikerlab/lightweight-registration

Installs the Python libraries listed in requirements.txt (or similar).

✅ If it runs without errors and prints output in the terminal, it worked.

Pulled directly from this repo's README.

// repository documentation

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# LWReg: a lightweight chemical registration system

[![Lwreg](https://img.shields.io/badge/DOI-10.1021/acs.jcim.3c00800-blue)](https://pubs.acs.org/doi/10.1021/acs.jcim.4c01133)
[![ReadTheDocs](https://readthedocs.org/projects/docs/badge/?version=latest)](https://lightweight-registration.readthedocs.io/en/)
[![RDKit](https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC)](https://www.rdkit.org/)
![TOC Image](https://github.com/rinikerlab/lightweight-registration/blob/main/Lwreg.png)

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 psycopg
```

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.set_default_config(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')}

```