Python API · stjames models · API example
Rowan's strain calculation estimates the energy cost of a molecular pose, such as a docked ligand conformation. It gently relaxes the submitted geometry under positional restraints, then compares its energy with the lowest-energy conformer found in a conformer search. Both are scored using the same final method and solvent settings. The reported strain is an energy difference in kcal/mol; the restraint penalty itself is excluded.
Positional restraints let bond lengths and angles relax toward the chosen method's preferences while discouraging major changes to the pose. This reduces artificially high energies caused by small geometric differences between, for example, a docking force field and the energy method. Inspect the relaxed structure to check that it still represents the pose you intended to evaluate.
Results include the strain energy, the restrained geometry, and the reference conformers. The reference is the best conformer found, rather than a guaranteed global minimum. If the relaxed pose lies below the search minimum, an additional free optimization helps update the reference.
Strain describes the molecule's internal energetic cost under the selected model. It is not a binding affinity or a conformational free energy. Compare results using consistent protonation states, methods, solvent settings, and restraint strengths.