Process Ligand API

The Process Ligand API generates conformers and parameters of ligands, which can be analyzed on their own or used for other ligand workflows, like Ligand Analyzer, where it is necessary to model ligand flexibility. This command takes a SMILES string or SDF file as input and generates:

  • Multiple conformers of the ligand
  • Parameter files for molecular dynamics
  • Output files in various formats

Command Line Interface

Examples

Run process ligand on a SMILES input

lev engine submit process-ligand \
    --smiles "CC(=O)OC1=CC=CC=C1C(=O)O"

*Run process ligand on an SDF input

lev engine submit process-ligand \
    --sdf-file ligand.sdf

Generate more conformers than default (10)

lev engine submit process-ligand \
    --smiles "CC(=O)OC1=CC=CC=C1C(=O)O" \
    --n-conformers 20

Flags

  • --ligand-sdf (str) (default “null”)
    • Path to input SDF file
  • --smiles (str) (default “null”)
    • SMILES string of the ligand to process
  • --n-conformers (int32) (default 10)
    • Number of conformers to generate

Outputs

  • ligand.sdf
    • Structural data file containing the ligand
  • ligand.params
    • Stores precomputed information about the geometry and chemistry of the ligand
  • conformers.pdb
    • A library of ligand conformers, formatted as a PDB file containing the coordinates of each conformer

Updated: