Bond Assignment#

enerzyme bond assigns chemical bonds to PDB cluster structures, typically from QuantumPDB workflows.

Command#

enerzyme bond -p cluster.pdb -m cluster.mol -i cluster.png -t ligands.sdf

Arguments#

  • -p — input PDB (cluster build output)

  • -m — output MOL with bond orders

  • -i — optional 2D depiction image

  • -t — template SDF (e.g. QuantumPDB ligands.sdf)

Implementation#

enerzyme/bond/bond.py:

  • pdb2mol() — RDKit PDB import

  • bond_with_template() — match ligand connectivity from template SDF

  • Residue-specific fixes (e.g. carboxylate protonation on ASP/GLU)

  • Metal/ligand handling heuristics

Use cases#

  • Prepare cluster.mol as Extractor.reference_mol_path

  • Generate chemically consistent inputs for QM suppliers

  • Visualize cluster connectivity (-i)

Requirements#

RDKit (included in standard Enerzyme conda env). Template quality strongly affects ligand bond orders in heterogeneous clusters.