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PDB Connector

Vernalis PDB Connector KNIME nodes package version 1.24.4.v201912051245 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:

  • Advanced Search (http://www.rcsb.org/pdb/rest/search)
  • Custom Report (http://www.rcsb.org/pdb/rest/customReport)

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 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)
Ligand Image Size
Select the ligand image size to use in the generation of ligand image URLs (applies to Ligand Image field only).
Use POST Query method (Faster)
Select the POST or GET service. GET is older, but may limit number of report fields which can be returned, and is slower.
Max. Report request size
If using the GET option, the maximum URL length can be set between 2000 and 8000. Higher values allow more fields to be returned, and result in fewer calls to the webservice, but may fall foul of proxy servers. For POST request, longer requests can be sent, but may exceed an internal limit on the remote server or use too much memory
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

Report Options

Select report
Use the dropdown menu to select from a number of predefined standard reports. Select 'Customizable Table' to allow fine-grained selection of all custom report fields, using the individual and group field selectors.
Select All
Initialise a Customizable Table with all report fields.
Clear All
Initialise a Customizable Table with no report fields.

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
Custom report fields.

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)

Workflows

Installation

To use this node in KNIME, install Vernalis KNIME Nodes from the following update site:

KNIME 4.1
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