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cheminformatics

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Perform operations on chemical structures using Python.

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# cheminformatics
## Perform operations on chemical structures using Python.

### Introduction
**_pdb_ligand_id-to-smi.ipynb_** notebook demonstrates how to obtain SMILES of ligands using ligand ID from PDB.

**_ligand-id-to-str-in-pdb-format.ipynb_** will download 3D ligand structures from PDB in SDF format and then will convert them into PDB format.

**_sdftosmi.py_** script will convert molecules in sdf format into their corresponding SMILES. All molecules are provided in a single SDF file as input.

**_smitostr.py_** will convert smiles to structure.

**_swarm-plot.ipynb_** plots swarm boxplot of docking score of ligands.

### Requirements
It requires Python3. This script uses RDKit and some additional packages. Install them using the following commands.

`conda create -c conda-forge -n my-rdkit-env rdkit`

`conda install pandas`

### Usage
To get SMILES and/or structures from ligand IDs, save all ligand IDs in a CSV file (lig-ids.csv) and run the notebook(s).
The other two scripts are simple Python scripts that you can easily run in a terminal.

For more information, read this article:
https://bioinformaticsreview.com/20221120/how-to-obtain-smiles-of-ligands-using-pdb-ligand-ids/

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