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PDB Connector Query Only

Vernalis PDB Connector KNIME nodes package version 1.17.3.v201808160901 by Vernalis (R&D), UK

The PDB Connector Query Only source node provides connections to the RESTful Web Service for searching for information from the Protein Data Bank at http://www.rcsb.org/pdb/rest/search

The user interface dialog options are designed to be a close mimic of the interactive web-based search and reporting options provided at http://www.pdb.org/pdb/search/advSearch.do and the user is encouraged to explore this resource for a full explanation of each search option. Alternatively, use the PDB Connector Query only (XML Query) node to paste an XML query directly from the "Query Details" link in the query results pages on the PDB page. The XML Query is made available as a flow variable ( xmlQuery ) after node execution.

The PDB Connector Query Only 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

Options

Query Options

Remove Similar Sequences
Control the (optional) sequence similarity filter, used to remove similar sequences from the search hits.
Match multiple query terms using
Control the composite query logic (individual query options can be either ANDed or ORed together)
Clear Query
Clear all query options
Test Query
Test the current query, with display of xml query string and result count. NB The 'Test' button uses the query configured in the dialog, without reference to flow variable settings.
Messages
Messages relating to the Test Query button are displayed in this area
XML Query string
The xml query string generated from the user settings is displayed here when the 'Test' button has been pressed

Other query option tabs

Selected
To select a query option, either check the "Selected" checkbox or click anywhere on one of the individual query parameters. To unselect a query option, uncheck the "Selected" checkbox.
Value(s)
Enter values for the query term in the box(es) provided

Output Ports

One-column table of PDB IDs that match query

Views

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

Best Friends (Incoming)

Best Friends (Outgoing)

Update Site

To use this node in KNIME, install Vernalis PDB Connector KNIME nodes package from the following update site:

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