MolMiner
MolMiner consolidates tools for small-molecule virtual screening. It includes custom scripts for data preprocessing, molecular docking (Autodock Vina), and ML/DL model development (Scikit-Learn and Keras). Using MolMiner is optional and was created to streamline environment setup without manually sourcing relevant Python project packages.
Installation
MolMiner installs a light cheminformatics core by default. Additional modules can be installed if needed.
pip install MolMiner
Additional modules
| Install | Adds | Usage |
|---|---|---|
pip install MolMiner |
rdkit, pandas, datamol, scikit-learn, splito, umap-learn, matplotlib/seaborn | fingerprints, BRICS/RECAP fragmentation, molecule drawing, chemical space (PCA/t-SNE/UMAP), clustering, plots, ROC/PR curves |
pip install "MolMiner[ml]" |
torch, keras, xgboost, optuna | mminer.models, mminer.hyperparams |
pip install "MolMiner[docking]" |
prolif, meeko | mminer.docking interaction analysis and ligand prep, requires Autodock Vina installation using Conda or Pixi |
pip install "MolMiner[safe]" |
safe-mol, transformers | slicer='safe', SAFEbuild, Draw.safe_highlight, Matching |
pip install "MolMiner[all]" |
all of the above | everything except AutoDock Vina (see below) |
Installing additional modules at once: pip install "MolMiner[ml,safe]".
Using a feature whose extra is missing reports what to install rather than failing with a bare
ModuleNotFoundError:
Molecular Docking
Vina is not included in [all], because it cannot be installed by pip on every platform. Installation of Vina
should be done directly using Conda or Pixi before the associated MolMiner modules can be used.
Quickstart
Tutorials will be forthcoming.
1 maintainer
Release files for MolMiner 0.0.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| molminer-0.0.3.tar.gz | 6.0 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| molminer-0.0.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 12.1 MB
Release files / molminer-0.0.3.tar.gz
| Download URL | molminer-0.0.3.tar.gz |
|---|---|
| Size | 6.0 MB |
| Tags | Source |
|
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Release files / molminer-0.0.3-py3-none-any.whl
| Download URL | molminer-0.0.3-py3-none-any.whl |
|---|---|
| Size | 6.0 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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