__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.
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