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PDB Connector Query Only (XML Query)

Vernalis PDB Connector KNIME nodes package version 1.27.2.v202010191232 by Vernalis (R&D), UK

The PDB Connector Query Only (XML Query) node provides connections to the RESTful Web Service for searching the Protein Data Bank.

The query is entered as a single XML string in this node (For a user-friendly query builder version, see the original PDB Connector node). This query can be copied and pasted from the "Query Details" link on a PDB query results page at the RCSB PDB . The XML Query is made available as a flow variable ( xmlQuery ) after node execution. Worked examples of using the node using these methods are provided here .

The PDB Connector Query Only (XML Query String) node was developed by Vernalis (Cambridge, UK) , based on the original PDB Connector node developed by Enspiral Discovery in collaboration with Vernalis (Cambridge, UK) . For feedback and more information, please contact knime@vernalis.com


Query Options

Clear Query
Clear all query options. If a flow variable has been set for the XML Query, this will also be un-set
Test Query
Test the current query, with display of result count. If a flow variable has been specified for the xml query, it's value will be used in the test. (NB This behaviour is different from that in the PDB Connector node, where the 'Test' button uses the query configured in the dialog, without reference to flow variable settings.). This button also lays out the XML clearly in the XML Query String box
Messages relating to the Test Query button are displayed in this area
XML Query string
The PDB XML advanced query text should be entered here. See above for details

Input Ports

Optional flow variable connection, which could contain the XML query in a flow variable

Output Ports

One-column table of PDB IDs that match query


XML Query
A view of the combined XML Query
Logical Query
A 'logical' view of the combined Query

Best Friends (Incoming)

Best Friends (Outgoing)



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