In openbabel, I have to upload a SMILES file (with extension. smi). I don't know how to save SMILES string (e.g.: C12C3C4C1C5C4C3C25) into SMILES file in my computer. I have tried in cactus (https://cactus.nci.nih.gov/translate/) but many of the times it ended up showing "Invalid SMILES". Can anyone suggest how I can fix it?
in openbable http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html using this link select input smiles and output as s
df than click on convert, as a result it gives some text copy that text and paste in notepad now save file ex filename.sdf
Sukhpreet Singh , Thanks.
It can be done by selecting a file (or folder) in the output file. After clicking 'convert' you will get the converted file with the .sdf extension. That's why, you don't need to copy and paste the converted results into notepad.
Use openeye
a=oechem.oemolistream('Input_SMILES_file')
b=oechem.oemolostream('output_file.pdb')
for mol in a.GetOEGraphMols():
oechem.OEWriteMolecule(b, mol)
You can use openbabel too
Regards
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