rdkit/README.md

# Molecular Fingerprinting

*author: shiyu*

<br />

## Desription

Molecular Fingerprinting encodes a Simplified Molecular Input Line Entry Specification (SMILES) as a fingerprint. The fingerprint can represent elements, atom pairs, or functional groups, etc., and are often used for substructure searches and similarity searches in drug discovery. 

This operator uses [RDKit](https://www.rdkit.org/docs/index.html) to generate the molecular fingerprint.



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## Code Example

An example that use the Morgan algorithm to generate a fingerprint of the molecular formula 'Cc1ccc(cc1)S(=O)(=O)N'.

*Write a same pipeline with explicit inputs/outputs name specifications:*

```python
from towhee.dc2 import pipe, ops, DataCollection

p = (
    pipe.input('smiles')
        .map('smiles', 'fingerprint', ops.molecular_fingerprinting.rdkit())
        .output('smiles', 'fingerprint')
)

DataCollection(p('Cc1ccc(cc1)S(=O)(=O)N')).show()
```
<img src="./result2.png" height="75px"/>



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## Factory Constructor

Create the operator via the following factory method:

***molecular_fingerprinting.rdkit( algorithm: str = 'morgan', size: int = 2048)***



**Parameters:**

***algorithm:*** *str*

Which algorithm to use for fingerprinting, including 'morgan', 'daylight', 'ap', 'maccs', defaluts to 'morgan', and there is the [list of available fingerprints](https://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-fingerprints).



***size:*** *int*

The bit vector size just for morgan and daylight algorithm, defaults to 2048.



<br />



## Interface

An molecular fingerprinting operator takes a SMILES as input.
It uses the RDKit specified by algorithm name to generate a SMILES fingerprint.

**Parameters:**

***smiles:*** *str*

A Simplified Molecular Input Line Entry Specification (SMILES).



**Returns:** *bytes*

The molecular fingerprint.