Vernalis PDB Connector KNIME nodes package version 1.27.0.v202008190633 by Vernalis (R&D), UK
The PDB Connector source node provides connections to two RESTful Web Services for search and retrieval of information from the Protein Data Bank:
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 (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 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 new PDB Connector 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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