reset ( self,  **kw )

Reset interpolation (just remove all but first coordset)

minimizeCallback ( self,  mol )

interpolateCallback ( self,  mol )

interpolate (
        self,
        m,
        **kw,
        )

Interpolate to new conformation m.

trajectory ( self )

__init__ (
        self,
        m,
        **kw,
        )

Compute a trajectory that transforms molecule conformation m. Subsequent calls to interpolate must supply molecules that have the exact same set of atoms as m. Currently support keyword options are:

method string, default "corkscrew" Use interpolation method method. Known methods are "corkscrew", "independent" and "linear". rate string, default "linear" Interpolate frames so that the trajectory motion appears to be "rate": either "linear" (constant motion throughout) or "sinusoidal" (fast in middle, slow at ends). frames integer, default 20 Number of intermediate frames to generate in trajectory minimize boolean, default False Run energy minimization for each trajectory frame when it is created. steps integer, default 60 If "minimize" is True, run "steps" steps of minimization for each frame.

If "minimize" is True, the steepest descent minimizer from MMTK is used for minimization with the Amber94 forcefield. Non-standard residues are parameterized using DockPrep and Parmchk, which generates GAFF parameters. mStart and mEnd must have hydrogens already added (this is to provide flexibility for caller to control hydrogen addition conditions).

Note that this class assumes that the hydrogens have already been added. This is because the hydrogen addition code (AddH) may put different number of hydrogens on different conformations because they have different hydrogen bonding patterns. To avoid this, all conformations must use the same idatmType for all atoms, and there is no way for this class to guarantee for that to happen. So we punt the problem to the caller.