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draw_structures
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| from rdkit import Chem | |
| from rdkit.Chem import AllChem | |
| from rdkit.Chem import Draw | |
| import os | |
| import pandas as pd | |
| import argparse | |
| def get_all_file(path): | |
| filename_list=[] | |
| files = os.listdir(path) | |
| for filename in files: | |
| filename_list.append(filename) | |
| return filename_list | |
| if __name__ == "__main__": | |
| parser = argparse.ArgumentParser(description='filename') | |
| parser.add_argument('filename') | |
| args = parser.parse_args() | |
| data = pd.read_csv(args.filename) | |
| smiles = data["smiles"] | |
| index=0 | |
| for smile in smiles: | |
| index+=1 | |
| print(smile) | |
| try: | |
| mols_suppl = Chem.MolFromSmiles(smile) | |
| Draw.MolToFile(mols_suppl,'.//png//'+str(index)+"."+smile+'.png',kekulize=True) | |
| except Exception as identifier: | |
| print(index, " is None.") |
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What is it?
This is a script that uses rdkit library to convert molecules to images.
What are its requirements?
python3
rdkit
pandas
The input file must be in "CSV" format and it must have a png directory.
It can only be used in the Anaconda Prompt because the rdkit library only is supported in Anaconda.
How to use it in the command line?
python draw_structures.py yourfilename.csv