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PDB Connector Custom Report

DeprecatedVernalis PDB Connector KNIME nodes package version 1.30.2.v202105121103 by Vernalis (R&D), UK

This node is no longer functional due to the shutdown of the remote webservices - Please use the new 'PDB Connector Structure Standard Report' node instead

The new PDB Connector Custom Report 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

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

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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Incoming table containing a column of PDB structure IDs

Output Ports

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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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