Fast perturbation calculation using covariance updates

[stratixs]

The basic premise for this change lies in the applicability of the Woodbury-Matrix-Identity to the pseudo-inverse. This allows to update the covariance matrix based on a rank-one update to the kirchhoff/hessian matrix instead of creating a new model and expensively recalculating the pseudo-inverse. A rank-one update describes the change in interactions strength between two atoms.

Features

• Adds a new base class ENMUpdate which allows to modify the interaction strength of a GNM's or ANM's contact pair in-place (changing the class attributes accordingly) using ENMUpdate.modify_contact().
• ENMUpdate.modify_atom() allows to switch on/off a whole atom thereby changing the contact to every connected atom. Also allows to change the amino acid residue type which may result in a change to the underlying ForceField.
• Instead of changing the model one might only want to see the effect of a interaction strength change on specific NMA functionality. So nma_update provides logic to do that without changing the model. The update to the msqf calculation for example only requires to calculate the update to the covariance diagonal (if the full subset is selected).