0 ×

PDB Property Extractor

StreamableVernalis custom KNIME nodes package version 1.27.2.v202010191232 by Vernalis (R&D), UK

This node attempts to extract one or more properties from a PDB cell column.
Note that not all properties might be available depending on the structure type, in which case a missing value will be returned.
The available properties at present are:
  • PDB Structure ID
  • Title
  • Experimental Method
  • Resolution
  • Number of Models
  • R
  • Rfree
  • Space Group
  • REMARK 1
  • REMARK 2
  • REMARK 3
The Number of Models is retrieved from the optional 'NUMMDL' PDB field. If this field is absent, but the file contains either ATOM or HETATM fields, this value is set to 1, as is the default interpretation in the PDB file format description.
Multi-line text fields (e.g. TITLE, REMARK 1 etc.) are converted to single-line strings.

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 contaning the PDB cells
Data to Extract
Select one or more options from the list

Input Ports

Icon
Input data table containing a column of pdb cells

Output Ports

Icon
Output data table with appended properties

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Vernalis KNIME Nodes from the following update site:

KNIME 4.2
Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform.

Developers

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.