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PDB Saver

StreamableVernalis custom KNIME nodes package version 1.24.4.v201912051245 by Vernalis (R&D), UK

This node saves a copy of the PDB files held in a table column to filepaths held in a second column.
A rudimentary attempt is made to validate the filepaths - which must be complete paths, e.g. C:\Temp\myfile.pdb If the full folder path does not exist, an attempt is made to create it.
The returned column will contain a missing value if either of the input columns is a missing value, ' true ' if the file was successfully written, and ' false ' if it was not written (i.e. because overwrite was set to off, and the file existed, or because the directory could not be created or was not a valid path.)

This node was developed by Vernalis (Cambridge, UK) . For feedback and more information, please contact knime@vernalis.com

Options

Select a column containing the PDB cells
The column containing the content to be written to the file
Enter name of column for file paths
The column containing the full path to the output files
Save all files in parent folder
If checked, then the file path folder is assumed to contain sub-paths, or simply filenames, and will be relative to the indicated parent folder. Filenames not ending '.pdb' will be suffixed with this extension
Parent Directory
The optional parent folder to save files in
Overwrite files?
If checked, existing files are overwritten without warning
Enter name of column for save successful flag
The name of a boolean column for the outcome to be put in

Input Ports

The input table containing a column with pdb text and a column with filepaths

Output Ports

The input table with a boolean column indicating the outcome of local save added

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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Developers

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