This node queries the PDB (www.rcsb.org) webservice described briefly here. The query accepts a SMILES or SMARTS query string, and can perform a variety of query types:
- Exact Match
- Substructure
- Superstructure
- Similarity
The SMILES string is only validated by sending it to the service - if the service is unable to correctly interpret the supplied string, then an execution error will result. The service will return a list of chemical components, along with all the structures each component is found in, and a number of details about the chemical component(s), as specified in the node dialogue. The second and third output tables provide a sorted list of the chemical component and structure IDs respectively.
NOTE Queries are sent un-encrypted to the service, and so could be intercepted by 3rd parties.
The PDB SMILES Query node was developed by Vernalis (Cambridge, UK). For feedback and more information, please contact knime@vernalis.com
Options
Output Ports
- Output table containing at the very least a list of all the Heterogen ID:Structure ID pairs found for ligands matching the query entered, plus additional columns relating to the ligand properties
- A list of the ligand IDs matching the query entered
- A list of the structure IDs containing ligands matching the query entered
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