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Add Hydrogens

Adds hydrogen atoms to produce an all-atom structure.

Backend implementation

utilities/applyhtreat
The command line tool applyhtreat is used to implement this node.

Options

Column containing structure

Select column in the data input table containing the structures

Output Column Structure

Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaces Input - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Input Ports

: Molecules in Maestro, Sd, Mol2 or Pdb format

Output Ports

: Molecules with hydrogens added in Maestro, Sd, Mol2 or Smiles format

Views

Std output/error of Apply H Treatment: Std output/error of Apply H Treatment

Workflows

Developers

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Installation

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

v5.2

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

Plugin provider: Schrödinger

Plugin version: 24.3.138.v202407300410

On NodePit since: 2023-12-06

Last update: 2024-11-20

KNIME versions: 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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