PDB Saver

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

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Installation

To use this node in KNIME, install the extension Vernalis KNIME Nodes from the below update site following our NodePit Product and Node Installation Guide:

v5.3

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

Plugin provider: Vernalis Research, UK

Plugin version: 1.36.7.v202405281205

On NodePit since: 2024-07-11

Last update: 2024-11-21

Tags: Streamable

KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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