datamol-io / molfeat-padel

A molfeat plugin that adds support for PaDEL descriptors

🧩 molfeat-PaDEL

A molfeat plugin that adds support for PaDEL-Descriptors

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🧩 molfeat-PaDEL - A molfeat plugin that adds support for PaDEL-Descriptors

Docs | Homepage

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Overview

molfeat-padel is an extension to molfeat that adds support for PaDEL descriptors. The PaDEL descriptors are a mix of molecular descriptors (663 1D, 2D descriptors, 134 3D descriptors) and structural fingerprints based on the Chemistry Development Kit (CDK).

• To learn more about PaDEL descriptors, please refer to the following paper: Yap, 2010

• To learn more about molfeat, please visit https://molfeat.datamol.io/.

• To learn more about the plugin system of molfeat, please see extending molfeat

Installation

You can install molfeat-padel with:

mamba install -c conda-forge molfeat

or

pip install molfeat-padel

molfeat-padel depends on molfeat and padelpy

Usage

The following example shows how to use the molfeat-padel plugin package automatically when installed. All scenarios highlighted in this example are valid:

1. initializing the calculator from the plugin package

from molfeat.trans import MoleculeTransformer

from molfeat_padel.calc import PadelDescriptors
mol_transf = MoleculeTransformer(featurizer=PadelDescriptors())

2. auto registration of PadelDescriptors to the list of calculators

from molfeat.trans import MoleculeTransformer
import molfeat_padel

mol_transf = MoleculeTransformer(featurizer="PadelDescriptors")
# works because PadelDescriptors is imported in the root init of molfeat_padel

3. enable autodiscovery and addition of the PadelDescriptors as importable attribute to the entry point group molfeat.calc

# put this somewhere in you code
from molfeat.trans import MoleculeTransformer
from molfeat.plugins import load_registered_plugins
load_registered_plugins(add_submodules=True)

# this is now possible
from molfeat.calc import PadelDescriptors
mol_transf = MoleculeTransformer(featurizer=PadelDescriptors())

# this is also possible
mol_transf = MoleculeTransformer(featurizer="PadelDescriptors")

Dependencies

The only dependencies of molfeat-padel are padelpy and molfeat

Changelog

See the latest changelogs at CHANGELOG.rst.

Maintainers

• @maclandrol

License

Under the Apache-2.0 license. See LICENSE.