Chem Func

Useful functions and scripts for working with small molecules.

Installation

Optionally, create a conda environment.

conda create -y -n chemfunc python=3.12
conda activate chemfunc

Install the latest version of Chem Func using pip.

pip install chemfunc

Alternatively, clone the repository and install the local version of the package.

git clone https://github.com/swansonk14/chemfunc.git
cd chemfunc
pip install -e .

Note: If you get the issue ImportError: libXrender.so.1: cannot open shared object file: No such file or directory, run conda install -c conda-forge xorg-libxrender.

Features

Chem Func contains a variety of useful functions and scripts for working with small molecules.

Functions can be imported from the chemfunc package. For example:

from pathlib import Path
from chemfunc.sdf_to_smiles import sdf_to_smiles

sdf_to_smiles(
    data_path=Path('molecules.sdf'),
    save_path=Path('molecules.csv')
)

Most modules can also be run as scripts from the command line using the chemfunc command along with the appropriate function name. For example:

chemfunc sdf_to_smiles \
    --data_path molecules.sdf \
    --save_path molecules.csv

To see a list of available scripts, run chemfunc -h.

For each script, run chemfunc <script_name> -h to see a description of the arguments for that script.

Contents

Below is a list of the contents of the package.

canonicalize_smiles.py (function, script)

Canonicalizes SMILES using RDKit canonicalization and optionally strips salts.

chemical_diversity.py (function, script)

Computes the chemical diversity of a set of molecules in terms of Tanimoto distances.

cluster_molecules.py (function, script)

Performs k-means clustering to cluster molecules based on Morgan fingerprints.

compute_properties.py (function, script)

Computes one or more molecular properties for a set of molecules.

convert_sdf.py (functions)

Functions to convert SDF files to SMILES or SMARTS. Used by sdf_to_smiles and sdf_to_smarts.

deduplicate_smiles.py (function, script)

Deduplicate a CSV files by SMILES.

filter_molecules.py (function, script)

Filters molecules to those with values in a certain range.

measure_experimental_reproducibility.py (function, script)

Measures the experimental reproducibility of two biological replicates by using one replicate to predict the other.

molecular_fingerprints.py (functions, script)

Contains functions to compute fingerprints for molecules. Parallelized for speed. The function save_fingerprints can be used as a script to compute fingerprints from a CSV file and save them as an NPZ file.

molecular_properties.py (functions)

Contains functions to compute molecular properties. Parallelized for speed.

molecular_similarities.py (functions)

Contains functions to compute similarities between molecules. Parallelized for speed.

nearest_neighbor.py (function, script)

Given a dataset of molecules, computes the nearest neighbor molecule in a second dataset using one of several similarity metrics.

plot_property_distribution.py (function, script)

Plots the distribution of molecular properties of a set of molecules.

plot_tsne.py (function, script)

Runs a t-SNE on molecular fingerprints from one or more chemical libraries.

regression_to_classification.py (function, script)

Converts regression data to classification data using given thresholds.

sample_molecules.py (function, script)

Samples molecules from a CSV file, either uniformly at random across the entire dataset or uniformly at random from each cluster within the data.

sdf_to_smarts.py (function, script)

Converts an SDF file to a CSV file with SMARTS.

sdf_to_smiles.py (function, script)

Converts an SDF file to a CSV file with SMILES.

select_from_clusters.py (function, script)

Selects the best molecule from each cluster.

smiles_to_svg.py (function, script)

Converts a SMILES string to an SVG image of the molecule.

visualize_molecules.py(function, script)

Converts a file of SMILES to images of molecular structures.

visualize_reactions.py (function, script)

Converts a file of reaction SMARTS to images of chemical reactions.