Posit How to

Ignore Nitrogen stereo

Nitrogen stereo can be ignored in Posit by constructing OEPosit with an OEPositOptions object that has the OEPositOptions.SetIgnoreNitrogenStereo method set to True.

Prepare molecules for Posit

With default settings, Posit internally generates the required input conformers and Posit can be used with 2D input molecules. However, if it is desired to pass a pre-generated set of conformers to Posit, following are the recommended ways to supply or prepare molecules for POSIT.

1. Use OMEGA or the OMEGA toolkit to prepare molecules or expand the stereo chemistry using OEFlipper. POSIT is guaranteed to work correctly if the input molecules have been generated by OMEGA.

2. Set the OEPositOptions fullConformationalSearch option to be false. See the section OEPositOptions for more details. This method of running POSIT is not recommended as a large portion of the flexible methodology will be deactivated.

Use multiple receptors

Multiple receptors can be passed to Posit by calling the AddReceptor with each of the receptors as shown in the example, Listing 5. The OEPosit will automatically detect the best receptor for the ligand in action and dock to it.

One of the difficulties of docking to multiple receptors, is that they can consume quite a large amount of memory so holding multiple docking objects at the same time can be problematic. This can be controlled with the SetPoserCacheCount method, based on the available hardware capacity and the size of the receptors in use.

Obtain clash-free pose

Pose generated from Posit with the default options can sometimes contain clashes. Users have the option to perform pose relaxation, either on the clashed poses or on all generated poses, with the appropriate option using the SetPoseRelaxMode method.