I have a large database and I am trying to filter out ring structures which contain a particular functional group, for example, thiophene. It has to be within the core ring structures, not outside. Is there a node in Knime that I could use? or maybe a way to script it out in python?
Any help would be appreciated.
If you use Python, you can install RDKit ( https://www.rdkit.org/docs/Install.html ).
Then you can build molecules. For example:
- from rdkit import Chem
- molecule = Chem.MolFromSmiles('c1c(CCO)csc1')
Once you have a molecule, you can see if it matches a pattern that has been expressed as SMARTS notation:
- pattern = Chem.MolFromSmarts('c2ccsc2') # (i.e. thiophene)
- molecule.HasSubstructMatch(pattern)
- >>True
Documentation for SMARTS: https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
Documentation for RDKit: https://www.rdkit.org/docs/GettingStartedInPython.html
There may be a module in KNIME to do the same as I have described.
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