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Proteax as_molfile

The chemical 2D structure that the supplied protein entry represents. The structure is represented in MDL molfile format (V2000 or V3000 depending on molecule size).

Options

Protein text or molfile: Protein entry in UniProt, PLN, GPMAW, FASTA, or MDL molfile format.
Molfile options: Controls molfile generation. Available options are 'expansion-mode=all|condensed|minimal residue-proxy-atom=<atom-symbol> proxy-atom-chain-maxlen=<integer> (>= 3) explicit-hydrogen-mask=<mask> x-proxy-atom=<atom-symbol>'. The default 'expansion-mode' is 'all'.
Result column name: Name of appended column with result.
Add error column: Adds a column with any error messages. The error column is always named like the output column plus " - error". If the error column is not added, all errors will be logged to the KNIME console instead.

Input Ports

: Table with at least one column that has a protein entry or molfile.

Output Ports

: Table with an appended column containing the calculated result.

Popular Predecessors

Proteax as_pln100 %

Popular Successors

Molecule Type Cast100 %

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Installation

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

v5.2

Plugin provider: Biochemfusion ApS

Plugin version: 2.0.0.20130511

On NodePit since: 2023-12-06

Last update: 2026-01-01

KNIME versions: From v3.6 to v5.2

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