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PDB Connector (XML Query String)

DeprecatedVernalis PDB Connector KNIME nodes package version 1.30.1.v202103301200 by Vernalis (R&D), UK

This node has been deprecated as the remote webservices have been shut down - please use the new family of PDB Connector nodes instead

Options

Query Options

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. If using the GET option, the maximum URL length can be set
Max. Report GET URL Length
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.
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.)
Messages
Messages relating to the Test Query button are displayed in this area
XML Query
The PDB XML advanced query text should be entered here. See above for details

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.

Input Ports

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

Output Ports

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One-column table of PDB IDs that match query
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Custom report fields.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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