University of Vienna
Question
Asked 3rd May, 2017
Is there any tool for determining functional groups in a given compound?
I'm looking for a tool that can give how many methyl groups, hydroxyl groups etc. are in a compound from it's SMILES, SDF or MOL2 format.
Most recent answer
The methyl group is not a functional group, but just a substructure. If you are interested in the functional groups of a molecule (in MDL molfile format), you might try checkmol: https://homepage.univie.ac.at/norbert.haider/cheminf/cmmm.html
Use the -ep option, e.g. checkmol -ep caffeine.mol
1 Recommendation
Popular answers (1)
Healx
If you are familiar with Python, you might want to try SMILES/SMARTS pattern matching in RDKit:
[in]>>from rdkit import Chem
[in]>>mol = Chem.MolFromSmiles('COC(=O)CNC(=O)CCCO')
[in]>>functional_group = Chem.MolFromSmarts('C=O')
[in]>>matches = mol.GetSubstructMatches(functional_group)
[in]>>len(matches)
[out]>>2
4 Recommendations
All Answers (7)
Healx
If you are familiar with Python, you might want to try SMILES/SMARTS pattern matching in RDKit:
[in]>>from rdkit import Chem
[in]>>mol = Chem.MolFromSmiles('COC(=O)CNC(=O)CCCO')
[in]>>functional_group = Chem.MolFromSmarts('C=O')
[in]>>matches = mol.GetSubstructMatches(functional_group)
[in]>>len(matches)
[out]>>2
4 Recommendations
Shahjalal University of Science and Technology
Thanks, how can I find SMARTS format of various functional groups?
Technische Universität Hamburg
I know this question is ancient and you probably implemented something yourself. But I wrote a paper on automatically fragmenting molecules. And applied it as an example on to UNIFAC:
University of Vienna
The methyl group is not a functional group, but just a substructure. If you are interested in the functional groups of a molecule (in MDL molfile format), you might try checkmol: https://homepage.univie.ac.at/norbert.haider/cheminf/cmmm.html
Use the -ep option, e.g. checkmol -ep caffeine.mol
1 Recommendation
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