obabel error on reading "Cl" as "l"

[zubairhussain123]

while converting the **smi** files to other formats like **pdb** or **mol** sometimes the obabel can't read **Cl** atoms in the smiles becuase they are not in the proper format or the **Cl** is sometimes written as **l**. To fix this error use python code as given below:

with open("list.txt", "r") as input_file: # replace list.txt according to your file name
    smiles_data = input_file.read()

# Replace 'l' with 'Cl' in the SMILES data
modified_smiles_data = smiles_data.replace("l", "Cl")

# Save the modified SMILES data to a new file
with open("modified_smiles.txt", "w") as output_file:
    output_file.write(modified_smiles_data)

This code will generate a new fixed file named as 'modified_smiles.txt'.

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[nbehrnd]

@zubairhussain123 As suggested by the issue template, to ease a replication and potential improvement of obabel, share

• a typical input file which leads to these observations
• a report of version of OpenBabel you used and the hosting operating system

[fredrikw]

I'm sorry but I fail to see why it's an issue with OpenBabel that you have broken SMILES strings. And running this code will produce garbage if you have a proper SMILES since every instance of "Cl" will be "CCl"...