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Assign Bond Orders

Schrödinger extension for KNIME Workbench version 20.3.139.202008121324 by Schrödinger

Assigns double and triple bonds to input structures based on molecular geometry (bond length, bond angles, and dihedral angles). Useful when importing ligands from PDBs into Maestro.Please check the output structure for errors and compare it to the molecular formula.

Backend implementation

$SCHRODINGER/run -FROM maestro fix_bond_orders.py

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

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Molecules in Maestro, Sd, Mol2 or Pdb format

Output Ports

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Molecules in Maestro, Sd, Mol2, Pdb or SMILES format

Views

Std output/error of Fix Bond Orders
Std output/error of Fix Bond Orders

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:

KNIME 4.2
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