Identify ligands

This protocol tries to identify a set of Small Molecules based on the SMILES string for each of them. To do so, it uses the PubChem API. If no exact match is found, it looks for similar compounds (which are specified in a summary file) and outputs the most similar. The protocol further identifies the small molecule by using the PubChem cross references to extract the ID from other databases (currently ZINC and ChEMBL). All this identifiers are stored in the object, and the user can choose to switch the main molecule name by one of them.

Input

Note

All parameters include a help button that gives further information for each of them.

Identify ligands form

The result of this protocol is a SetOfSmallMolecules which includes the found identifiers for each molecule.

Identify ligands output

Test

This protocol has an integrated test that can be run using the following command:

scipion3 tests pwchem.tests.tests_databases.TestIdentifyLigands