Vernalis PDB Connector KNIME nodes package version 1.24.2.v201911141223 by Vernalis (R&D), UK
The PDB Connector (XML Query) node provides connections to two RESTful Web Services for search and retrieval of information from 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, or the new PDB Connector XML Query Builder ). 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 node also allows for simple generation of a second report format table from a query run in either this or the PDB Connector node, as both nodes provide the query xml as a flow variable at the output ports.
The node provides options to use either POST or GET report webservice variants. The POST option is newer, and should be used unless machine memory is an issue (The node will download the entire report to memory). The GET service requires multiple requests of the webservice, and URL length limits the number of hits which can be processed in each call, and the number of available report fields. Lower values for the maximum URL length (2000-8000) will result in more calls, and fewer fields being available, but is more reliable when running through a proxy server. Higher values should be used where possible. Multiple calls to the GET service are likely to be intercepted by the PDB server "Robot Blocker", adding further time to the query. The GET service should be avoided wherever possible. The node will make a number of retries at increasing delay intervals (0, 1, 5, 10, 30, 60, 300, 600 seconds) to download each block of report data during the second part of the execution (There is an additional delay, defaulting to 1 second, on each attempt, which can be adjusted by adding the line -Dknime.url.timeout= followed by a value in milliseconds - e.g. 5000 for 5 seconds to the knime.ini file).
The PDB Connector (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 firstname.lastname@example.org
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