https://github.com/ijpulidos/fruitfly

Utilities and CLI for molbloom filters
https://github.com/ijpulidos/fruitfly

Last synced: 11 days ago
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Utilities and CLI for molbloom filters

• Host: GitHub
• URL: https://github.com/ijpulidos/fruitfly
• Owner: ijpulidos
• License: mit
• Created: 2024-04-03T20:32:08.000Z (9 months ago)
• Default Branch: main
• Last Pushed: 2024-04-04T04:45:19.000Z (9 months ago)
• Last Synced: 2024-04-04T05:32:26.126Z (9 months ago)
• Language: Python
• Size: 2.93 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# fruitfly

Utilities and CLI for molbloom filters.

THIS IS A WORK IN PROGRESS. Several changes are expected.

**Note:** To date this is just a convenient script with a CLI that wraps

around `molbloom` to help finding matches of compounds in `.bloom` files,

given an input SMILES (`.smi`) file.

## Installing dependencies

The recommended way is to use conda/mamba (or similar) to create an environment

with the required tools. 

After you clone this repository, you can create the conda environment using 

the following command (note that we recommend `mamba` but you can change the

command to use `conda` instead of `mamba`, if desired):

```bash

mamba env create -f environmentl.yml -n fruitfly-env

```

## How to use

To use it you would just activate the created environment with 

`conda activate fruitfly-env`, and call the script like the following in the

same directory where you cloned this repository:

```bash

python fruitfly.py find-matches --glob-exp "filters/*.bloom" --smiles-file input.smi --out-file results.json

```

Please note that the quotes in the `glob-exp` are required for the shell to not interpret

wildcards (`*`).

The `glob-exp` argument is an expression to match the filters files.

Additional arguments can be specified, for more information please use 

`python fruitfly find-matches --help`.

## Results

The results are stored in a generated `json` file, which has as keys the base names

of the filters you used, and the matching smiles as values for each of the filters.

This is convenient in order to know from which bloom filter the matches were obtained.

Additionally, if you specified the `--include-unmatched True` argument, a key `unmatched`

will be generated with the unmatched SMILES as the values.

## Future work

In the near future, commands to easily create your own filters from `.smi` files will

be added. Improving the CLI and overall modularity of the project is also planned.