Class TrajFlexSlave

Calculate the pairwise rmsd between frames of a trajectory.

Instance Methods

initialize(self, params)
Expects:

array __getFrames(self, f)
Load coordinate frames from file or take them from own cache

1|0 requested(self, i, j)
Checks if the rmsd of two frames i and j are to be calculated:

[float] calcRmsd(self, window, f1, f2)
Calulate the rmsd between two frame chunks.

[float] go(self, jobs)
Run job.

reportError(self, msg, window)
Report errors.

Method Details

Expects:

 {'ferror':str,
  'trajMap':[int],
  'only_off_diagonal':1|0,
  'only_cross_member':1|0}

Load coordinate frames from file or take them from own cache

Checks if the rmsd of two frames i and j are to be calculated:

 requested( int_f1, int_f2 ) -> 1|0

Calulate the rmsd between two frame chunks.

window (((int, int),(int,int))) - start and end of two frame chunks within the whole trajectory
f1 (array) - frame chunk
f2 (array) - frame chunk

Run job.

jobs ({((int,int),(int,int)) : (str, str)}) - { ((int,int),(int,int)) : (str, str) }, maps start and end position of two chunks of coordinate frames to the files where the two chunks are pickled.

Report errors.

msg (str) - error message
window (((int, int),(int,int))) - start and end of two frame chunks within the whole trajectory