Vernalis PDB Connector KNIME nodes package version 1.30.1.v202103301200 by Vernalis (R&D), UK
This node provides access to the RCSB PDB advanced query webservice, in an interface which closely follows the web UI at http://www.rcsb.org/search/advanced Queries comprise nested fields and subgroups (which themselves can contain fields / subgroups to an arbitrary depth). The items in each field are combined using the indicated logic operator
Fields can be removed by clicking on the 'X' button at the left-hand side of the field, and added by clicking the 'Add Field' button at the bottom of the relevant group.
Subgroups can be added by clicking the 'Add SubGroup' button at the bottom of the relevant parent group panel, and removed by clicking the 'Remove Group' button at the bottom of the subgroup. The top-most 'parent' group cannot be removed, although it can be left empty.
Individual fields can be reset by clicking the 'Clear' button at the right-hand side of the field. Clicking on the 'Clear' button at the bottom of a subgroup panel removes all fields and subgroups from that panel
Queries can be tested by pressing the 'Count' button, either at the right-hand side of the field or the bottom of the group panel. In either case, the button text is replaced with the count for the relevant part of the query (field, subgroup or entire query). The button remains unavailable for repeated counting until the query it relates to is changed in some way.
Many of the input boxes will provide live drop-downs of possible options once text entry has started.
The relationship between Text, Structure and Sequence queries is always 'AND'
Perform chemical ligand searches
To use this node in KNIME, install Vernalis KNIME Nodes from the following update site:
A zipped version of the software site can be downloaded here.
You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.
You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.
Do you have feedback, questions, comments about NodePit, want to support this platform, or want your own nodes or workflows listed here as well? Do you think, the search results could be improved or something is missing? Then please get in touch! Alternatively, you can send us an email to firstname.lastname@example.org, follow @NodePit on Twitter, or chat on Gitter!
Please note that this is only about NodePit. We do not provide general support for KNIME — please use the KNIME forums instead.