0 ×

Assign Bond Orders

Schrödinger extension for KNIME Workbench version 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


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 in Maestro, Sd, Mol2, Pdb or SMILES format


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

Best Friends (Incoming)

Best Friends (Outgoing)



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


You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

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. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.


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.