PCA buildCovariance and app do not superpose well for projections

[yasirkhanqu]

The prody pca app uses DCDFile when the number of frames > 1000 (

ProDy/prody/apps/prody_apps/prody_pca.py

Line 96 in 454c40c

if len(dcd) > 1000:

) and uses the aligned kwarg of buildCovariance to control whether the trajectory frames should be superposed (

ProDy/prody/dynamics/pca.py

Line 124 in 454c40c

frame.superpose()

).

This works for updating the frames themselves outside the DCDFile trajectory object, giving the right PCA, but does not update the DCDFile coordinates, so the projections are wrong from this DCDFile.

One should find a way to update the DCDFile or extract the frame coordinates into a new array, perhaps as an attribute of the PCA object, which can be used for the projections.

[yasirkhanqu]

It would also be good to write a new aligned trajectory file