msmbuilder.cfep.contact_reaction_coordinate

msmbuilder.cfep.contact_reaction_coordinate(trajectory, weights)

Computes a residue-contact based reaction coordinate.

Specifically, the reaction coordinate is a weighted linear combination of the alpha carbon distances for each residue. Weights can take any value, including negative and zero values.

Parameters:

trajectory : msmbuilder trajectory

The trajectory along which to compute the reaction coordinate value

weights : nd_array, float

The weights to apply to all the inter-residue (Ca-Ca) distances

Returns:

rc_value : nd_array, float

The reaction coordinate value for each snapshot of trajectory