Optimizes the geometry for an input RDKit Mol column and calculates the molecule's energy in kcal/mol. If the passed in molecules have no conformation, it will be calculated. The optimization is based on a particular force field and a number of iterations. It is also possible to turn off optimization completely by iterating 0 times. Optionally already available coordinates can be removed in order to calculate new ones from scratch. The following force fields are supported:
- UFF: Universal force field is an all atom potential containing parameters for every atom. The force field parameters are estimated using general rules based only on the element, its hybridization, and its connectivity. Published in: UFF, a Full Periodic Table Force Field for Molecular Mechanics and Molecular Dynamics Simulations by A.K. Rappe, C.J. Casewit, K.S. Colwell, W.A. Goddard III, W.M. Skiff, J.Am. Chem. Soc. 114 (1992) 10024–10035
- MMFF94: Merck molecular force field. Published in: Basis, form, scope, parameterization, and performance of MMFF94, Thomas A. Halgren, J. Comp. Chem.; 1996; 490-519
- MMFF94S: Static variant of MMFF94. MMFF94S incorporates altered out of plane bending parameters that yield planar (or nearly planar) energy-minimized geometries at unstrained delocalized trigonal nitrogen centers. Published in: MMFF VI. MMFF94s option for energy minimization studies, Thomas A. Halgren; 1999; J. Comput. Chem., 20: 720–729
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