This namespace contains constants describing the type of optimization run.
Indicates a single-point geometry run.
Optimization in torsional coordinates. In the case of a ligand in the protein active
site, translational and rotational degrees of freedom are included in the optimization.
torsional coordinates defines a set of rotors in the molecules. Numerical
torsional coordinates are dihedral angles defined by Cartesian coordinates
of 4 bonded atoms
a-b-c-d where the middle bond between atoms b and c is a
rotatable bond. Please look at the OEChem documentation for the definition of
rotatable bond. Bonds a-b and c-d are selected arbitrarily but uniquely, so a single
dihedral angle is assigned to each torsional coordinate.
Torsional coordinates are
a subset of
torsional space, however usually the latter term is used
synonymously with the former.
Optimization in atomic Cartesian coordinates.
This flag applies only for the optimization of a ligand inside the protein. Both
translational and rotational degrees of freedom are optimized. Term
optimization means that only 6 degrees of freedom are allowed to change during
optimization. Those are 3 translational and 3 rotational degrees of freedom.
In our implementation 3 rotational degrees of freedom are described by 4 quaternions.
Please consult any molecular physics or mechanics textbook for the definition of
translational-rotational degrees of freedom and