Assign Bond Orders

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


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




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