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Rxn to RInChI

StreamableReaction extension for KNIME Workbench version 1.0.0.qualifer by Lhasa Limited

In 2011, the first prototype of RInChI was introduced as version 0.02 based on Python programming (Grethe, Goodman, Allen, 2013). To make the resulting libraries comparable with InChI deliveries, to increase the search ability of RInChIKeys in the Web by the introduction of the Web-RInChIKey and to fix a number of bugs and development gaps in the former version this new version (version number 1.00) has been created. This version is supposed to be published for general usage by the InChI Trust.

For more details see: http://www-rinchi.ch.cam.ac.uk/.

RInchi
The RInChI format is a hierarchical, layered description of a reaction with different levels based on the Standard InChI representation (version 1.04) of each structural component participating in the reaction.

Inchi Key
RInChIKeys are hashed representations of the RInChI strings. The hashing process creates shorter strings that are unique representations of the original (longer) RInChIs. However, RInChIs (and therefore the original RXN and/or RD file) cannot be rebuilt out of the hashed string. That makes RInChIKeys an encrypted unique depiction of chemical reactions especially suitable for database processes and web operations. For the anticipated usage, three different types of RInChIKeys have been developed:

  1. Long-RInChIKeys are strings concatenated from the InChIKeys of each reaction component. The length of Long-RInChIKeys is flexible.
  2. Short-RInChIKeys are created by hashing the major and minor layers of InChIs for each group of RInChI to a fixed length string
  3. Web-RInChIKeys deduplicate InChIs over all groups and hash all major and minor InChI layers into a fixed length string ignoring the specific role of the reaction components.
All RInChIKeys are generated using the sha2 hashing functionality used by and provided with the InChI algorithm.

Input format
Accepts RXN or RDF input. Note: If agents occur, the RXN file format is not sufficient as agents in an rxn string are ignored by the RInChI library.

Instead, the reaction must be described in the RD file format that contains catalysts, solvents and other reagents as molfiles following the reaction section in RXN format within the RD file section.


For example:

$DTYPE RXN:AGENTS(1):MOLECULES(1):MOLSTRUCTURE
$DATUM $MFMT
... molfile....
$DTYPE RXN:AGENTS(1):MOLECULES(2):MOLSTRUCTURE
$DATUM $MFMT
... molfile....

Options

RXN
The reaction (please note the requirement for agent handling))
Force equilibrium
To handle a reaction as equilibrium reaction, the related parameter “in_force_equilibrium” of the function rinchi_from_file_text or rinchikey_from_file_text must be set to TRUE (default FALSE). Note: There is no defined place for the equilibrium parameter in the RXN file definition. For equilibrium reactions the comment “NOTE: Reaction is an equilibrium reaction.” is returned in the comment section of the rebuilt RXN/RD file

Input Ports

Icon
Input reactions in RXN or RDF format. Please note the requirement for agent handling.

Output Ports

Icon
The RInChI, AUX info, and all 3 keys (web, long, shorT))

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install Lhasa reaction contributions from the following update site:

KNIME 4.3

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

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