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drfp-0.3.6
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مشاهده بیشترتوضیحات
An NLP-inspired chemical reaction fingerprint based on basic set arithmetic.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | drfp-0.3.6 |
| نام | drfp |
| نسخه کتابخانه | 0.3.6 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Daniel Probst |
| ایمیل نویسنده | daniel.probst@hey.com |
| آدرس صفحه اصلی | https://github.com/reymond-group/drfp |
| آدرس اینترنتی | https://pypi.org/project/drfp/ |
| مجوز | MIT |
[](https://doi.org/10.5281/zenodo.5268144)
# DRFP
An NLP-inspired chemical reaction fingerprint based on basic set arithmetic.
Read the associated [open access article](https://pubs.rsc.org/en/content/articlehtml/2022/dd/d1dd00006c)
## Description
Predicting the nature and outcome of reactions using computational methods is an important tool to accelerate chemical research. The recent application of deep learning-based learned fingerprints to reaction classification and reaction yield prediction has shown an impressive increase in performance compared to previous methods such as DFT- and structure-based fingerprints. However, learned fingerprints require large training data sets, are inherently biased, and are based on complex deep learning architectures. Here we present the differential reaction fingerprint *DRFP*. The *DRFP* algorithm takes a reaction SMILES as an input and creates a binary fingerprint based on the symmetric difference of two sets containing the circular molecular n-grams generated from the molecules listed left and right from the reaction arrow, respectively, without the need for distinguishing between reactants and reagents. We show that *DRFP* outperforms DFT-based fingerprints in reaction yield prediction and other structure-based fingerprints in reaction classification, and reaching the performance of state-of-the-art learned fingerprints in both tasks while being data-independent.
## Getting Started
The best way to start exploring DRFP is on binder.
A notebook that gets you started on creating and using DRFP:
[](https://mybinder.org/v2/gh/reymond-group/drfp/HEAD?filepath=notebooks%2F01_fingerprinting.ipynb)
A notbook that explains how you can use SHAP to analyse and interpret your machine learning models when using DRFP:
[](https://mybinder.org/v2/gh/reymond-group/drfp/HEAD?filepath=notebooks%2F02_model_explainability.ipynb)
## Installation and Usage
*DRFP* can be installed from pypi using `pip install drfp`. However, it depends on [RDKit](https://www.rdkit.org/) which is best [installed using conda](https://www.rdkit.org/docs/Install.html).
Once DRFP is installed, there are two ways you can use it. You can use the cli app `drfp` or the library provided by the package.
### CLI
```bash
drfp my_rxn_smiles.txt my_rxn_fps.pkl -d 512
```
This will create a pickle dump containing an numpy ndarray containing DRFP fingerprints with a dimensionality of 512. To also export the mapping, use the flag `--mapping`. This will create the additional file `my_rxn_fps.map.pkl`. You can call `drfp --help` to show all available flags and options.
### Library
Following is a basic exmple of how to use DRFP in a Python script.
```python
from drfp import DrfpEncoder
rxn_smiles = [
"CO.O[C@@H]1CCNC1.[C-]#[N+]CC(=O)OC>>[C-]#[N+]CC(=O)N1CC[C@@H](O)C1",
"CCOC(=O)C(CC)c1cccnc1.Cl.O>>CCC(C(=O)O)c1cccnc1",
]
fps = DrfpEncoder.encode(rxn_smiles)
```
The variable `fps` now points to a list containing the fingerprints for the two reaction SMILES as numpy arrays.
## Documentation
The library contains the class `DrfpEncoder` with one public method `encode`.
| `DrfpEncoder.encode()` | Description | Type | Default |
|-|-|-|-|
| `X` | An iterable (e.g. a list) of reaction SMILES or a single reaction SMILES to be encoded | `Iterable` or `str` | |
| `n_folded_length` | The folded length of the fingerprint (the parameter for the modulo hashing) | `int` | `2048` |
| `min_radius` | The minimum radius of a substructure (0 includes single atoms) | `int` | `0` |
| `radius` | The maximum radius of a substructure | `int` | `3` |
| `rings` | Whether to include full rings as substructures | `bool` | `True` |
| `mapping` | Return a feature to substructure mapping in addition to the fingerprints. If true, the return signature of this method is `Tuple[List[np.ndarray], Dict[int, Set[str]]]` | `bool` | `False` |
| `atom_index_mapping` | Return the atom indices of mapped substructures for each reaction | `bool` | `False` |
| `root_central_atom` | Whether to root the central atom of substructures when generating SMILES | `bool` | `True` |
| `include_hydrogens` | Whether to explicitly include hydrogens in the molecular graph | `bool` | `False` |
| `show_progress_bar` | Whether to show a progress bar when encoding reactions | `bool` | `False` |
# Reproduce
Want to reproduce the results in our paper? You can find all the data in the `data` folder and encoding and training scripts in the `scripts` folder.
# Cite Us
```
@article{probst2022reaction,
title={Reaction Classification and Yield Prediction using the Differential Reaction Fingerprint DRFP},
author={Probst, Daniel and Schwaller, Philippe and Reymond, Jean-Louis},
journal={Digital Discovery},
year={2022},
publisher={Royal Society of Chemistry}
}
```
نیازمندی
| مقدار | نام |
|---|---|
| - | rdkit-pypi |
| - | tqdm |
| >=1.21.0 | numpy |
| >=8.0.1 | click |
| - | importlib-metadata |
| - | tox |
| - | setuptools |
| - | setuptools-scm |
| - | pytest |
| - | pytest-cov |
| - | black |
نحوه نصب
نصب پکیج whl drfp-0.3.6:
pip install drfp-0.3.6.whl
نصب پکیج tar.gz drfp-0.3.6:
pip install drfp-0.3.6.tar.gz