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PDB Loader

StreamableVernalis custom KNIME nodes package version 1.12.0.v201708101336 by Vernalis (R&D), UK

Loads PDB files specified by a valid full file path or URL into a table.
Files may be local or remote, as long as the URL is accessible.
Only paths ending .pdb or .pdb.gz will be loaded. The resulting column will be cast as PDBCells.

File encoding is attempted as follows:

  1. Firstly, the URL connection to the supplied file is inspected for encoding information.
  2. If none is available, then the first 4 bytes of the file are inspected for any BOM present, and if so, the following are recognised:
    • UTF-8
    • UTF-16 (Big- and Little Endian)
    • UTF-32 (Big- and Little Endian)
  3. Finally, the default (UTF-8) is assumed. As UTF-8 is not required to provide a BOM, this is a reasonable guess in most cases.
A console INFO entry is added for each file format detected, and a WARN entry added when the default is used because none could be detected. If manual control of the file encoding is required, then the Load text-based files node should be used, followed by a Molecule Type Cast node

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

Options

Select a column contaning the PDB paths
Select the column containing the file paths or URLs
PDB File column name
Enter name of column for PDB cells

Input Ports

Input table containing paths or URLs to pdb files to load

Output Ports

Output table with pdb files loaded

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Update Site

To use this node in KNIME, install Vernalis custom KNIME nodes package from the following update site:

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