smiles_to_structure

This script reads a list of SMILES (Simplified Molecular Input Line Entry System) strings from a file, converts them into chemical structures using RDKit, and displays the structures as images directly within a Jupyter notebook.

https://github.com/quantaosun/smiles_to_structure

Science Score: 44.0%

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Low similarity (9.4%) to scientific vocabulary

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Repository

Basic Info

Host: GitHub
Owner: quantaosun
Language: Jupyter Notebook
Default Branch: main
Homepage:
Size: 4.8 MB

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Open Issues: 0
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Created almost 2 years ago · Last pushed over 1 year ago

Metadata Files

Readme Citation

README.md

SmilestoStructure

This script reads a list of SMILES (Simplified Molecular Input Line Entry System) strings from a raw SMILES file, converts them into chemical structures using RDKit, and displays the resulting structures as images directly within a Jupyter notebook. Each structure is labeled with its corresponding entry number for easy identification.

Tutorial: 1. Generate a csv file, for example, for a specific protein target, you can download a csv file from Chembl database

Open this csv file with your excel or Mac number software, export it to csv again, since the downloaded csv may have some minor format issue not recognised by this code.
Upload this new csv file to the code via the Colab budge link, and it is ready to process through the SMILES inside the csv you provided.
read the file by modifying the file name df = pd.read_csv('11.csv') df
Change the column number based on where is your SMILES in the csv file, if they are stored at 9th column, it should be !awk -F "\"*,\"*" '{print $8}' 11.csv > smile.smi

(6. Delete rows that not a SMILES, and export the new smiles string to a new csv file.)

Display the molecules as images inside Jupyter Notebook

Owner

Name: Sun
Login: quantaosun
Kind: user
Location: China

Repositories: 218
Profile: https://github.com/quantaosun

Medicinal Chemistry/Modelling

Citation (CITATION.cff)

cff-version: 0.0.1
message: "If you use this software, please cite it as below."
authors:
- family-names: "Sun"
  given-names: "Quantao"
title: "smiles_to_structures"
version: 0.0.1
date-released: 2024-7-24
repository-code: https://github.com/quantaosun/Smiles_to_Structure
keywords:
  - "rdkit"
  - "jupyter notebook"
  - "smiles structure"
license: MIT
url: https://github.com/quantaosun/Smiles_to_Structure

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